Starting phenix.real_space_refine on Sat Sep 12 08:15:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4x_24838/09_2026/7s4x_24838.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 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 161 5.49 5 Mg 5 5.21 5 S 23 5.16 5 C 8614 2.51 5 N 2546 2.21 5 O 3142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14491 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 11090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1354, 11079 Classifications: {'peptide': 1354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 1318} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 1354, 11079 Classifications: {'peptide': 1354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 1318} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 11262 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNAv2': 98} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 52, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 556 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.50 Time building chain proxies: 4.70, per 1000 atoms: 0.32 Number of scatterers: 14491 At special positions: 0 Unit cell: (89.1, 134.46, 131.22, 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 23 16.00 P 161 15.00 Mg 5 11.99 O 3142 8.00 N 2546 7.00 C 8614 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: 1.03 Conformation dependent library (CDL) restraints added in 862.1 milliseconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 55.4% alpha, 8.2% beta 56 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.799A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.049A 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: 3.707A 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 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.726A pdb=" N ALA A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.586A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 292 through 306 removed outlier: 5.047A pdb=" N ASP A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.576A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.733A 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: 3.529A 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: 4.013A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.035A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.745A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.698A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.966A 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 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.613A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.067A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.319A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.506A 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 removed outlier: 3.741A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.525A pdb=" N LYS A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.175A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.390A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.522A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1087 removed outlier: 3.898A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.672A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 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 removed outlier: 3.505A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.908A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 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: 7.185A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.644A 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: 9.943A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 836 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.596A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.503A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 503 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.46 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: 2929 1.33 - 1.45: 4075 1.45 - 1.57: 7714 1.57 - 1.69: 317 1.69 - 1.81: 44 Bond restraints: 15079 Sorted by residual: bond pdb=" C3' DA C 19 " pdb=" O3' DA C 19 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.73e+00 bond pdb=" C3' DC C 18 " pdb=" O3' DC C 18 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.07e+00 bond pdb=" CA ARG A 976 " pdb=" C ARG A 976 " ideal model delta sigma weight residual 1.522 1.484 0.039 1.38e-02 5.25e+03 7.79e+00 bond pdb=" C3' DT c 32 " pdb=" O3' DT c 32 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.75e+00 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 5.96e+00 ... (remaining 15074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 20030 1.53 - 3.07: 818 3.07 - 4.60: 159 4.60 - 6.14: 33 6.14 - 7.67: 4 Bond angle restraints: 21044 Sorted by residual: angle pdb=" O4' DC c 26 " pdb=" C4' DC c 26 " pdb=" C3' DC c 26 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 angle pdb=" O4' DC C 21 " pdb=" C4' DC C 21 " pdb=" C3' DC C 21 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" O4' DC c 29 " pdb=" C4' DC c 29 " pdb=" C3' DC c 29 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 21039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 8205 31.84 - 63.69: 543 63.69 - 95.53: 47 95.53 - 127.37: 0 127.37 - 159.22: 3 Dihedral angle restraints: 8798 sinusoidal: 4811 harmonic: 3987 Sorted by residual: dihedral pdb=" C4' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " pdb=" C1' G B 43 " ideal model delta sinusoidal sigma weight residual 36.34 -37.31 73.65 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' A B 88 " pdb=" C3' A B 88 " pdb=" C2' A B 88 " pdb=" C1' A B 88 " ideal model delta sinusoidal sigma weight residual 36.34 -36.93 73.27 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' U B 44 " pdb=" C3' U B 44 " pdb=" C2' U B 44 " pdb=" C1' U B 44 " ideal model delta sinusoidal sigma weight residual 36.35 -36.12 72.47 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 8795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1925 0.059 - 0.118: 324 0.118 - 0.177: 41 0.177 - 0.236: 85 0.236 - 0.295: 35 Chirality restraints: 2410 Sorted by residual: chirality pdb=" C2' C B 55 " pdb=" C3' C B 55 " pdb=" O2' C B 55 " pdb=" C1' C B 55 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2' U B 44 " pdb=" C3' U B 44 " pdb=" O2' U B 44 " pdb=" C1' U B 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' G B 43 " pdb=" C3' G B 43 " pdb=" O2' G B 43 " pdb=" C1' G B 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 2407 not shown) Planarity restraints: 2107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 75 " -0.023 2.00e-02 2.50e+03 1.10e-02 3.33e+00 pdb=" N9 A B 75 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A B 75 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 75 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 75 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 75 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 75 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 75 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B 75 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 42 " -0.023 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 A B 42 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 42 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 42 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 42 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 42 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 42 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 42 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 54 " 0.022 2.00e-02 2.50e+03 9.52e-03 2.72e+00 pdb=" N9 G B 54 " -0.023 2.00e-02 2.50e+03 pdb=" C8 G B 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 54 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 54 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 54 " -0.004 2.00e-02 2.50e+03 ... (remaining 2104 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 76 2.48 - 3.09: 9975 3.09 - 3.69: 23748 3.69 - 4.30: 36736 4.30 - 4.90: 56487 Nonbonded interactions: 127022 Sorted by model distance: nonbonded pdb=" OP1 DC D 34 " pdb="MG MG A1402 " model vdw 1.878 2.170 nonbonded pdb=" OE1 GLU A 762 " pdb="MG MG A1401 " model vdw 1.915 2.170 nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1402 " model vdw 1.956 2.170 nonbonded pdb=" OD1 ASP A 10 " pdb="MG MG A1401 " model vdw 2.010 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1402 " model vdw 2.091 2.250 ... (remaining 127017 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.390 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.090 Find NCS groups from input model: 0.070 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 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 : 0.006 0.055 15079 Z= 0.347 Angle : 0.728 7.670 21044 Z= 0.449 Chirality : 0.067 0.295 2410 Planarity : 0.003 0.038 2107 Dihedral : 18.476 159.217 6218 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1351 helix: 0.57 (0.20), residues: 646 sheet: -0.55 (0.46), residues: 117 loop : -0.37 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1019 TYR 0.016 0.002 TYR A1265 PHE 0.021 0.002 PHE A1327 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.35 (15079) covalent geometry : angle 0.72754 / 0.45 (21044) hydrogen bonds : bond 0.14069 / 9.82 ( 642) hydrogen bonds : angle 5.95173 / 4.18 ( 1717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.496 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.8134 time to fit residues: 64.2965 Evaluate side-chains 52 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.066446 restraints weight = 47131.357| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.69 r_work: 0.2777 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15079 Z= 0.182 Angle : 0.929 24.051 21044 Z= 0.415 Chirality : 0.078 1.143 2410 Planarity : 0.004 0.044 2107 Dihedral : 18.889 162.581 3328 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.74 % Allowed : 3.86 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1351 helix: 0.96 (0.20), residues: 644 sheet: -0.79 (0.43), residues: 120 loop : -0.22 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.017 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (15079) covalent geometry : angle 0.92917 / 0.41 (21044) hydrogen bonds : bond 0.04503 / 3.04 ( 642) hydrogen bonds : angle 4.83740 / 3.42 ( 1717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 837 ASP cc_start: 0.8197 (p0) cc_final: 0.7948 (p0) REVERT: A 905 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7381 (ptp90) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.8638 time to fit residues: 62.5225 Evaluate side-chains 61 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1062 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 38 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 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 = 0.3583 r_free = 0.3583 target = 0.103375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.068458 restraints weight = 40923.944| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.55 r_work: 0.2812 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15079 Z= 0.139 Angle : 0.699 12.184 21044 Z= 0.333 Chirality : 0.058 0.672 2410 Planarity : 0.003 0.044 2107 Dihedral : 18.997 169.659 3328 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.66 % Allowed : 5.34 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1351 helix: 1.20 (0.20), residues: 646 sheet: -0.83 (0.43), residues: 133 loop : -0.07 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1058 TYR 0.014 0.001 TYR A 814 PHE 0.016 0.001 PHE A1327 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (15079) covalent geometry : angle 0.69889 / 0.33 (21044) hydrogen bonds : bond 0.03957 / 2.69 ( 642) hydrogen bonds : angle 4.57591 / 3.23 ( 1717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 674 GLN cc_start: 0.8854 (tp40) cc_final: 0.8624 (mm110) REVERT: A 905 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7320 (ptp90) REVERT: A 1019 ARG cc_start: 0.7227 (mmm160) cc_final: 0.7027 (mmm160) REVERT: A 1271 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7547 (tp30) REVERT: A 1275 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7186 (mm-30) outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.8257 time to fit residues: 59.8997 Evaluate side-chains 60 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 1018 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 0.0050 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 GLN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064699 restraints weight = 49768.981| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.77 r_work: 0.2722 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15079 Z= 0.273 Angle : 0.750 16.126 21044 Z= 0.356 Chirality : 0.060 0.587 2410 Planarity : 0.004 0.046 2107 Dihedral : 19.000 162.444 3328 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.07 % Allowed : 6.32 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1351 helix: 1.10 (0.20), residues: 647 sheet: -0.79 (0.43), residues: 133 loop : -0.15 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1058 TYR 0.017 0.002 TYR A 155 PHE 0.019 0.002 PHE A1327 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (15079) covalent geometry : angle 0.74991 / 0.36 (21044) hydrogen bonds : bond 0.04246 / 2.84 ( 642) hydrogen bonds : angle 4.55214 / 3.21 ( 1717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 190 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 674 GLN cc_start: 0.8863 (tp40) cc_final: 0.8464 (mm110) REVERT: A 837 ASP cc_start: 0.8177 (p0) cc_final: 0.7929 (p0) REVERT: A 905 ARG cc_start: 0.7575 (ptp90) cc_final: 0.7232 (ptp90) REVERT: A 1271 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7546 (tp30) REVERT: A 1275 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7266 (mm-30) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.8697 time to fit residues: 61.0618 Evaluate side-chains 64 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1062 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.102633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067658 restraints weight = 40381.171| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.53 r_work: 0.2795 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15079 Z= 0.148 Angle : 0.676 14.497 21044 Z= 0.324 Chirality : 0.055 0.533 2410 Planarity : 0.003 0.045 2107 Dihedral : 19.024 165.448 3328 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.99 % Allowed : 6.98 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1351 helix: 1.26 (0.20), residues: 646 sheet: -0.61 (0.45), residues: 123 loop : -0.13 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1058 TYR 0.011 0.001 TYR A 155 PHE 0.017 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (15079) covalent geometry : angle 0.67615 / 0.32 (21044) hydrogen bonds : bond 0.03688 / 2.49 ( 642) hydrogen bonds : angle 4.45686 / 3.15 ( 1717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 190 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 674 GLN cc_start: 0.8871 (tp40) cc_final: 0.8623 (mm110) REVERT: A 905 ARG cc_start: 0.7601 (ptp90) cc_final: 0.7223 (ptp90) REVERT: A 1078 ARG cc_start: 0.7530 (ptt90) cc_final: 0.7191 (ptt90) REVERT: A 1271 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7443 (tp30) REVERT: A 1275 GLU cc_start: 0.7869 (mm-30) cc_final: 0.6973 (mm-30) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.8386 time to fit residues: 59.9975 Evaluate side-chains 62 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 1018 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 74 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065893 restraints weight = 44691.006| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.63 r_work: 0.2755 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15079 Z= 0.221 Angle : 0.707 15.353 21044 Z= 0.337 Chirality : 0.056 0.572 2410 Planarity : 0.003 0.046 2107 Dihedral : 18.997 165.087 3328 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.90 % Allowed : 7.39 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1351 helix: 1.21 (0.20), residues: 647 sheet: -0.61 (0.45), residues: 123 loop : -0.16 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.015 0.001 TYR A 155 PHE 0.018 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (15079) covalent geometry : angle 0.70657 / 0.34 (21044) hydrogen bonds : bond 0.03890 / 2.60 ( 642) hydrogen bonds : angle 4.43510 / 3.13 ( 1717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8728 (tt) REVERT: A 190 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 627 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: A 674 GLN cc_start: 0.8885 (tp40) cc_final: 0.8512 (mm110) REVERT: A 905 ARG cc_start: 0.7585 (ptp90) cc_final: 0.7184 (ptp90) REVERT: A 1029 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 1271 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7457 (tp30) REVERT: A 1275 GLU cc_start: 0.7928 (mm-30) cc_final: 0.6994 (mm-30) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 0.9167 time to fit residues: 63.2460 Evaluate side-chains 62 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 117 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 ASN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.064066 restraints weight = 38443.150| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.45 r_work: 0.2724 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 15079 Z= 0.320 Angle : 0.785 15.821 21044 Z= 0.372 Chirality : 0.061 0.728 2410 Planarity : 0.004 0.058 2107 Dihedral : 19.111 162.213 3328 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.31 % Allowed : 7.80 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1351 helix: 1.04 (0.21), residues: 647 sheet: -0.92 (0.42), residues: 133 loop : -0.21 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1078 TYR 0.019 0.002 TYR A 155 PHE 0.021 0.002 PHE A1327 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.32 (15079) covalent geometry : angle 0.78527 / 0.37 (21044) hydrogen bonds : bond 0.04357 / 2.91 ( 642) hydrogen bonds : angle 4.52947 / 3.20 ( 1717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 576 ASP cc_start: 0.8818 (m-30) cc_final: 0.8596 (m-30) REVERT: A 674 GLN cc_start: 0.8920 (tp40) cc_final: 0.8525 (mm110) REVERT: A 905 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7153 (ptp90) REVERT: A 1078 ARG cc_start: 0.7624 (ptt90) cc_final: 0.7293 (ptt90) REVERT: A 1271 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7503 (tp30) REVERT: A 1275 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7017 (mm-30) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 0.8333 time to fit residues: 64.0929 Evaluate side-chains 61 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.066931 restraints weight = 40639.051| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.52 r_work: 0.2781 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15079 Z= 0.151 Angle : 0.685 13.327 21044 Z= 0.328 Chirality : 0.054 0.621 2410 Planarity : 0.003 0.046 2107 Dihedral : 19.167 165.204 3328 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.82 % Allowed : 8.13 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1351 helix: 1.23 (0.21), residues: 647 sheet: -0.77 (0.44), residues: 125 loop : -0.16 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1078 TYR 0.012 0.001 TYR A 155 PHE 0.017 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15079) covalent geometry : angle 0.68497 / 0.33 (21044) hydrogen bonds : bond 0.03700 / 2.49 ( 642) hydrogen bonds : angle 4.43192 / 3.13 ( 1717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 576 ASP cc_start: 0.8772 (m-30) cc_final: 0.8550 (m-30) REVERT: A 627 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: A 674 GLN cc_start: 0.8880 (tp40) cc_final: 0.8491 (mm110) REVERT: A 879 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5689 (mtt) REVERT: A 905 ARG cc_start: 0.7523 (ptp90) cc_final: 0.7109 (ptp90) REVERT: A 1078 ARG cc_start: 0.7587 (ptt90) cc_final: 0.7260 (ptt90) REVERT: A 1271 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7427 (tp30) REVERT: A 1275 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7025 (mm-30) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.8685 time to fit residues: 62.8537 Evaluate side-chains 67 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.067374 restraints weight = 44606.783| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.64 r_work: 0.2787 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15079 Z= 0.154 Angle : 0.663 12.445 21044 Z= 0.319 Chirality : 0.053 0.626 2410 Planarity : 0.003 0.045 2107 Dihedral : 19.117 168.272 3328 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.90 % Allowed : 8.05 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1351 helix: 1.37 (0.21), residues: 646 sheet: -0.73 (0.44), residues: 125 loop : -0.11 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1019 TYR 0.012 0.001 TYR A 155 PHE 0.017 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15079) covalent geometry : angle 0.66267 / 0.32 (21044) hydrogen bonds : bond 0.03582 / 2.41 ( 642) hydrogen bonds : angle 4.35258 / 3.08 ( 1717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 298 ASP cc_start: 0.7819 (m-30) cc_final: 0.7594 (m-30) REVERT: A 576 ASP cc_start: 0.8760 (m-30) cc_final: 0.8560 (m-30) REVERT: A 674 GLN cc_start: 0.8893 (tp40) cc_final: 0.8506 (mm110) REVERT: A 837 ASP cc_start: 0.8093 (p0) cc_final: 0.7889 (p0) REVERT: A 879 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5660 (mtt) REVERT: A 905 ARG cc_start: 0.7512 (ptp90) cc_final: 0.7100 (ptp90) REVERT: A 1019 ARG cc_start: 0.7067 (mmm160) cc_final: 0.6762 (mmp-170) REVERT: A 1029 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7578 (pp) REVERT: A 1078 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7235 (ptt90) REVERT: A 1271 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7520 (tp30) REVERT: A 1275 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7032 (mm-30) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.8634 time to fit residues: 67.3599 Evaluate side-chains 70 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 82 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 11 optimal weight: 0.0370 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069718 restraints weight = 46717.897| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.70 r_work: 0.2837 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15079 Z= 0.118 Angle : 0.634 11.212 21044 Z= 0.306 Chirality : 0.051 0.521 2410 Planarity : 0.003 0.046 2107 Dihedral : 19.040 171.474 3328 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.74 % Allowed : 8.46 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1351 helix: 1.56 (0.21), residues: 646 sheet: -0.60 (0.45), residues: 123 loop : -0.11 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.011 0.001 TYR A 568 PHE 0.016 0.001 PHE A1327 TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (15079) covalent geometry : angle 0.63361 / 0.31 (21044) hydrogen bonds : bond 0.03379 / 2.30 ( 642) hydrogen bonds : angle 4.27429 / 3.03 ( 1717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8039 (pp30) REVERT: A 298 ASP cc_start: 0.7748 (m-30) cc_final: 0.7539 (m-30) REVERT: A 306 LEU cc_start: 0.7265 (mt) cc_final: 0.6924 (pp) REVERT: A 576 ASP cc_start: 0.8713 (m-30) cc_final: 0.8513 (m-30) REVERT: A 674 GLN cc_start: 0.8867 (tp40) cc_final: 0.8478 (mm110) REVERT: A 781 MET cc_start: 0.8779 (tpp) cc_final: 0.8456 (tpt) REVERT: A 879 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5659 (mtt) REVERT: A 905 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7175 (ptp90) REVERT: A 990 ASN cc_start: 0.9079 (m-40) cc_final: 0.8739 (m-40) REVERT: A 1029 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7460 (pp) REVERT: A 1271 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7533 (tp30) REVERT: A 1275 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7002 (mm-30) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.8031 time to fit residues: 60.0118 Evaluate side-chains 68 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.069164 restraints weight = 36893.220| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.42 r_work: 0.2834 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15079 Z= 0.141 Angle : 0.758 38.843 21044 Z= 0.355 Chirality : 0.051 0.518 2410 Planarity : 0.004 0.109 2107 Dihedral : 18.984 171.828 3328 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.57 % Allowed : 8.87 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1351 helix: 1.58 (0.21), residues: 646 sheet: -0.52 (0.45), residues: 123 loop : -0.11 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 653 TYR 0.011 0.001 TYR A 155 PHE 0.015 0.001 PHE A1327 TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (15079) covalent geometry : angle 0.75792 / 0.36 (21044) hydrogen bonds : bond 0.03428 / 2.31 ( 642) hydrogen bonds : angle 4.23973 / 3.01 ( 1717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.07 seconds wall clock time: 82 minutes 13.78 seconds (4933.78 seconds total)