Starting phenix.real_space_refine on Mon Jul 6 18:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2f_52583/07_2026/9i2f_52583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2f_52583/07_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_52583/07_2026/9i2f_52583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2f_52583/07_2026/9i2f_52583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2f_52583/07_2026/9i2f_52583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2f_52583/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.59, per 1000 atoms: 0.18 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: 3.80 Conformation dependent library (CDL) restraints added in 945.4 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: 7.33 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: 10.33 Time building geometry restraints manager: 5.15 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: 67437 1.84 - 3.68: 1317 3.68 - 5.53: 34 5.53 - 7.37: 3 7.37 - 9.21: 2 Bond angle restraints: 68793 Sorted by residual: 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=" N3 DT G 64 " pdb=" C4 DT G 64 " pdb=" O4 DT G 64 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT G 57 " pdb=" C4 DT G 57 " pdb=" O4 DT G 57 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+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: 2713 0.043 - 0.085: 449 0.085 - 0.128: 144 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 43.670 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.510 ------------------------------------------------------------------------------- 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= 0.277 Angle : 0.596 9.209 29108 Z= 0.444 Chirality : 0.044 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 0.00373 / 0.28 (20689) covalent geometry : angle 0.59639 / 0.44 (29108) hydrogen bonds : bond 0.13095 / 14.41 ( 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 : 0.950 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: 0.9515 (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: 0.8529 (tmtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.3162 time to fit residues: 179.0029 Evaluate side-chains 91 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.3769 r_free = 0.3769 target = 0.098478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062105 restraints weight = 121653.203| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.65 r_work: 0.2850 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20689 Z= 0.169 Angle : 0.515 6.789 29108 Z= 0.302 Chirality : 0.039 0.279 3405 Planarity : 0.004 0.067 2709 Dihedral : 21.965 178.284 5660 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.01 % Favored : 96.87 % Rotamer: Outliers : 0.51 % Allowed : 4.22 % Favored : 95.27 % 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: 1.08 (0.18), residues: 810 sheet: 0.06 (0.41), residues: 182 loop : -1.22 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.018 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 0.00334 / 0.17 (20689) covalent geometry : angle 0.51473 / 0.30 (29108) hydrogen bonds : bond 0.05592 / 6.12 ( 894) hydrogen bonds : angle 5.19102 / 6.63 ( 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 97 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.043 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: symmetry clash REVERT: C 216 MET cc_start: 0.9530 (mmp) cc_final: 0.9284 (mmm) REVERT: C 317 ASP cc_start: 0.8978 (m-30) cc_final: 0.8771 (m-30) REVERT: C 414 LYS cc_start: 0.8981 (tttp) cc_final: 0.8583 (ttmm) REVERT: C 514 MET cc_start: 0.8605 (ttp) cc_final: 0.8063 (ttp) REVERT: A 417 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 489 MET cc_start: 0.8058 (mtp) cc_final: 0.7688 (mtp) REVERT: A 551 MET cc_start: 0.8866 (ptm) cc_final: 0.8603 (ptm) REVERT: B 551 MET cc_start: 0.6984 (ptm) cc_final: 0.6448 (ptm) REVERT: B 560 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8440 (tptp) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.2721 time to fit residues: 136.3058 Evaluate side-chains 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 5.9990 chunk 162 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.095710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059069 restraints weight = 121218.246| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.64 r_work: 0.2769 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20689 Z= 0.283 Angle : 0.524 6.951 29108 Z= 0.312 Chirality : 0.040 0.270 3405 Planarity : 0.004 0.058 2709 Dihedral : 22.054 179.256 5660 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 0.77 % Allowed : 5.18 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1726 helix: 1.45 (0.18), residues: 810 sheet: 0.30 (0.41), residues: 185 loop : -0.87 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.019 0.001 TYR B 273 PHE 0.012 0.001 PHE A 97 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 (20689) covalent geometry : angle 0.52380 / 0.31 (29108) hydrogen bonds : bond 0.05435 / 5.91 ( 894) hydrogen bonds : angle 4.95765 / 6.36 ( 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 99 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.864 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: 0.9520 (mmp) cc_final: 0.9298 (mmm) REVERT: C 414 LYS cc_start: 0.9049 (tttp) cc_final: 0.8642 (ttpp) REVERT: A 417 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8780 (mm-30) REVERT: A 489 MET cc_start: 0.8085 (mtp) cc_final: 0.7685 (mtp) REVERT: A 551 MET cc_start: 0.8881 (ptm) cc_final: 0.8634 (ptm) REVERT: B 551 MET cc_start: 0.7104 (ptm) cc_final: 0.6644 (ptm) REVERT: B 560 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8447 (tptp) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 1.2629 time to fit residues: 134.9685 Evaluate side-chains 88 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 B residue 120 ASP Chi-restraints excluded: chain B residue 383 LYS 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: 20.0000 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.096193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059531 restraints weight = 120173.428| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.61 r_work: 0.2781 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20689 Z= 0.182 Angle : 0.484 5.629 29108 Z= 0.287 Chirality : 0.038 0.267 3405 Planarity : 0.004 0.049 2709 Dihedral : 22.120 179.720 5660 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 0.58 % Allowed : 6.07 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1726 helix: 1.61 (0.18), residues: 810 sheet: 0.19 (0.40), residues: 185 loop : -0.75 (0.24), 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 0.010 0.001 PHE B 357 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (20689) covalent geometry : angle 0.48442 / 0.29 (29108) hydrogen bonds : bond 0.05050 / 5.47 ( 894) hydrogen bonds : angle 4.74392 / 6.07 ( 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 95 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.935 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 414 LYS cc_start: 0.9083 (tttp) cc_final: 0.8648 (ttpp) REVERT: C 514 MET cc_start: 0.8658 (ttp) cc_final: 0.8173 (ttp) REVERT: A 417 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8803 (mm-30) REVERT: A 489 MET cc_start: 0.8176 (mtp) cc_final: 0.7831 (mtp) REVERT: A 551 MET cc_start: 0.8858 (ptm) cc_final: 0.8609 (ptm) REVERT: B 551 MET cc_start: 0.7100 (ptm) cc_final: 0.6646 (ptm) REVERT: B 560 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8408 (tptp) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 1.1734 time to fit residues: 122.8908 Evaluate side-chains 82 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 171 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 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: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.095433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058717 restraints weight = 120563.524| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.61 r_work: 0.2758 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20689 Z= 0.218 Angle : 0.491 7.195 29108 Z= 0.290 Chirality : 0.038 0.261 3405 Planarity : 0.004 0.062 2709 Dihedral : 22.134 179.695 5660 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 0.45 % Allowed : 6.46 % Favored : 93.09 % 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: 0.84 (0.21), residues: 1726 helix: 1.72 (0.18), residues: 811 sheet: 0.03 (0.40), residues: 185 loop : -0.60 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.018 0.001 TYR B 273 PHE 0.011 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (20689) covalent geometry : angle 0.49115 / 0.29 (29108) hydrogen bonds : bond 0.04961 / 5.35 ( 894) hydrogen bonds : angle 4.63693 / 5.94 ( 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 89 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 1.093 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: 0.9130 (tttp) cc_final: 0.8694 (ttpp) REVERT: C 514 MET cc_start: 0.8687 (ttp) cc_final: 0.8263 (ttp) REVERT: A 489 MET cc_start: 0.8185 (mtp) cc_final: 0.7836 (mtp) REVERT: A 551 MET cc_start: 0.8829 (ptm) cc_final: 0.8585 (ptm) REVERT: B 518 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6836 (t80) REVERT: B 551 MET cc_start: 0.7109 (ptm) cc_final: 0.6687 (ptm) REVERT: B 560 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8439 (tptp) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 1.2855 time to fit residues: 129.0257 Evaluate side-chains 79 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 372 ILE 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: 10.0000 chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.095160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058427 restraints weight = 120727.583| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.61 r_work: 0.2756 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1838 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= 0.202 Angle : 0.487 8.643 29108 Z= 0.287 Chirality : 0.038 0.263 3405 Planarity : 0.004 0.078 2709 Dihedral : 22.177 179.789 5660 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.32 % Allowed : 7.23 % Favored : 92.46 % 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: 0.87 (0.21), residues: 1726 helix: 1.74 (0.18), residues: 810 sheet: -0.08 (0.39), residues: 185 loop : -0.53 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 473 TYR 0.017 0.001 TYR B 273 PHE 0.010 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (20689) covalent geometry : angle 0.48673 / 0.29 (29108) hydrogen bonds : bond 0.04883 / 5.26 ( 894) hydrogen bonds : angle 4.58574 / 5.88 ( 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 80 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.960 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 414 LYS cc_start: 0.9147 (tttp) cc_final: 0.8714 (ttpp) REVERT: A 551 MET cc_start: 0.8805 (ptm) cc_final: 0.8601 (ptm) REVERT: B 518 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6777 (t80) REVERT: B 551 MET cc_start: 0.7139 (ptm) cc_final: 0.6718 (ptm) REVERT: B 560 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8432 (tptp) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 1.1873 time to fit residues: 108.0794 Evaluate side-chains 73 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain B residue 518 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.095463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058805 restraints weight = 120384.514| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.59 r_work: 0.2759 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1916 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= 0.166 Angle : 0.477 8.080 29108 Z= 0.280 Chirality : 0.038 0.262 3405 Planarity : 0.004 0.071 2709 Dihedral : 22.168 179.698 5660 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 0.32 % Allowed : 7.54 % Favored : 92.14 % 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: 1.82 (0.18), residues: 810 sheet: -0.10 (0.39), residues: 185 loop : -0.49 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 332 TYR 0.028 0.001 TYR A 273 PHE 0.009 0.001 PHE A 97 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (20689) covalent geometry : angle 0.47662 / 0.28 (29108) hydrogen bonds : bond 0.04738 / 5.10 ( 894) hydrogen bonds : angle 4.50263 / 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 79 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.902 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: 0.9149 (tttp) cc_final: 0.8708 (ttpp) REVERT: C 514 MET cc_start: 0.8716 (ttp) cc_final: 0.8317 (ttp) REVERT: A 551 MET cc_start: 0.8818 (ptm) cc_final: 0.8559 (ptm) REVERT: B 518 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6652 (t80) REVERT: B 551 MET cc_start: 0.7131 (ptm) cc_final: 0.6740 (ptm) REVERT: B 560 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8426 (tptp) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 1.1171 time to fit residues: 101.0461 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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=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: 0.9990 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.094584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.058067 restraints weight = 119897.914| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.56 r_work: 0.2771 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20689 Z= 0.156 Angle : 0.469 8.572 29108 Z= 0.276 Chirality : 0.037 0.262 3405 Planarity : 0.003 0.052 2709 Dihedral : 22.143 179.628 5660 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.19 % Allowed : 7.93 % Favored : 91.88 % 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: 1.05 (0.21), residues: 1726 helix: 1.88 (0.18), residues: 810 sheet: -0.09 (0.40), residues: 185 loop : -0.41 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 332 TYR 0.024 0.001 TYR A 273 PHE 0.008 0.001 PHE A 97 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (20689) covalent geometry : angle 0.46931 / 0.28 (29108) hydrogen bonds : bond 0.04640 / 4.99 ( 894) hydrogen bonds : angle 4.43724 / 5.68 ( 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 82 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.975 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 414 LYS cc_start: 0.9184 (tttp) cc_final: 0.8744 (ttpp) REVERT: C 514 MET cc_start: 0.8732 (ttp) cc_final: 0.8337 (ttp) REVERT: A 551 MET cc_start: 0.8771 (ptm) cc_final: 0.8112 (ptm) REVERT: A 555 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8394 (mtp-110) REVERT: B 551 MET cc_start: 0.7058 (ptm) cc_final: 0.6636 (ptm) REVERT: B 560 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8430 (tptp) outliers start: 3 outliers final: 0 residues processed: 80 average time/residue: 1.1971 time to fit residues: 111.2134 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 194 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.094477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057763 restraints weight = 121277.950| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.60 r_work: 0.2738 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20689 Z= 0.234 Angle : 0.504 9.314 29108 Z= 0.294 Chirality : 0.038 0.261 3405 Planarity : 0.004 0.050 2709 Dihedral : 22.144 179.567 5660 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 0.26 % Allowed : 8.06 % 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: 1.00 (0.21), residues: 1726 helix: 1.80 (0.18), residues: 810 sheet: 0.00 (0.40), residues: 183 loop : -0.40 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 473 TYR 0.036 0.001 TYR A 273 PHE 0.013 0.001 PHE A 570 HIS 0.004 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 (20689) covalent geometry : angle 0.50370 / 0.29 (29108) hydrogen bonds : bond 0.04847 / 5.22 ( 894) hydrogen bonds : angle 4.51419 / 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 80 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.008 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: 0.9211 (tttp) cc_final: 0.8779 (ttpp) REVERT: A 489 MET cc_start: 0.8180 (mtp) cc_final: 0.7832 (mtp) REVERT: A 551 MET cc_start: 0.8728 (ptm) cc_final: 0.8052 (ptm) REVERT: A 555 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8391 (mtp-110) REVERT: B 560 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8505 (tmtt) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 1.2446 time to fit residues: 110.8786 Evaluate side-chains 76 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 174 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 547 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059866 restraints weight = 125665.173| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.56 r_work: 0.2707 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20689 Z= 0.223 Angle : 0.496 9.807 29108 Z= 0.289 Chirality : 0.038 0.264 3405 Planarity : 0.004 0.047 2709 Dihedral : 22.187 179.809 5660 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.13 % Allowed : 8.38 % 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: 0.96 (0.21), residues: 1726 helix: 1.77 (0.18), residues: 810 sheet: -0.07 (0.39), residues: 183 loop : -0.41 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 473 TYR 0.034 0.001 TYR A 273 PHE 0.012 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (20689) covalent geometry : angle 0.49578 / 0.29 (29108) hydrogen bonds : bond 0.04846 / 5.21 ( 894) hydrogen bonds : angle 4.51365 / 5.79 ( 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 75 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.972 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: 0.9202 (tttp) cc_final: 0.8745 (ttpp) REVERT: A 551 MET cc_start: 0.8685 (ptm) cc_final: 0.8061 (ptm) REVERT: B 560 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8486 (tmtt) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 1.1550 time to fit residues: 99.0507 Evaluate side-chains 75 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 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: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.094027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057730 restraints weight = 121402.952| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.58 r_work: 0.2691 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20689 Z= 0.194 Angle : 0.488 9.866 29108 Z= 0.285 Chirality : 0.038 0.263 3405 Planarity : 0.004 0.041 2709 Dihedral : 22.179 179.608 5660 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 0.26 % Allowed : 8.44 % Favored : 91.30 % 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: 1.01 (0.21), residues: 1726 helix: 1.80 (0.18), residues: 810 sheet: -0.05 (0.39), residues: 183 loop : -0.38 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 332 TYR 0.025 0.001 TYR A 273 PHE 0.010 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (20689) covalent geometry : angle 0.48773 / 0.28 (29108) hydrogen bonds : bond 0.04756 / 5.12 ( 894) hydrogen bonds : angle 4.46147 / 5.72 ( 2425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9687.42 seconds wall clock time: 165 minutes 28.83 seconds (9928.83 seconds total)