Starting phenix.real_space_refine on Wed Mar 4 11:54:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2m_51812/03_2026/9h2m_51812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2m_51812/03_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_51812/03_2026/9h2m_51812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2m_51812/03_2026/9h2m_51812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h2m_51812/03_2026/9h2m_51812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2m_51812/03_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-dev-5986/lib/python3.9/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: 3.48, per 1000 atoms: 0.26 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: 1.31 Conformation dependent library (CDL) restraints added in 436.2 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: 2.08 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: 3.75 Time building geometry restraints manager: 1.71 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=" P DC D 27 " pdb=" OP1 DC D 27 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" P DC E 11 " pdb=" OP1 DC E 11 " ideal model delta sigma weight residual 1.480 1.500 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" P DT D 10 " pdb=" OP1 DT D 10 " ideal model delta sigma weight residual 1.480 1.500 -0.020 2.00e-02 2.50e+03 9.72e-01 bond pdb=" P DG E 17 " pdb=" OP1 DG E 17 " ideal model delta sigma weight residual 1.480 1.500 -0.020 2.00e-02 2.50e+03 9.70e-01 bond pdb=" P DC D 2 " pdb=" OP1 DC D 2 " ideal model delta sigma weight residual 1.480 1.500 -0.020 2.00e-02 2.50e+03 9.60e-01 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18761 2.03 - 4.07: 463 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 - 0.053: 1904 0.053 - 0.107: 212 0.107 - 0.160: 83 0.160 - 0.214: 52 0.214 - 0.267: 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 2.35 -2.61 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU A1227 " pdb=" CB LEU A1227 " pdb=" CD1 LEU A1227 " pdb=" CD2 LEU A1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.98e-01 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 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.73e-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: 0.720 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.470 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.003 0.047 13768 Z= 0.155 Angle : 0.702 10.172 19294 Z= 0.398 Chirality : 0.047 0.267 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 covalent geometry : bond 0.00344 (13768) covalent geometry : angle 0.70168 (19294) hydrogen bonds : bond 0.19964 ( 631) hydrogen bonds : angle 6.50078 ( 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 : 0.491 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: 0.1565 time to fit residues: 21.0753 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 : 0.438 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 861 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN A1191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.069179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.045158 restraints weight = 64305.393| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.57 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 13768 Z= 0.243 Angle : 0.599 6.774 19294 Z= 0.323 Chirality : 0.038 0.228 2252 Planarity : 0.004 0.049 1936 Dihedral : 20.684 92.235 3457 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.19 % Allowed : 20.30 % Favored : 76.51 % 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: 0.39 (0.22), residues: 1331 helix: 0.98 (0.19), residues: 687 sheet: -0.42 (0.49), residues: 112 loop : -0.42 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 224 TYR 0.033 0.002 TYR A 347 PHE 0.015 0.002 PHE A1114 TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00518 (13768) covalent geometry : angle 0.59906 (19294) hydrogen bonds : bond 0.04410 ( 631) hydrogen bonds : angle 4.52361 ( 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 : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9310 (pt) cc_final: 0.9007 (mm) REVERT: A 859 ILE cc_start: 0.9264 (mp) cc_final: 0.8851 (tp) outliers start: 30 outliers final: 8 residues processed: 68 average time/residue: 0.1216 time to fit residues: 12.3601 Evaluate side-chains 40 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3745 r_free = 0.3745 target = 0.067976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044628 restraints weight = 60920.847| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.78 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13768 Z= 0.183 Angle : 0.533 8.131 19294 Z= 0.289 Chirality : 0.036 0.186 2252 Planarity : 0.004 0.051 1936 Dihedral : 21.068 92.529 3457 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.91 % Allowed : 21.47 % 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: 0.81 (0.23), residues: 1331 helix: 1.41 (0.20), residues: 694 sheet: -0.34 (0.52), residues: 101 loop : -0.37 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1328 TYR 0.015 0.001 TYR A1008 PHE 0.011 0.001 PHE A 946 TRP 0.011 0.002 TRP A 890 HIS 0.003 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00388 (13768) covalent geometry : angle 0.53290 (19294) hydrogen bonds : bond 0.03814 ( 631) hydrogen bonds : angle 4.30397 ( 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 52 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9388 (pt) cc_final: 0.9052 (mm) REVERT: A 37 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8107 (p0) REVERT: A 693 MET cc_start: 0.8518 (ttp) cc_final: 0.7918 (tmm) REVERT: A 859 ILE cc_start: 0.9051 (mp) cc_final: 0.8651 (tp) REVERT: A 1100 GLU cc_start: 0.8416 (mp0) cc_final: 0.8060 (pm20) outliers start: 18 outliers final: 9 residues processed: 50 average time/residue: 0.1092 time to fit residues: 8.8283 Evaluate side-chains 38 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 405 PHE 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 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1114 PHE 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: 0.9980 chunk 93 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 601 ASN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.065870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042082 restraints weight = 65197.316| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.52 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13768 Z= 0.239 Angle : 0.553 7.887 19294 Z= 0.298 Chirality : 0.037 0.187 2252 Planarity : 0.004 0.044 1936 Dihedral : 21.069 93.894 3457 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.23 % Allowed : 21.36 % 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: 0.79 (0.23), residues: 1331 helix: 1.42 (0.20), residues: 697 sheet: -0.29 (0.51), residues: 103 loop : -0.43 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.016 0.002 TYR A 155 PHE 0.014 0.001 PHE A1114 TRP 0.011 0.002 TRP A1074 HIS 0.005 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00505 (13768) covalent geometry : angle 0.55276 (19294) hydrogen bonds : bond 0.03914 ( 631) hydrogen bonds : angle 4.37878 ( 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 48 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 27 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9341 (pt) cc_final: 0.9083 (mm) REVERT: A 37 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8305 (p0) REVERT: A 402 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: A 693 MET cc_start: 0.8677 (ttp) cc_final: 0.8023 (tmm) REVERT: A 859 ILE cc_start: 0.9154 (mp) cc_final: 0.8761 (tp) REVERT: A 1030 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9045 (mtmm) outliers start: 21 outliers final: 15 residues processed: 46 average time/residue: 0.0986 time to fit residues: 7.7142 Evaluate side-chains 42 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 405 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 823 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1288 ASN Chi-restraints excluded: chain A residue 1348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 110 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 43 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3656 r_free = 0.3656 target = 0.065247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041868 restraints weight = 62057.915| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.69 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13768 Z= 0.146 Angle : 0.477 8.229 19294 Z= 0.256 Chirality : 0.035 0.176 2252 Planarity : 0.003 0.048 1936 Dihedral : 20.892 94.020 3457 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.08 (0.23), residues: 1331 helix: 1.71 (0.20), residues: 695 sheet: -0.28 (0.54), residues: 97 loop : -0.36 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.011 0.001 TYR A 567 PHE 0.011 0.001 PHE A 946 TRP 0.004 0.001 TRP A 658 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00311 (13768) covalent geometry : angle 0.47729 (19294) hydrogen bonds : bond 0.03197 ( 631) hydrogen bonds : angle 4.14018 ( 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 45 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9382 (pt) cc_final: 0.9107 (mm) REVERT: A 37 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8350 (p0) REVERT: A 693 MET cc_start: 0.8607 (ttp) cc_final: 0.7946 (tmm) REVERT: A 829 MET cc_start: 0.8882 (mpp) cc_final: 0.8600 (mpp) REVERT: A 859 ILE cc_start: 0.9130 (mp) cc_final: 0.8699 (tp) REVERT: A 1030 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9021 (mtmm) outliers start: 19 outliers final: 10 residues processed: 43 average time/residue: 0.1066 time to fit residues: 7.5756 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 : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 405 PHE 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 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 14 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.064181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.040935 restraints weight = 61853.164| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.66 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13768 Z= 0.195 Angle : 0.504 9.504 19294 Z= 0.269 Chirality : 0.036 0.191 2252 Planarity : 0.003 0.044 1936 Dihedral : 20.820 94.373 3457 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.70 % Allowed : 22.00 % 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: 1.10 (0.23), residues: 1331 helix: 1.74 (0.20), residues: 690 sheet: -0.26 (0.56), residues: 92 loop : -0.35 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.014 0.001 TYR A 155 PHE 0.013 0.001 PHE A 946 TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00412 (13768) covalent geometry : angle 0.50359 (19294) hydrogen bonds : bond 0.03493 ( 631) hydrogen bonds : angle 4.16475 ( 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 41 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9399 (pt) cc_final: 0.9131 (mm) REVERT: A 37 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8460 (p0) REVERT: A 690 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8543 (mtm110) REVERT: A 693 MET cc_start: 0.8640 (ttp) cc_final: 0.7974 (tmm) REVERT: A 829 MET cc_start: 0.8919 (mpp) cc_final: 0.8636 (mpp) REVERT: A 859 ILE cc_start: 0.9184 (mp) cc_final: 0.8758 (tp) REVERT: A 1030 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9013 (mtmm) REVERT: A 1100 GLU cc_start: 0.8478 (pm20) cc_final: 0.8235 (pm20) outliers start: 16 outliers final: 10 residues processed: 40 average time/residue: 0.1094 time to fit residues: 7.0771 Evaluate side-chains 37 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1288 ASN 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: 7.9990 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3638 r_free = 0.3638 target = 0.064161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040823 restraints weight = 62711.678| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.56 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.5368 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= 0.248 Angle : 0.543 9.750 19294 Z= 0.290 Chirality : 0.037 0.186 2252 Planarity : 0.004 0.056 1936 Dihedral : 20.891 96.814 3457 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.02 % Allowed : 21.89 % Favored : 76.09 % 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: 1.61 (0.20), residues: 692 sheet: -0.09 (0.53), residues: 103 loop : -0.43 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.017 0.002 TYR A 155 PHE 0.015 0.001 PHE A1114 TRP 0.007 0.002 TRP A 890 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00520 (13768) covalent geometry : angle 0.54260 (19294) hydrogen bonds : bond 0.03890 ( 631) hydrogen bonds : angle 4.38599 ( 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: 19 poor density : 24 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9389 (pt) cc_final: 0.9124 (mm) REVERT: A 690 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8490 (mtm110) REVERT: A 693 MET cc_start: 0.8665 (ttp) cc_final: 0.7997 (tmm) REVERT: A 829 MET cc_start: 0.9039 (mpp) cc_final: 0.8726 (mpp) REVERT: A 1006 LYS cc_start: 0.9299 (mttt) cc_final: 0.9030 (ttpp) REVERT: A 1030 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9052 (mtmm) outliers start: 19 outliers final: 12 residues processed: 40 average time/residue: 0.1267 time to fit residues: 7.6933 Evaluate side-chains 37 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1288 ASN 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: 0.0370 chunk 29 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3649 r_free = 0.3649 target = 0.064400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041293 restraints weight = 62039.501| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.57 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13768 Z= 0.212 Angle : 0.507 11.085 19294 Z= 0.271 Chirality : 0.036 0.178 2252 Planarity : 0.003 0.044 1936 Dihedral : 20.736 95.989 3457 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 22.32 % 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: 1.00 (0.23), residues: 1331 helix: 1.68 (0.20), residues: 689 sheet: -0.10 (0.57), residues: 92 loop : -0.46 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.015 0.001 TYR A 155 PHE 0.013 0.001 PHE A 946 TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00445 (13768) covalent geometry : angle 0.50750 (19294) hydrogen bonds : bond 0.03479 ( 631) hydrogen bonds : angle 4.25079 ( 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 42 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9408 (pt) cc_final: 0.9130 (mm) REVERT: A 690 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8426 (mtm110) REVERT: A 693 MET cc_start: 0.8605 (ttp) cc_final: 0.7954 (tmm) REVERT: A 829 MET cc_start: 0.9064 (mpp) cc_final: 0.8709 (mpp) REVERT: A 1030 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9044 (mtmm) outliers start: 19 outliers final: 14 residues processed: 41 average time/residue: 0.1019 time to fit residues: 6.7738 Evaluate side-chains 38 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1288 ASN 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: 7.9990 chunk 139 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3628 r_free = 0.3628 target = 0.063558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.040679 restraints weight = 62736.150| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.48 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13768 Z= 0.258 Angle : 0.551 11.711 19294 Z= 0.292 Chirality : 0.037 0.164 2252 Planarity : 0.004 0.045 1936 Dihedral : 20.770 96.794 3457 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.02 % Allowed : 22.32 % 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: 0.93 (0.24), residues: 1331 helix: 1.62 (0.20), residues: 689 sheet: -0.15 (0.57), residues: 97 loop : -0.48 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.017 0.002 TYR A 155 PHE 0.015 0.001 PHE A1114 TRP 0.007 0.002 TRP A 476 HIS 0.003 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00540 (13768) covalent geometry : angle 0.55090 (19294) hydrogen bonds : bond 0.03930 ( 631) hydrogen bonds : angle 4.38535 ( 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: 19 poor density : 23 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9432 (pt) cc_final: 0.9169 (mm) REVERT: A 690 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8516 (mtm110) REVERT: A 693 MET cc_start: 0.8644 (ttp) cc_final: 0.7996 (tmm) REVERT: A 829 MET cc_start: 0.9041 (mpp) cc_final: 0.8719 (mpp) REVERT: A 1030 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9083 (mtmm) outliers start: 19 outliers final: 15 residues processed: 39 average time/residue: 0.1159 time to fit residues: 7.2038 Evaluate side-chains 40 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1030 LYS Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1114 PHE Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1288 ASN Chi-restraints excluded: chain A residue 1348 VAL 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: 7.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN ** A1241 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 = 0.3679 r_free = 0.3679 target = 0.065195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041982 restraints weight = 62679.647| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.79 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13768 Z= 0.120 Angle : 0.462 11.472 19294 Z= 0.245 Chirality : 0.035 0.163 2252 Planarity : 0.003 0.033 1936 Dihedral : 20.520 95.481 3457 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.59 % Allowed : 22.95 % 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: 1.24 (0.24), residues: 1331 helix: 1.92 (0.21), residues: 688 sheet: -0.04 (0.59), residues: 92 loop : -0.40 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.012 0.001 TYR A 567 PHE 0.012 0.001 PHE A 946 TRP 0.004 0.001 TRP A 18 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00254 (13768) covalent geometry : angle 0.46175 (19294) hydrogen bonds : bond 0.03059 ( 631) hydrogen bonds : angle 4.05087 ( 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 38 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9414 (pt) cc_final: 0.9133 (mm) REVERT: A 690 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8353 (mtm110) REVERT: A 829 MET cc_start: 0.9044 (mpp) cc_final: 0.8627 (mpp) outliers start: 15 outliers final: 11 residues processed: 36 average time/residue: 0.0989 time to fit residues: 5.7792 Evaluate side-chains 34 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 845 ILE 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 1114 PHE 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: 40.0000 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3662 r_free = 0.3662 target = 0.064730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041903 restraints weight = 62223.485| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.50 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13768 Z= 0.157 Angle : 0.475 12.058 19294 Z= 0.252 Chirality : 0.035 0.160 2252 Planarity : 0.003 0.032 1936 Dihedral : 20.465 95.346 3457 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.59 % Allowed : 23.49 % Favored : 74.92 % 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: 1.27 (0.24), residues: 1331 helix: 1.93 (0.20), residues: 688 sheet: -0.02 (0.57), residues: 97 loop : -0.36 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 652 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A 946 TRP 0.004 0.001 TRP A 18 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00332 (13768) covalent geometry : angle 0.47504 (19294) hydrogen bonds : bond 0.03233 ( 631) hydrogen bonds : angle 4.05935 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.77 seconds wall clock time: 48 minutes 38.84 seconds (2918.84 seconds total)