Starting phenix.real_space_refine on Thu Aug 6 04:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2m_51812/08_2026/9h2m_51812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2m_51812/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9h2m_51812/08_2026/9h2m_51812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2m_51812/08_2026/9h2m_51812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h2m_51812/08_2026/9h2m_51812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2m_51812/08_2026/9h2m_51812.map" } 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-2.2rc3-6140/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, 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: 1.41 Conformation dependent library (CDL) restraints added in 601.8 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: 1.85 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: 3.88 Time building geometry restraints manager: 1.85 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: 18570 2.03 - 4.07: 654 4.07 - 6.10: 64 6.10 - 8.14: 5 8.14 - 10.17: 1 Bond angle restraints: 19294 Sorted by residual: angle pdb=" O5' C C 58 " pdb=" C5' C C 58 " pdb=" C4' C C 58 " ideal model delta sigma weight residual 109.40 112.24 -2.84 8.00e-01 1.56e+00 1.26e+01 angle pdb=" O5' A B -1 " pdb=" C5' A B -1 " pdb=" C4' A B -1 " ideal model delta sigma weight residual 109.40 112.20 -2.80 8.00e-01 1.56e+00 1.22e+01 angle pdb=" O5' U C 41 " pdb=" C5' U C 41 " pdb=" C4' U C 41 " ideal model delta sigma weight residual 109.40 112.13 -2.73 8.00e-01 1.56e+00 1.17e+01 angle pdb=" O5' A C 32 " pdb=" C5' A C 32 " pdb=" C4' A C 32 " ideal model delta sigma weight residual 109.40 112.13 -2.73 8.00e-01 1.56e+00 1.16e+01 angle pdb=" O5' C C 35 " pdb=" C5' C C 35 " pdb=" C4' C C 35 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.12e+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: 1893 0.055 - 0.111: 206 0.111 - 0.166: 97 0.166 - 0.222: 55 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.380 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- 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= 0.262 Angle : 0.753 10.172 19294 Z= 0.520 Chirality : 0.052 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 0.00397 / 0.26 (13768) covalent geometry : angle 0.75282 / 0.52 (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 : 0.459 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: 0.8533 (tp) outliers start: 4 outliers final: 0 residues processed: 97 average time/residue: 0.1494 time to fit residues: 20.4478 Evaluate side-chains 39 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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** A1191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.071769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047963 restraints weight = 63641.170| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.59 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1643 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= 0.228 Angle : 0.666 10.892 19294 Z= 0.353 Chirality : 0.045 0.161 2252 Planarity : 0.005 0.048 1936 Dihedral : 21.054 88.693 3457 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.08 % Allowed : 20.09 % 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: 0.20 (0.22), residues: 1331 helix: 0.86 (0.19), residues: 684 sheet: -0.33 (0.49), residues: 112 loop : -0.61 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 340 TYR 0.024 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 0.66636 / 0.35 (19294) hydrogen bonds : bond 0.04859 / 3.29 ( 631) hydrogen bonds : angle 4.71090 / 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 68 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9234 (pt) cc_final: 0.8921 (mm) REVERT: A 764 MET cc_start: 0.8379 (mmm) cc_final: 0.8139 (mmt) REVERT: A 848 ILE cc_start: 0.9629 (mt) cc_final: 0.9356 (tt) REVERT: A 859 ILE cc_start: 0.9218 (mp) cc_final: 0.8776 (tp) outliers start: 29 outliers final: 10 residues processed: 66 average time/residue: 0.1178 time to fit residues: 11.9172 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 : 0.453 ------------------------------------------------------------------------------- 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: 9.9990 chunk 50 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 overall best weight: 5.5186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.068710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.044849 restraints weight = 64942.544| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.54 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13768 Z= 0.248 Angle : 0.606 10.289 19294 Z= 0.328 Chirality : 0.041 0.154 2252 Planarity : 0.005 0.084 1936 Dihedral : 21.046 91.130 3457 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.41 (0.23), residues: 1331 helix: 1.13 (0.20), residues: 690 sheet: -0.44 (0.49), residues: 112 loop : -0.64 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 652 TYR 0.024 0.002 TYR A 347 PHE 0.017 0.002 PHE A1114 TRP 0.010 0.001 TRP A1074 HIS 0.006 0.002 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 (13768) covalent geometry : angle 0.60580 / 0.33 (19294) hydrogen bonds : bond 0.04571 / 3.09 ( 631) hydrogen bonds : angle 4.58626 / 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 : 0.452 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9284 (pt) cc_final: 0.8986 (mm) REVERT: A 37 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8100 (p0) REVERT: A 693 MET cc_start: 0.8636 (ttp) cc_final: 0.7974 (tmm) REVERT: A 859 ILE cc_start: 0.9274 (mp) cc_final: 0.8880 (tp) outliers start: 28 outliers final: 15 residues processed: 63 average time/residue: 0.1009 time to fit residues: 10.2997 Evaluate side-chains 46 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 93 optimal weight: 0.5980 chunk 142 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.069160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045251 restraints weight = 64632.848| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.54 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13768 Z= 0.150 Angle : 0.534 10.071 19294 Z= 0.286 Chirality : 0.039 0.185 2252 Planarity : 0.004 0.069 1936 Dihedral : 21.074 90.696 3457 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.02 % Allowed : 21.79 % Favored : 76.20 % 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: 0.66 (0.23), residues: 1331 helix: 1.40 (0.20), residues: 689 sheet: -0.69 (0.48), residues: 107 loop : -0.52 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.016 0.001 TYR A 25 PHE 0.013 0.001 PHE A 946 TRP 0.014 0.001 TRP A1074 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (13768) covalent geometry : angle 0.53421 / 0.29 (19294) hydrogen bonds : bond 0.03832 / 2.60 ( 631) hydrogen bonds : angle 4.32665 / 3.00 ( 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 50 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9231 (pt) cc_final: 0.9005 (mm) REVERT: A 32 MET cc_start: 0.9086 (mmm) cc_final: 0.8884 (mmm) REVERT: A 37 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8094 (p0) REVERT: A 218 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8326 (ptmm) REVERT: A 241 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 516 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8500 (mt-10) REVERT: A 630 MET cc_start: 0.9168 (tpp) cc_final: 0.8953 (tpt) REVERT: A 693 MET cc_start: 0.8595 (ttp) cc_final: 0.7922 (tmm) REVERT: A 829 MET cc_start: 0.8819 (mpp) cc_final: 0.8454 (mpp) REVERT: A 859 ILE cc_start: 0.9205 (mp) cc_final: 0.8797 (tp) REVERT: A 1100 GLU cc_start: 0.8195 (pm20) cc_final: 0.7781 (pm20) outliers start: 19 outliers final: 12 residues processed: 48 average time/residue: 0.0924 time to fit residues: 7.3248 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 : 0.465 ------------------------------------------------------------------------------- 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 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 1012 GLU Chi-restraints excluded: chain A residue 1063 ILE 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: 0.9980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.069808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045818 restraints weight = 64565.561| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.56 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3080 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= 0.102 Angle : 0.469 8.498 19294 Z= 0.257 Chirality : 0.036 0.160 2252 Planarity : 0.003 0.042 1936 Dihedral : 20.963 89.874 3457 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.70 % Allowed : 21.25 % 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: 0.91 (0.23), residues: 1331 helix: 1.59 (0.20), residues: 695 sheet: -0.44 (0.50), residues: 101 loop : -0.44 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.010 0.001 TYR A1145 PHE 0.010 0.001 PHE A 946 TRP 0.011 0.001 TRP A1074 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (13768) covalent geometry : angle 0.46889 / 0.26 (19294) hydrogen bonds : bond 0.03370 / 2.27 ( 631) hydrogen bonds : angle 4.13489 / 2.87 ( 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 53 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9234 (pt) cc_final: 0.8995 (mm) REVERT: A 218 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8309 (ptmm) REVERT: A 241 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7274 (t80) REVERT: A 630 MET cc_start: 0.9118 (tpp) cc_final: 0.8867 (tpt) REVERT: A 693 MET cc_start: 0.8586 (ttp) cc_final: 0.7898 (tmm) REVERT: A 829 MET cc_start: 0.8827 (mpp) cc_final: 0.8362 (mpp) REVERT: A 859 ILE cc_start: 0.9069 (mp) cc_final: 0.8667 (tp) outliers start: 16 outliers final: 5 residues processed: 51 average time/residue: 0.0909 time to fit residues: 7.5489 Evaluate side-chains 35 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 928 LEU Chi-restraints excluded: chain A residue 1063 ILE 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: 9.9990 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 26 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.067648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.043733 restraints weight = 64694.715| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.48 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13768 Z= 0.219 Angle : 0.537 9.166 19294 Z= 0.288 Chirality : 0.038 0.142 2252 Planarity : 0.004 0.047 1936 Dihedral : 21.019 89.962 3457 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.85 (0.23), residues: 1331 helix: 1.54 (0.20), residues: 695 sheet: -0.45 (0.49), residues: 105 loop : -0.48 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1233 TYR 0.016 0.002 TYR A 155 PHE 0.012 0.001 PHE A 446 TRP 0.010 0.001 TRP A1074 HIS 0.005 0.001 HIS A 989 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (13768) covalent geometry : angle 0.53656 / 0.29 (19294) hydrogen bonds : bond 0.03812 / 2.60 ( 631) hydrogen bonds : angle 4.28067 / 2.98 ( 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 48 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 27 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9296 (pt) cc_final: 0.9028 (mm) REVERT: A 37 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8268 (p0) REVERT: A 218 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8364 (ptmm) REVERT: A 241 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 402 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: A 630 MET cc_start: 0.9220 (tpp) cc_final: 0.9009 (tpt) REVERT: A 693 MET cc_start: 0.8615 (ttp) cc_final: 0.7938 (tmm) REVERT: A 829 MET cc_start: 0.8836 (mpp) cc_final: 0.8437 (mpp) REVERT: A 859 ILE cc_start: 0.9070 (mp) cc_final: 0.8681 (tp) outliers start: 21 outliers final: 11 residues processed: 48 average time/residue: 0.0895 time to fit residues: 7.1201 Evaluate side-chains 41 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 928 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 1180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 0.0000 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 90 optimal weight: 50.0000 chunk 106 optimal weight: 8.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.068470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044551 restraints weight = 63944.079| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.51 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13768 Z= 0.116 Angle : 0.481 11.238 19294 Z= 0.258 Chirality : 0.036 0.278 2252 Planarity : 0.003 0.040 1936 Dihedral : 21.008 90.433 3457 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.59 % Allowed : 21.68 % Favored : 76.73 % 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: 1.03 (0.23), residues: 1331 helix: 1.72 (0.20), residues: 683 sheet: -0.40 (0.51), residues: 101 loop : -0.37 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.010 0.001 TYR A 25 PHE 0.011 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 0.00239 / 0.12 (13768) covalent geometry : angle 0.48128 / 0.26 (19294) hydrogen bonds : bond 0.03418 / 2.30 ( 631) hydrogen bonds : angle 4.13328 / 2.88 ( 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 43 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9228 (pt) cc_final: 0.9005 (mm) REVERT: A 37 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8222 (p0) REVERT: A 218 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8364 (ptmm) REVERT: A 241 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7333 (t80) REVERT: A 630 MET cc_start: 0.9134 (tpp) cc_final: 0.8888 (tpt) REVERT: A 693 MET cc_start: 0.8605 (ttp) cc_final: 0.7917 (tmm) REVERT: A 829 MET cc_start: 0.8773 (mpp) cc_final: 0.8321 (mpp) REVERT: A 859 ILE cc_start: 0.9083 (mp) cc_final: 0.8683 (tp) outliers start: 15 outliers final: 9 residues processed: 40 average time/residue: 0.0796 time to fit residues: 5.5860 Evaluate side-chains 37 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 482 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE 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 1114 PHE Chi-restraints excluded: chain A residue 1242 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 49 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.065984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.042087 restraints weight = 64664.578| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.53 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.172 13768 Z= 0.267 Angle : 0.598 10.610 19294 Z= 0.321 Chirality : 0.040 0.173 2252 Planarity : 0.004 0.051 1936 Dihedral : 21.092 90.901 3457 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.02 % Allowed : 21.79 % Favored : 76.20 % 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: 1331 helix: 1.35 (0.20), residues: 698 sheet: -0.54 (0.52), residues: 103 loop : -0.59 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.019 0.002 TYR A 155 PHE 0.016 0.002 PHE A 188 TRP 0.019 0.003 TRP A1074 HIS 0.008 0.002 HIS A 989 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (13768) covalent geometry : angle 0.59832 / 0.32 (19294) hydrogen bonds : bond 0.04479 / 3.07 ( 631) hydrogen bonds : angle 4.46864 / 3.11 ( 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 45 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9315 (pt) cc_final: 0.9030 (mm) REVERT: A 37 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8325 (p0) REVERT: A 241 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7424 (t80) REVERT: A 402 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: A 693 MET cc_start: 0.8673 (ttp) cc_final: 0.8008 (tmm) REVERT: A 829 MET cc_start: 0.8864 (mpp) cc_final: 0.8420 (mpp) REVERT: A 859 ILE cc_start: 0.9204 (mp) cc_final: 0.8839 (tp) REVERT: A 1169 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9184 (p) outliers start: 19 outliers final: 12 residues processed: 44 average time/residue: 0.0962 time to fit residues: 7.2726 Evaluate side-chains 39 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 985 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1114 PHE 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: 20.0000 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.067319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.043356 restraints weight = 64136.889| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.53 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4083 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= 0.121 Angle : 0.491 11.646 19294 Z= 0.264 Chirality : 0.037 0.199 2252 Planarity : 0.003 0.045 1936 Dihedral : 21.074 91.403 3457 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.38 % Allowed : 22.85 % Favored : 75.77 % 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: 0.97 (0.23), residues: 1331 helix: 1.67 (0.20), residues: 690 sheet: -0.38 (0.55), residues: 97 loop : -0.45 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.012 0.001 TYR A 567 PHE 0.012 0.001 PHE A 946 TRP 0.013 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13768) covalent geometry : angle 0.49130 / 0.26 (19294) hydrogen bonds : bond 0.03551 / 2.40 ( 631) hydrogen bonds : angle 4.18726 / 2.91 ( 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 38 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9287 (pt) cc_final: 0.9032 (mm) REVERT: A 37 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 218 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8287 (ptmm) REVERT: A 241 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7410 (t80) REVERT: A 693 MET cc_start: 0.8628 (ttp) cc_final: 0.7968 (tmm) REVERT: A 829 MET cc_start: 0.8826 (mpp) cc_final: 0.8588 (mpp) REVERT: A 859 ILE cc_start: 0.9142 (mp) cc_final: 0.8732 (tp) REVERT: A 1169 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9174 (p) outliers start: 13 outliers final: 7 residues processed: 36 average time/residue: 0.1035 time to fit residues: 6.2123 Evaluate side-chains 36 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 482 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1114 PHE 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: 9.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.067894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044055 restraints weight = 63971.154| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.45 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4174 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= 0.105 Angle : 0.483 12.753 19294 Z= 0.255 Chirality : 0.036 0.206 2252 Planarity : 0.003 0.038 1936 Dihedral : 20.891 90.528 3457 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.85 % Allowed : 23.38 % Favored : 75.77 % 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: 1.16 (0.23), residues: 1331 helix: 1.87 (0.20), residues: 683 sheet: -0.21 (0.56), residues: 97 loop : -0.41 (0.26), residues: 551 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 A1332 TRP 0.010 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (13768) covalent geometry : angle 0.48289 / 0.25 (19294) hydrogen bonds : bond 0.03259 / 2.22 ( 631) hydrogen bonds : angle 4.06705 / 2.82 ( 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 34 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 37 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8367 (p0) REVERT: A 218 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: A 241 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 693 MET cc_start: 0.8654 (ttp) cc_final: 0.7974 (tmm) REVERT: A 829 MET cc_start: 0.8771 (mpp) cc_final: 0.8523 (mpp) REVERT: A 859 ILE cc_start: 0.9126 (mp) cc_final: 0.8679 (tp) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.0966 time to fit residues: 5.2888 Evaluate side-chains 29 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 624 ILE Chi-restraints excluded: chain A residue 1063 ILE 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: 2.9990 chunk 28 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.066655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.042748 restraints weight = 64324.958| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.54 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13768 Z= 0.184 Angle : 0.514 11.822 19294 Z= 0.273 Chirality : 0.037 0.194 2252 Planarity : 0.003 0.040 1936 Dihedral : 20.862 90.776 3457 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.17 % Allowed : 23.17 % Favored : 75.66 % 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: 1.06 (0.23), residues: 1331 helix: 1.75 (0.20), residues: 691 sheet: -0.28 (0.56), residues: 97 loop : -0.44 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.014 0.001 TYR A 155 PHE 0.015 0.001 PHE A1332 TRP 0.014 0.002 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (13768) covalent geometry : angle 0.51419 / 0.27 (19294) hydrogen bonds : bond 0.03640 / 2.47 ( 631) hydrogen bonds : angle 4.17958 / 2.90 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.06 seconds wall clock time: 45 minutes 50.46 seconds (2750.46 seconds total)