Starting phenix.real_space_refine on Fri Jul 3 09:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.map" model { file = "/net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2m_51812/07_2026/9h2m_51812.cif" } resolution = 3.06 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= 0.001 sd= 0.020 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 Ca 1 9.91 5 P 145 5.49 5 S 14 5.16 5 C 7956 2.51 5 N 2341 2.21 5 O 2754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10151 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PTRANS': 34, 'TRANS': 1302} Chain breaks: 2 Unresolved non-hydrogen bonds: 833 Unresolved non-hydrogen angles: 1028 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASN:plan1': 24, 'ASP:plan': 44, 'GLU:plan': 32, 'GLN:plan1': 12, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 5, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 474 Chain: "B" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 564 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1388 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 22} Link IDs: {'rna2p': 10, 'rna3p': 54} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 546 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.68, per 1000 atoms: 0.20 Number of scatterers: 13211 At special positions: 0 Unit cell: (92.4, 126.5, 122.1, 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) Ca 1 19.99 S 14 16.00 P 145 15.00 O 2754 8.00 N 2341 7.00 C 7956 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: 0.96 Conformation dependent library (CDL) restraints added in 417.7 milliseconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 12 sheets defined 53.9% alpha, 8.8% beta 53 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 60 through 94 removed outlier: 3.807A pdb=" N LYS A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.573A pdb=" N VAL A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.622A 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 180 through 197 removed outlier: 3.852A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.551A pdb=" N GLU A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.567A pdb=" N LYS A 392 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.618A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.745A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.742A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.758A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 removed outlier: 3.710A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 572 Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.569A pdb=" N ILE A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.966A pdb=" N LEU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.548A pdb=" N LYS A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 691 through 697 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.580A pdb=" N LYS A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 753 removed outlier: 3.950A pdb=" N GLY A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 793 removed outlier: 3.589A pdb=" N LEU A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 784 " --> pdb=" O GLN A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 814 Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.574A pdb=" N GLY A 872 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 886 Processing helix chain 'A' and resid 886 through 896 Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.550A pdb=" N GLU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 966 through 977 removed outlier: 4.141A pdb=" N VAL A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1008 removed outlier: 3.596A pdb=" N TYR A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1016 removed outlier: 4.397A pdb=" N PHE A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1034 removed outlier: 3.677A pdb=" N ARG A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.847A pdb=" N ILE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 3.786A pdb=" N ALA A1081 " --> pdb=" O GLU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1245 through 1257 removed outlier: 3.649A pdb=" N LEU A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A1257 " --> pdb=" O TYR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1274 through 1291 removed outlier: 4.325A pdb=" N GLU A1278 " --> pdb=" O LYS A1274 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A1279 " --> pdb=" O LYS A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1305 Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1312 through 1322 Processing helix chain 'A' and resid 1331 through 1335 Processing helix chain 'A' and resid 1359 through 1363 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 5.976A pdb=" N ILE A 760 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.054A pdb=" N GLU A1377 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 33 " --> pdb=" O GLU A1377 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ARG A1379 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU A 35 " --> pdb=" O ARG A1379 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A1381 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A1212 " --> pdb=" O ILE A1368 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A1211 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU A1235 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.718A pdb=" N LEU A 661 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.873A pdb=" N GLN A 538 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 844 through 847 removed outlier: 3.506A pdb=" N ASP A 846 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA8, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.819A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AB1, first strand: chain 'A' and resid 1131 through 1132 Processing sheet with id=AB2, first strand: chain 'A' and resid 1167 through 1178 removed outlier: 3.597A pdb=" N GLY A1158 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1157 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A1203 " --> pdb=" O LYS A1157 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR A1159 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A1201 " --> pdb=" O THR A1159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1343 through 1345 removed outlier: 3.627A pdb=" N PHE A1343 " --> pdb=" O ILE A1350 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 1.32 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: 2783 1.33 - 1.45: 3679 1.45 - 1.57: 6993 1.57 - 1.69: 286 1.69 - 1.81: 27 Bond restraints: 13768 Sorted by residual: bond pdb=" C1' DT D 22 " pdb=" N1 DT D 22 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C1' DT D 5 " pdb=" N1 DT D 5 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.25e+01 bond pdb=" C1' DT E 20 " pdb=" N1 DT E 20 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" C1' DT D 6 " pdb=" N1 DT D 6 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" C1' DT D 24 " pdb=" N1 DT D 24 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18783 2.03 - 4.07: 441 4.07 - 6.10: 64 6.10 - 8.14: 5 8.14 - 10.17: 1 Bond angle restraints: 19294 Sorted by residual: angle pdb=" O3' DT E 27 " pdb=" P DT E 28 " pdb=" O5' DT E 28 " ideal model delta sigma weight residual 104.00 98.12 5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" O3' DC E 8 " pdb=" P DA E 9 " pdb=" O5' DA E 9 " ideal model delta sigma weight residual 104.00 98.18 5.82 1.50e+00 4.44e-01 1.51e+01 angle pdb=" O3' DT E 28 " pdb=" P DG E 29 " pdb=" O5' DG E 29 " ideal model delta sigma weight residual 104.00 98.19 5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" O3' DG E 17 " pdb=" P DA E 18 " pdb=" O5' DA E 18 " ideal model delta sigma weight residual 104.00 98.19 5.81 1.50e+00 4.44e-01 1.50e+01 angle pdb=" O3' DG E 22 " pdb=" P DT E 23 " pdb=" O5' DT E 23 " ideal model delta sigma weight residual 104.00 98.20 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 19289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6729 18.06 - 36.13: 935 36.13 - 54.19: 329 54.19 - 72.25: 219 72.25 - 90.31: 23 Dihedral angle restraints: 8235 sinusoidal: 4300 harmonic: 3935 Sorted by residual: dihedral pdb=" CA TYR A1039 " pdb=" C TYR A1039 " pdb=" N SER A1040 " pdb=" CA SER A1040 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE A1038 " pdb=" C PHE A1038 " pdb=" N TYR A1039 " pdb=" CA TYR A1039 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ALA A1032 " pdb=" C ALA A1032 " pdb=" N THR A1033 " pdb=" CA THR A1033 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1988 0.055 - 0.111: 190 0.111 - 0.166: 19 0.166 - 0.222: 54 0.222 - 0.277: 1 Chirality restraints: 2252 Sorted by residual: chirality pdb=" P DC D 27 " pdb=" OP1 DC D 27 " pdb=" OP2 DC D 27 " pdb=" O5' DC D 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.61 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P DT D 26 " pdb=" OP1 DT D 26 " pdb=" OP2 DT D 26 " pdb=" O5' DT D 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" P DC E 16 " pdb=" OP1 DC E 16 " pdb=" OP2 DC E 16 " pdb=" O5' DC E 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 2249 not shown) Planarity restraints: 1936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1012 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A1013 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1013 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1013 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 916 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 917 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 917 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 917 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1138 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A1139 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1139 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1139 " -0.026 5.00e-02 4.00e+02 ... (remaining 1933 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1971 2.76 - 3.29: 12229 3.29 - 3.83: 23172 3.83 - 4.36: 27652 4.36 - 4.90: 44356 Nonbonded interactions: 109380 Sorted by model distance: nonbonded pdb=" NH2 ARG A 75 " pdb=" O4 U C 24 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP A 595 " pdb=" OH TYR A 655 " model vdw 2.230 3.040 nonbonded pdb=" N2 G C 48 " pdb=" OP2 A C 51 " model vdw 2.236 3.120 nonbonded pdb=" N ALA A 59 " pdb=" OP1 A B -8 " model vdw 2.243 3.120 nonbonded pdb=" O LEU A 101 " pdb=" O2' A C 21 " model vdw 2.245 3.040 ... (remaining 109375 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=1.00 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: 0.770 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: 0.040 Set scattering table: 0.030 Process input model: 13.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13768 Z= 0.257 Angle : 0.704 10.172 19294 Z= 0.493 Chirality : 0.045 0.277 2252 Planarity : 0.004 0.052 1936 Dihedral : 20.393 90.313 5695 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.43 % Allowed : 19.77 % Favored : 79.81 % 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: -0.03 (0.22), residues: 1331 helix: 0.49 (0.20), residues: 666 sheet: -0.52 (0.47), residues: 114 loop : -0.40 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 224 TYR 0.017 0.001 TYR A 81 PHE 0.010 0.001 PHE A1114 TRP 0.004 0.001 TRP A 476 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.26 (13768) covalent geometry : angle 0.70423 / 0.49 (19294) hydrogen bonds : bond 0.19964 / 13.47 ( 631) hydrogen bonds : angle 6.50078 / 4.66 ( 1693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 848 ILE cc_start: 0.9417 (mt) cc_final: 0.9183 (tt) REVERT: A 859 ILE cc_start: 0.9003 (mp) cc_final: 0.8532 (tp) outliers start: 4 outliers final: 0 residues processed: 97 average time/residue: 0.1252 time to fit residues: 16.9715 Evaluate side-chains 38 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 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 = 0.3774 r_free = 0.3774 target = 0.071752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.048002 restraints weight = 63684.654| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.65 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13768 Z= 0.229 Angle : 0.650 11.086 19294 Z= 0.350 Chirality : 0.044 0.168 2252 Planarity : 0.005 0.045 1936 Dihedral : 21.128 89.554 3457 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.19 % Allowed : 19.77 % Favored : 77.05 % 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: 0.17 (0.22), residues: 1331 helix: 0.82 (0.19), residues: 684 sheet: -0.32 (0.49), residues: 112 loop : -0.61 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1328 TYR 0.026 0.002 TYR A 347 PHE 0.018 0.002 PHE A1114 TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (13768) covalent geometry : angle 0.64964 / 0.35 (19294) hydrogen bonds : bond 0.04910 / 3.33 ( 631) hydrogen bonds : angle 4.70595 / 3.27 ( 1693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9242 (pt) cc_final: 0.8938 (mm) REVERT: A 764 MET cc_start: 0.8384 (mmm) cc_final: 0.8143 (mmt) REVERT: A 848 ILE cc_start: 0.9630 (mt) cc_final: 0.9360 (tt) REVERT: A 859 ILE cc_start: 0.9225 (mp) cc_final: 0.8785 (tp) outliers start: 30 outliers final: 10 residues processed: 67 average time/residue: 0.1006 time to fit residues: 10.0411 Evaluate side-chains 44 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 143 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 861 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN A1101 GLN A1191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.068702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044712 restraints weight = 64947.474| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.66 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 13768 Z= 0.247 Angle : 0.590 10.426 19294 Z= 0.326 Chirality : 0.040 0.174 2252 Planarity : 0.005 0.096 1936 Dihedral : 21.159 92.636 3457 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.98 % Allowed : 20.40 % Favored : 76.62 % 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: 0.44 (0.23), residues: 1331 helix: 1.14 (0.20), residues: 687 sheet: -0.45 (0.49), residues: 112 loop : -0.59 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 653 TYR 0.022 0.002 TYR A 347 PHE 0.017 0.002 PHE A 553 TRP 0.010 0.001 TRP A1074 HIS 0.006 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (13768) covalent geometry : angle 0.59021 / 0.33 (19294) hydrogen bonds : bond 0.04613 / 3.13 ( 631) hydrogen bonds : angle 4.59032 / 3.19 ( 1693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9323 (pt) cc_final: 0.9007 (mm) REVERT: A 37 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8141 (p0) REVERT: A 693 MET cc_start: 0.8559 (ttp) cc_final: 0.7946 (tmm) REVERT: A 859 ILE cc_start: 0.9279 (mp) cc_final: 0.8883 (tp) outliers start: 28 outliers final: 14 residues processed: 63 average time/residue: 0.0844 time to fit residues: 8.6577 Evaluate side-chains 45 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 76 optimal weight: 30.0000 chunk 127 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 142 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.069770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.045803 restraints weight = 64460.985| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.57 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13768 Z= 0.116 Angle : 0.520 9.600 19294 Z= 0.279 Chirality : 0.038 0.259 2252 Planarity : 0.004 0.059 1936 Dihedral : 21.160 92.220 3457 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 22.00 % Favored : 76.41 % 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: 0.70 (0.23), residues: 1331 helix: 1.44 (0.20), residues: 687 sheet: -0.73 (0.49), residues: 103 loop : -0.50 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.016 0.001 TYR A 25 PHE 0.011 0.001 PHE A 946 TRP 0.012 0.001 TRP A1074 HIS 0.003 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (13768) covalent geometry : angle 0.52002 / 0.28 (19294) hydrogen bonds : bond 0.03718 / 2.53 ( 631) hydrogen bonds : angle 4.28752 / 2.96 ( 1693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.396 Fit side-chains REVERT: A 21 ILE cc_start: 0.9353 (pt) cc_final: 0.9066 (mm) REVERT: A 37 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8051 (p0) REVERT: A 241 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 516 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8489 (mt-10) REVERT: A 693 MET cc_start: 0.8550 (ttp) cc_final: 0.7884 (tmm) REVERT: A 829 MET cc_start: 0.8782 (mpp) cc_final: 0.8422 (mpp) REVERT: A 859 ILE cc_start: 0.9189 (mp) cc_final: 0.8772 (tp) REVERT: A 1006 LYS cc_start: 0.9261 (mttt) cc_final: 0.8973 (mtpt) outliers start: 15 outliers final: 7 residues processed: 46 average time/residue: 0.0739 time to fit residues: 5.8200 Evaluate side-chains 37 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1242 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 110 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 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 = 0.3698 r_free = 0.3698 target = 0.068083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044116 restraints weight = 65160.199| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.59 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13768 Z= 0.189 Angle : 0.523 8.660 19294 Z= 0.287 Chirality : 0.038 0.180 2252 Planarity : 0.004 0.048 1936 Dihedral : 21.158 91.885 3457 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.44 % Allowed : 21.25 % Favored : 76.30 % 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: 0.77 (0.23), residues: 1331 helix: 1.46 (0.20), residues: 688 sheet: -0.50 (0.49), residues: 105 loop : -0.46 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 62 TYR 0.014 0.001 TYR A 155 PHE 0.014 0.001 PHE A1114 TRP 0.011 0.001 TRP A1074 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (13768) covalent geometry : angle 0.52280 / 0.29 (19294) hydrogen bonds : bond 0.03865 / 2.64 ( 631) hydrogen bonds : angle 4.36722 / 3.04 ( 1693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 28 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9263 (pt) cc_final: 0.9020 (mm) REVERT: A 37 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8209 (p0) REVERT: A 218 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8332 (ptmm) REVERT: A 241 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 693 MET cc_start: 0.8610 (ttp) cc_final: 0.7934 (tmm) REVERT: A 829 MET cc_start: 0.8827 (mpp) cc_final: 0.8463 (mpp) REVERT: A 859 ILE cc_start: 0.9126 (mp) cc_final: 0.8739 (tp) outliers start: 23 outliers final: 14 residues processed: 50 average time/residue: 0.0990 time to fit residues: 7.9350 Evaluate side-chains 43 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1097 LYS Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1242 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 14 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 ASN A 933 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.068770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.044828 restraints weight = 64318.298| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.53 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13768 Z= 0.119 Angle : 0.480 10.481 19294 Z= 0.262 Chirality : 0.037 0.178 2252 Planarity : 0.003 0.038 1936 Dihedral : 21.226 92.130 3457 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.23 % Allowed : 21.15 % Favored : 76.62 % 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: 1.01 (0.23), residues: 1331 helix: 1.68 (0.20), residues: 687 sheet: -0.50 (0.50), residues: 101 loop : -0.35 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1233 TYR 0.012 0.001 TYR A 25 PHE 0.012 0.001 PHE A 946 TRP 0.011 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (13768) covalent geometry : angle 0.47964 / 0.26 (19294) hydrogen bonds : bond 0.03426 / 2.32 ( 631) hydrogen bonds : angle 4.17874 / 2.90 ( 1693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9332 (pt) cc_final: 0.9046 (mm) REVERT: A 37 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8236 (p0) REVERT: A 218 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8288 (ptmm) REVERT: A 241 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7278 (t80) REVERT: A 402 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8277 (mp10) REVERT: A 693 MET cc_start: 0.8579 (ttp) cc_final: 0.7905 (tmm) REVERT: A 829 MET cc_start: 0.8831 (mpp) cc_final: 0.8383 (mpp) REVERT: A 859 ILE cc_start: 0.9047 (mp) cc_final: 0.8647 (tp) REVERT: A 862 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (mttt) outliers start: 21 outliers final: 9 residues processed: 46 average time/residue: 0.0828 time to fit residues: 6.4587 Evaluate side-chains 40 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1242 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 75 optimal weight: 0.0570 chunk 96 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.067247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.043257 restraints weight = 64546.527| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.57 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13768 Z= 0.197 Angle : 0.523 10.985 19294 Z= 0.283 Chirality : 0.038 0.274 2252 Planarity : 0.004 0.043 1936 Dihedral : 21.211 92.007 3457 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 21.15 % 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 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: 0.86 (0.23), residues: 1331 helix: 1.53 (0.20), residues: 697 sheet: -0.50 (0.53), residues: 97 loop : -0.44 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.015 0.001 TYR A 155 PHE 0.012 0.001 PHE A 946 TRP 0.014 0.002 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (13768) covalent geometry : angle 0.52256 / 0.28 (19294) hydrogen bonds : bond 0.03836 / 2.62 ( 631) hydrogen bonds : angle 4.30771 / 2.99 ( 1693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9264 (pt) cc_final: 0.9034 (mm) REVERT: A 37 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8237 (p0) REVERT: A 241 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 402 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: A 693 MET cc_start: 0.8623 (ttp) cc_final: 0.7945 (tmm) REVERT: A 829 MET cc_start: 0.8822 (mpp) cc_final: 0.8407 (mpp) REVERT: A 859 ILE cc_start: 0.9103 (mp) cc_final: 0.8687 (tp) REVERT: A 862 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8723 (mttt) outliers start: 19 outliers final: 12 residues processed: 45 average time/residue: 0.0856 time to fit residues: 6.4276 Evaluate side-chains 41 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 49 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.065478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041710 restraints weight = 64720.223| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.42 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13768 Z= 0.260 Angle : 0.578 11.979 19294 Z= 0.315 Chirality : 0.039 0.184 2252 Planarity : 0.004 0.054 1936 Dihedral : 21.366 93.707 3457 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.23 % Allowed : 21.79 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.23), residues: 1331 helix: 1.29 (0.20), residues: 699 sheet: -0.40 (0.51), residues: 110 loop : -0.63 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.018 0.002 TYR A 155 PHE 0.016 0.002 PHE A 446 TRP 0.027 0.003 TRP A1074 HIS 0.007 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (13768) covalent geometry : angle 0.57772 / 0.31 (19294) hydrogen bonds : bond 0.04215 / 2.86 ( 631) hydrogen bonds : angle 4.51851 / 3.15 ( 1693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9286 (pt) cc_final: 0.9047 (mm) REVERT: A 37 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8376 (p0) REVERT: A 241 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7574 (t80) REVERT: A 693 MET cc_start: 0.8645 (ttp) cc_final: 0.7981 (tmm) REVERT: A 829 MET cc_start: 0.8874 (mpp) cc_final: 0.8428 (mpp) REVERT: A 859 ILE cc_start: 0.9174 (mp) cc_final: 0.8819 (tp) REVERT: A 862 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8771 (ptpt) REVERT: A 1169 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9184 (p) outliers start: 21 outliers final: 13 residues processed: 47 average time/residue: 0.0929 time to fit residues: 7.1058 Evaluate side-chains 41 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 133 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 49 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.066573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.042719 restraints weight = 64391.062| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.44 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13768 Z= 0.147 Angle : 0.495 11.806 19294 Z= 0.268 Chirality : 0.037 0.185 2252 Planarity : 0.003 0.047 1936 Dihedral : 21.228 94.016 3457 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.70 % Allowed : 22.95 % Favored : 75.35 % 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: 0.91 (0.23), residues: 1331 helix: 1.61 (0.20), residues: 690 sheet: -0.41 (0.56), residues: 97 loop : -0.47 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.012 0.001 TYR A 567 PHE 0.013 0.001 PHE A 946 TRP 0.012 0.002 TRP A1074 HIS 0.003 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (13768) covalent geometry : angle 0.49461 / 0.27 (19294) hydrogen bonds : bond 0.03648 / 2.47 ( 631) hydrogen bonds : angle 4.26219 / 2.96 ( 1693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9312 (pt) cc_final: 0.9047 (mm) REVERT: A 37 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8385 (p0) REVERT: A 241 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7556 (t80) REVERT: A 693 MET cc_start: 0.8638 (ttp) cc_final: 0.7958 (tmm) REVERT: A 829 MET cc_start: 0.8868 (mpp) cc_final: 0.8613 (mpp) REVERT: A 859 ILE cc_start: 0.9135 (mp) cc_final: 0.8759 (tp) REVERT: A 862 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8727 (ptpt) REVERT: A 1169 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9182 (p) outliers start: 16 outliers final: 12 residues processed: 40 average time/residue: 0.0843 time to fit residues: 5.6197 Evaluate side-chains 41 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1169 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 85 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 54 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.065889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042112 restraints weight = 64733.699| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.43 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13768 Z= 0.203 Angle : 0.524 13.128 19294 Z= 0.282 Chirality : 0.037 0.177 2252 Planarity : 0.003 0.041 1936 Dihedral : 21.116 93.763 3457 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.70 % Allowed : 22.95 % Favored : 75.35 % 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: 1331 helix: 1.61 (0.20), residues: 691 sheet: -0.35 (0.56), residues: 97 loop : -0.47 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.015 0.001 TYR A 155 PHE 0.014 0.001 PHE A 946 TRP 0.017 0.002 TRP A1074 HIS 0.011 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (13768) covalent geometry : angle 0.52446 / 0.28 (19294) hydrogen bonds : bond 0.03792 / 2.58 ( 631) hydrogen bonds : angle 4.31118 / 3.00 ( 1693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9326 (pt) cc_final: 0.9057 (mm) REVERT: A 37 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8481 (p0) REVERT: A 241 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7558 (t80) REVERT: A 693 MET cc_start: 0.8671 (ttp) cc_final: 0.7989 (tmm) REVERT: A 829 MET cc_start: 0.8867 (mpp) cc_final: 0.8610 (mpp) REVERT: A 859 ILE cc_start: 0.9142 (mp) cc_final: 0.8762 (tp) REVERT: A 862 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8723 (ptpt) REVERT: A 1169 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9177 (p) outliers start: 16 outliers final: 11 residues processed: 39 average time/residue: 0.0879 time to fit residues: 5.6307 Evaluate side-chains 39 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 79 optimal weight: 30.0000 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 130 optimal weight: 0.0050 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 overall best weight: 3.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.065759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042618 restraints weight = 61379.457| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.66 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13768 Z= 0.150 Angle : 0.485 12.443 19294 Z= 0.262 Chirality : 0.036 0.198 2252 Planarity : 0.003 0.038 1936 Dihedral : 21.028 94.362 3457 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.38 % Allowed : 23.17 % Favored : 75.45 % 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: 1.10 (0.23), residues: 1331 helix: 1.79 (0.20), residues: 685 sheet: -0.28 (0.56), residues: 97 loop : -0.40 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.011 0.001 TYR A 567 PHE 0.012 0.001 PHE A 946 TRP 0.007 0.001 TRP A1074 HIS 0.003 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (13768) covalent geometry : angle 0.48523 / 0.26 (19294) hydrogen bonds : bond 0.03465 / 2.35 ( 631) hydrogen bonds : angle 4.17962 / 2.90 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.06 seconds wall clock time: 41 minutes 2.58 seconds (2462.58 seconds total)