Starting phenix.real_space_refine on Sun Aug 9 20:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2f_52583/08_2026/9i2f_52583.map" } resolution = 2.8 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= 0.008 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 273 5.49 5 S 63 5.16 5 C 11600 2.51 5 N 3426 2.21 5 O 4403 1.98 5 H 17371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 37136 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1067 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain breaks: 2 Chain: "I" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1001 Classifications: {'DNA': 32} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 2 Chain: "C" Number of atoms: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 9460 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 1 Chain: "A" Number of atoms: 9486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9486 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 19, 'TRANS': 560} Chain breaks: 1 Chain: "B" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9487 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 19, 'TRANS': 560} Chain breaks: 1 Chain: "E" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1867 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 15} Link IDs: {'rna2p': 20, 'rna3p': 37} Chain breaks: 1 Chain: "H" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1067 Classifications: {'DNA': 34} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 33} Chain breaks: 2 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1897 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 12, 'rna3p_pur': 22, 'rna3p_pyr': 14} Link IDs: {'rna2p': 22, 'rna3p': 36} Chain breaks: 1 Chain: "F" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1804 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 12, 'rna3p_pur': 21, 'rna3p_pyr': 12} Link IDs: {'rna2p': 22, 'rna3p': 33} Chain breaks: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.13 Number of scatterers: 37136 At special positions: 0 Unit cell: (119.9, 161.7, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 273 15.00 O 4403 8.00 N 3426 7.00 C 11600 6.00 H 17371 1.00 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: 3.45 Conformation dependent library (CDL) restraints added in 901.9 milliseconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 26 sheets defined 52.5% alpha, 13.3% beta 70 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.759A pdb=" N ALA C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.856A pdb=" N LEU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 62 through 88 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 169 through 193 removed outlier: 3.590A pdb=" N ILE C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 302 through 326 removed outlier: 3.933A pdb=" N LEU C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 416 through 424 Processing helix chain 'C' and resid 428 through 445 removed outlier: 4.496A pdb=" N LYS C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 476 removed outlier: 4.017A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.529A pdb=" N ARG C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 566 through 586 Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.811A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 169 through 193 removed outlier: 3.654A pdb=" N ILE A 173 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 302 through 327 removed outlier: 3.653A pdb=" N LEU A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.059A pdb=" N LEU A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 346' Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.655A pdb=" N TYR A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 416 through 424 Processing helix chain 'A' and resid 428 through 445 removed outlier: 4.371A pdb=" N LYS A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.795A pdb=" N LEU A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 518 " --> pdb=" O MET A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.936A pdb=" N ILE A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 566 through 586 Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.514A pdb=" N ALA B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.868A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 170 through 193 removed outlier: 4.603A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 302 through 328 removed outlier: 3.897A pdb=" N LEU B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 4.290A pdb=" N PHE B 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 428 through 446 removed outlier: 4.219A pdb=" N LYS B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.609A pdb=" N LEU B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 518 " --> pdb=" O MET B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.578A pdb=" N PHE B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 566 through 586 removed outlier: 4.281A pdb=" N LEU B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 48 Processing sheet with id=AA2, first strand: chain 'C' and resid 195 through 199 removed outlier: 4.769A pdb=" N GLU C 240 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 195 through 199 Processing sheet with id=AA4, first strand: chain 'C' and resid 217 through 220 Processing sheet with id=AA5, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AA6, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AA7, first strand: chain 'C' and resid 411 through 412 removed outlier: 5.977A pdb=" N THR C 370 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 495 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 500 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS C 493 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 50 removed outlier: 3.743A pdb=" N GLY A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.666A pdb=" N GLU A 240 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AB3, first strand: chain 'A' and resid 217 through 220 Processing sheet with id=AB4, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AB5, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AB6, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.742A pdb=" N PHE A 495 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 500 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A 493 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.620A pdb=" N GLU A 407 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 49 Processing sheet with id=AC1, first strand: chain 'B' and resid 195 through 199 removed outlier: 4.770A pdb=" N GLU B 240 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AC3, first strand: chain 'B' and resid 217 through 220 Processing sheet with id=AC4, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AC5, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AC6, first strand: chain 'B' and resid 411 through 412 removed outlier: 3.508A pdb=" N VAL B 501 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 459 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 495 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE B 500 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B 493 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 748 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 340 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 9.59 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17338 1.03 - 1.23: 148 1.23 - 1.42: 9059 1.42 - 1.62: 11422 1.62 - 1.81: 93 Bond restraints: 38060 Sorted by residual: bond pdb=" N THR C 4 " pdb=" H THR C 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 4 " pdb=" H THR B 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR A 4 " pdb=" H THR A 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C3' DT I 57 " pdb=" C2' DT I 57 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C1' DT H 57 " pdb=" N1 DT H 57 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.51e+00 ... (remaining 38055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 67140 1.84 - 3.68: 1613 3.68 - 5.53: 35 5.53 - 7.37: 3 7.37 - 9.21: 2 Bond angle restraints: 68793 Sorted by residual: angle pdb=" O5' G F 59 " pdb=" C5' G F 59 " pdb=" C4' G F 59 " ideal model delta sigma weight residual 109.40 113.43 -4.03 8.00e-01 1.56e+00 2.53e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT H 57 " pdb=" C4 DT H 57 " pdb=" O4 DT H 57 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT H 64 " pdb=" C4 DT H 64 " pdb=" O4 DT H 64 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" O5' C E 13 " pdb=" C5' C E 13 " pdb=" C4' C E 13 " ideal model delta sigma weight residual 109.40 112.77 -3.37 8.00e-01 1.56e+00 1.78e+01 ... (remaining 68788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 16745 35.30 - 70.61: 863 70.61 - 105.91: 42 105.91 - 141.22: 0 141.22 - 176.52: 13 Dihedral angle restraints: 17663 sinusoidal: 11636 harmonic: 6027 Sorted by residual: dihedral pdb=" O4' C E 39 " pdb=" C1' C E 39 " pdb=" N1 C E 39 " pdb=" C2 C E 39 " ideal model delta sinusoidal sigma weight residual 200.00 23.48 176.52 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C F 46 " pdb=" C1' C F 46 " pdb=" N1 C F 46 " pdb=" C2 C F 46 " ideal model delta sinusoidal sigma weight residual 200.00 48.66 151.34 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' U D 18 " pdb=" C1' U D 18 " pdb=" N1 U D 18 " pdb=" C2 U D 18 " ideal model delta sinusoidal sigma weight residual -128.00 45.16 -173.16 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 17660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2536 0.043 - 0.085: 459 0.085 - 0.128: 311 0.128 - 0.170: 90 0.170 - 0.213: 9 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CA GLU A 235 " pdb=" N GLU A 235 " pdb=" C GLU A 235 " pdb=" CB GLU A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3' DC I 67 " pdb=" C4' DC I 67 " pdb=" O3' DC I 67 " pdb=" C2' DC I 67 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" C3' DG G 65 " pdb=" C4' DG G 65 " pdb=" O3' DG G 65 " pdb=" C2' DG G 65 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 3402 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 575 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ASP B 575 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP B 575 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 576 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " -0.244 9.50e-02 1.11e+02 8.17e-02 7.38e+00 pdb=" NE ARG A 270 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 270 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 270 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 270 " -0.007 2.00e-02 2.50e+03 pdb="HH22 ARG A 270 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 74 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ASP A 74 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 74 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 75 " -0.014 2.00e-02 2.50e+03 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 513 2.10 - 2.72: 59644 2.72 - 3.35: 105049 3.35 - 3.97: 137181 3.97 - 4.60: 213572 Nonbonded interactions: 515959 Sorted by model distance: nonbonded pdb=" P DT G 1 " pdb=" O2' G D 15 " model vdw 1.470 3.200 nonbonded pdb=" O2' G E 15 " pdb=" P DT H 1 " model vdw 1.471 3.200 nonbonded pdb=" P DT I 1 " pdb=" O2' G F 15 " model vdw 1.488 3.200 nonbonded pdb="HH21 ARG A 270 " pdb=" HD2 TYR A 273 " model vdw 1.706 2.100 nonbonded pdb=" H1 G E 23 " pdb=" H5 C E 39 " model vdw 1.749 2.100 ... (remaining 515954 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 386 or (resid 387 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 388 through 535 or resid 541 through 586)) selection = (chain 'B' and (resid 4 through 109 or (resid 110 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 111 through 280 or (resid 281 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 282 through 535 or resid 541 through 586)) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 11 through 63 or resid 121 through 123)) selection = (chain 'E' and resid 11 through 123) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 27 or resid 54 through 67)) selection = (chain 'H' and (resid 1 through 27 or resid 54 through 67)) selection = chain 'I' } 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: 3.800 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: 0.210 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 39.200 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.041 20689 Z= 0.284 Angle : 0.651 9.209 29108 Z= 0.505 Chirality : 0.049 0.213 3405 Planarity : 0.005 0.106 2709 Dihedral : 18.661 176.520 9233 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 0.52 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -1.38 (0.20), residues: 1726 helix: -0.15 (0.18), residues: 798 sheet: -0.20 (0.41), residues: 182 loop : -1.92 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.023 0.001 TYR C 333 PHE 0.018 0.001 PHE B 397 HIS 0.010 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.28 (20689) covalent geometry : angle 0.65129 / 0.51 (29108) hydrogen bonds : bond 0.13095 / 14.44 ( 894) hydrogen bonds : angle 6.70530 / 8.45 ( 2425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.9515 (mmp) cc_final: 0.9284 (mmm) REVERT: C 268 ILE cc_start: 0.9285 (mp) cc_final: 0.8910 (mp) REVERT: C 414 LYS cc_start: 0.8958 (tttp) cc_final: 0.8567 (ttmm) REVERT: C 459 LEU cc_start: 0.9033 (mt) cc_final: 0.8775 (mt) REVERT: C 514 MET cc_start: 0.8568 (ttp) cc_final: 0.7991 (ttp) REVERT: A 417 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 475 LYS cc_start: 0.8837 (mppt) cc_final: 0.8580 (mptp) REVERT: A 489 MET cc_start: 0.8292 (mtp) cc_final: 0.7914 (mtp) REVERT: A 548 ILE cc_start: 0.9255 (mp) cc_final: 0.9017 (mp) REVERT: A 551 MET cc_start: 0.8880 (ptm) cc_final: 0.8415 (ptm) REVERT: B 551 MET cc_start: 0.6911 (ptm) cc_final: 0.6356 (ptm) REVERT: B 560 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8528 (tmtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.0656 time to fit residues: 145.6053 Evaluate side-chains 89 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.098625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062308 restraints weight = 121635.181| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.65 r_work: 0.2854 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20689 Z= 0.165 Angle : 0.528 6.931 29108 Z= 0.306 Chirality : 0.040 0.286 3405 Planarity : 0.004 0.064 2709 Dihedral : 21.943 178.698 5660 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 0.58 % Allowed : 4.41 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1726 helix: 1.05 (0.18), residues: 810 sheet: 0.06 (0.41), residues: 182 loop : -1.24 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.017 0.001 TYR B 273 PHE 0.008 0.001 PHE C 495 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (20689) covalent geometry : angle 0.52757 / 0.31 (29108) hydrogen bonds : bond 0.05687 / 6.25 ( 894) hydrogen bonds : angle 5.20480 / 6.65 ( 2425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.9527 (mmp) cc_final: 0.9271 (mmm) REVERT: C 414 LYS cc_start: 0.8970 (tttp) cc_final: 0.8573 (ttmm) REVERT: C 514 MET cc_start: 0.8597 (ttp) cc_final: 0.8054 (ttp) REVERT: A 417 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8774 (mm-30) REVERT: A 489 MET cc_start: 0.8042 (mtp) cc_final: 0.7669 (mtp) REVERT: A 551 MET cc_start: 0.8856 (ptm) cc_final: 0.8595 (ptm) REVERT: B 551 MET cc_start: 0.6989 (ptm) cc_final: 0.6454 (ptm) REVERT: B 560 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8439 (tptp) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 1.0321 time to fit residues: 109.3924 Evaluate side-chains 85 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 386 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 ASN B 321 ASN B 511 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058680 restraints weight = 120863.745| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.60 r_work: 0.2766 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20689 Z= 0.287 Angle : 0.546 6.528 29108 Z= 0.320 Chirality : 0.040 0.285 3405 Planarity : 0.004 0.061 2709 Dihedral : 22.059 179.420 5660 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 0.77 % Allowed : 5.24 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1726 helix: 1.42 (0.18), residues: 810 sheet: 0.26 (0.40), residues: 185 loop : -0.88 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 277 TYR 0.019 0.001 TYR B 273 PHE 0.013 0.001 PHE A 97 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.29 (20689) covalent geometry : angle 0.54637 / 0.32 (29108) hydrogen bonds : bond 0.05527 / 6.04 ( 894) hydrogen bonds : angle 4.98243 / 6.40 ( 2425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.9523 (mmp) cc_final: 0.9295 (mmm) REVERT: C 414 LYS cc_start: 0.9048 (tttp) cc_final: 0.8630 (ttpp) REVERT: A 417 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 489 MET cc_start: 0.8065 (mtp) cc_final: 0.7589 (mtp) REVERT: A 551 MET cc_start: 0.8881 (ptm) cc_final: 0.8636 (ptm) REVERT: B 551 MET cc_start: 0.7114 (ptm) cc_final: 0.6658 (ptm) REVERT: B 560 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8438 (tptp) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 1.0539 time to fit residues: 113.7567 Evaluate side-chains 89 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 386 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.096586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059853 restraints weight = 119977.458| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.60 r_work: 0.2782 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20689 Z= 0.156 Angle : 0.492 5.935 29108 Z= 0.287 Chirality : 0.038 0.280 3405 Planarity : 0.003 0.048 2709 Dihedral : 22.107 179.942 5660 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 0.70 % Allowed : 5.82 % Favored : 93.48 % 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: 0.68 (0.21), residues: 1726 helix: 1.59 (0.18), residues: 810 sheet: 0.15 (0.40), residues: 185 loop : -0.74 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.019 0.001 TYR B 273 PHE 0.009 0.001 PHE B 357 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (20689) covalent geometry : angle 0.49170 / 0.29 (29108) hydrogen bonds : bond 0.05096 / 5.54 ( 894) hydrogen bonds : angle 4.75807 / 6.10 ( 2425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 414 LYS cc_start: 0.9080 (tttp) cc_final: 0.8645 (ttpp) REVERT: A 417 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8799 (mm-30) REVERT: A 489 MET cc_start: 0.8078 (mtp) cc_final: 0.7679 (mtp) REVERT: A 551 MET cc_start: 0.8858 (ptm) cc_final: 0.8606 (ptm) REVERT: B 325 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8533 (ttmt) REVERT: B 551 MET cc_start: 0.7090 (ptm) cc_final: 0.6640 (ptm) REVERT: B 560 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8431 (tptp) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 0.9872 time to fit residues: 99.9910 Evaluate side-chains 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 120 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 162 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.095595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058729 restraints weight = 120567.627| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.60 r_work: 0.2759 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20689 Z= 0.221 Angle : 0.504 5.866 29108 Z= 0.295 Chirality : 0.039 0.274 3405 Planarity : 0.004 0.055 2709 Dihedral : 22.108 179.801 5660 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 0.26 % Allowed : 6.33 % Favored : 93.41 % 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 (0.21), residues: 1726 helix: 1.69 (0.18), residues: 810 sheet: 0.03 (0.40), residues: 185 loop : -0.65 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.018 0.001 TYR B 273 PHE 0.013 0.001 PHE B 471 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (20689) covalent geometry : angle 0.50439 / 0.29 (29108) hydrogen bonds : bond 0.05035 / 5.46 ( 894) hydrogen bonds : angle 4.68529 / 6.02 ( 2425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 ASP cc_start: 0.9036 (m-30) cc_final: 0.8836 (m-30) REVERT: C 414 LYS cc_start: 0.9124 (tttp) cc_final: 0.8689 (ttpp) REVERT: C 514 MET cc_start: 0.8682 (ttp) cc_final: 0.8248 (ttp) REVERT: A 489 MET cc_start: 0.8174 (mtp) cc_final: 0.7821 (mtp) REVERT: A 551 MET cc_start: 0.8854 (ptm) cc_final: 0.8608 (ptm) REVERT: B 518 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6620 (t80) REVERT: B 551 MET cc_start: 0.7107 (ptm) cc_final: 0.6673 (ptm) REVERT: B 560 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8426 (tptp) outliers start: 4 outliers final: 2 residues processed: 85 average time/residue: 1.0617 time to fit residues: 104.4511 Evaluate side-chains 77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain B residue 518 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 187 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.095204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058350 restraints weight = 120408.415| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.59 r_work: 0.2752 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20689 Z= 0.211 Angle : 0.502 8.987 29108 Z= 0.292 Chirality : 0.039 0.275 3405 Planarity : 0.004 0.056 2709 Dihedral : 22.168 179.989 5660 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 0.51 % Allowed : 6.71 % Favored : 92.77 % 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: 0.82 (0.21), residues: 1726 helix: 1.71 (0.18), residues: 810 sheet: -0.10 (0.39), residues: 185 loop : -0.58 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.024 0.001 TYR A 273 PHE 0.011 0.001 PHE A 97 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (20689) covalent geometry : angle 0.50198 / 0.29 (29108) hydrogen bonds : bond 0.04987 / 5.40 ( 894) hydrogen bonds : angle 4.63404 / 5.95 ( 2425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 414 LYS cc_start: 0.9148 (tttp) cc_final: 0.8716 (ttpp) REVERT: A 51 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6061 (tmtt) REVERT: A 489 MET cc_start: 0.8177 (mtp) cc_final: 0.7764 (mtp) REVERT: B 325 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8509 (ttmt) REVERT: B 551 MET cc_start: 0.7144 (ptm) cc_final: 0.6724 (ptm) REVERT: B 560 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8435 (tptp) outliers start: 8 outliers final: 2 residues processed: 83 average time/residue: 1.0905 time to fit residues: 105.2451 Evaluate side-chains 75 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 68 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059223 restraints weight = 120436.385| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.60 r_work: 0.2776 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20689 Z= 0.142 Angle : 0.484 8.358 29108 Z= 0.280 Chirality : 0.038 0.275 3405 Planarity : 0.004 0.074 2709 Dihedral : 22.146 179.935 5660 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 0.26 % Allowed : 7.67 % Favored : 92.07 % 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: 0.96 (0.21), residues: 1726 helix: 1.83 (0.18), residues: 810 sheet: -0.09 (0.39), residues: 185 loop : -0.50 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 473 TYR 0.027 0.001 TYR A 273 PHE 0.008 0.001 PHE A 97 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (20689) covalent geometry : angle 0.48382 / 0.28 (29108) hydrogen bonds : bond 0.04756 / 5.13 ( 894) hydrogen bonds : angle 4.49669 / 5.76 ( 2425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 ASP cc_start: 0.9032 (m-30) cc_final: 0.8826 (m-30) REVERT: C 414 LYS cc_start: 0.9128 (tttp) cc_final: 0.8684 (ttpp) REVERT: A 51 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6039 (tmtt) REVERT: A 551 MET cc_start: 0.8546 (ptm) cc_final: 0.8291 (ptm) REVERT: B 325 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8455 (ttmt) REVERT: B 551 MET cc_start: 0.7132 (ptm) cc_final: 0.6710 (ptm) REVERT: B 560 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8426 (tptp) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.9740 time to fit residues: 88.3366 Evaluate side-chains 78 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 327 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 3 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.095189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058225 restraints weight = 119813.531| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.60 r_work: 0.2764 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20689 Z= 0.210 Angle : 0.501 8.679 29108 Z= 0.290 Chirality : 0.038 0.273 3405 Planarity : 0.004 0.054 2709 Dihedral : 22.135 179.822 5660 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 0.38 % Allowed : 7.86 % Favored : 91.75 % 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: 0.98 (0.21), residues: 1726 helix: 1.83 (0.18), residues: 810 sheet: -0.11 (0.40), residues: 185 loop : -0.46 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 332 TYR 0.022 0.001 TYR A 273 PHE 0.010 0.001 PHE A 97 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (20689) covalent geometry : angle 0.50058 / 0.29 (29108) hydrogen bonds : bond 0.04832 / 5.23 ( 894) hydrogen bonds : angle 4.52952 / 5.81 ( 2425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 414 LYS cc_start: 0.9146 (tttp) cc_final: 0.8712 (ttpp) REVERT: C 514 MET cc_start: 0.8712 (ttp) cc_final: 0.8302 (ttp) REVERT: A 51 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6042 (tmtt) REVERT: A 489 MET cc_start: 0.8151 (mtp) cc_final: 0.7802 (mtp) REVERT: B 325 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8476 (ttmt) REVERT: B 551 MET cc_start: 0.7184 (ptm) cc_final: 0.6765 (ptm) REVERT: B 560 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8425 (tptp) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 1.0342 time to fit residues: 92.9892 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 486 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 194 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 185 optimal weight: 11.9990 chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 95 optimal weight: 0.0570 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058485 restraints weight = 121276.285| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.60 r_work: 0.2763 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20689 Z= 0.188 Angle : 0.494 9.376 29108 Z= 0.287 Chirality : 0.038 0.274 3405 Planarity : 0.004 0.053 2709 Dihedral : 22.147 179.847 5660 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 0.32 % Allowed : 7.99 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1726 helix: 1.84 (0.18), residues: 810 sheet: -0.05 (0.40), residues: 183 loop : -0.43 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 473 TYR 0.027 0.001 TYR A 273 PHE 0.009 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (20689) covalent geometry : angle 0.49418 / 0.29 (29108) hydrogen bonds : bond 0.04799 / 5.18 ( 894) hydrogen bonds : angle 4.50395 / 5.79 ( 2425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 414 LYS cc_start: 0.9152 (tttp) cc_final: 0.8722 (ttpp) REVERT: C 514 MET cc_start: 0.8710 (ttp) cc_final: 0.8298 (ttp) REVERT: A 51 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.5972 (tmtt) REVERT: A 489 MET cc_start: 0.8138 (mtp) cc_final: 0.7789 (mtp) REVERT: B 325 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8487 (ttmt) REVERT: B 551 MET cc_start: 0.7133 (ptm) cc_final: 0.6700 (ptm) REVERT: B 560 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8422 (tptp) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 1.1168 time to fit residues: 96.5483 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 486 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 174 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.096069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059294 restraints weight = 120562.672| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.61 r_work: 0.2780 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20689 Z= 0.136 Angle : 0.482 9.713 29108 Z= 0.278 Chirality : 0.038 0.274 3405 Planarity : 0.004 0.049 2709 Dihedral : 22.138 179.839 5660 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % 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 (0.21), residues: 1726 helix: 1.92 (0.18), residues: 811 sheet: -0.09 (0.40), residues: 185 loop : -0.39 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 473 TYR 0.027 0.001 TYR A 273 PHE 0.008 0.001 PHE B 357 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (20689) covalent geometry : angle 0.48187 / 0.28 (29108) hydrogen bonds : bond 0.04632 / 5.01 ( 894) hydrogen bonds : angle 4.40299 / 5.65 ( 2425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 414 LYS cc_start: 0.9163 (tttp) cc_final: 0.8728 (ttpp) REVERT: C 514 MET cc_start: 0.8711 (ttp) cc_final: 0.8289 (ttp) REVERT: A 489 MET cc_start: 0.8145 (mtp) cc_final: 0.7797 (mtp) REVERT: B 325 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8479 (ttmt) REVERT: B 551 MET cc_start: 0.7104 (ptm) cc_final: 0.6695 (ptm) REVERT: B 560 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8497 (tmtt) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.9589 time to fit residues: 84.4039 Evaluate side-chains 73 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 4 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056706 restraints weight = 120386.114| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.54 r_work: 0.2730 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20689 Z= 0.254 Angle : 0.525 9.612 29108 Z= 0.301 Chirality : 0.039 0.272 3405 Planarity : 0.004 0.049 2709 Dihedral : 22.116 179.639 5660 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1726 helix: 1.79 (0.18), residues: 810 sheet: -0.07 (0.40), residues: 183 loop : -0.39 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 473 TYR 0.036 0.001 TYR A 273 PHE 0.013 0.001 PHE A 97 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 (20689) covalent geometry : angle 0.52542 / 0.30 (29108) hydrogen bonds : bond 0.04957 / 5.37 ( 894) hydrogen bonds : angle 4.55339 / 5.87 ( 2425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8222.99 seconds wall clock time: 140 minutes 20.80 seconds (8420.80 seconds total)