Starting phenix.real_space_refine on Sat Mar 7 04:58:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2f_52583/03_2026/9i2f_52583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2f_52583/03_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_52583/03_2026/9i2f_52583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2f_52583/03_2026/9i2f_52583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2f_52583/03_2026/9i2f_52583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2f_52583/03_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-dev-5986/lib/python3.9/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: 6.55, 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: 2.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5.97 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: 9.10 Time building geometry restraints manager: 4.09 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=" CD GLU A 235 " pdb=" OE1 GLU A 235 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" C SER A 170 " pdb=" N PRO A 171 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.38e-02 5.25e+03 1.61e+00 ... (remaining 38055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 67593 1.84 - 3.68: 1164 3.68 - 5.53: 31 5.53 - 7.37: 3 7.37 - 9.21: 2 Bond angle restraints: 68793 Sorted by residual: angle pdb=" C3' DA G 9 " pdb=" C2' DA G 9 " pdb=" C1' DA G 9 " ideal model delta sigma weight residual 101.60 105.83 -4.23 1.50e+00 4.44e-01 7.95e+00 angle pdb=" N GLU A 235 " pdb=" CA GLU A 235 " pdb=" CB GLU A 235 " ideal model delta sigma weight residual 110.16 114.11 -3.95 1.48e+00 4.57e-01 7.12e+00 angle pdb=" CA LEU B 386 " pdb=" CB LEU B 386 " pdb=" CG LEU B 386 " ideal model delta sigma weight residual 116.30 125.51 -9.21 3.50e+00 8.16e-02 6.92e+00 angle pdb=" C LYS A 577 " pdb=" N GLU A 578 " pdb=" CA GLU A 578 " ideal model delta sigma weight residual 120.31 116.40 3.91 1.52e+00 4.33e-01 6.62e+00 angle pdb=" N GLU A 578 " pdb=" CA GLU A 578 " pdb=" CB GLU A 578 " ideal model delta sigma weight residual 110.28 114.19 -3.91 1.55e+00 4.16e-01 6.36e+00 ... (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: 2730 0.043 - 0.085: 502 0.085 - 0.128: 156 0.128 - 0.170: 16 0.170 - 0.213: 1 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=" CG LEU B 386 " pdb=" CB LEU B 386 " pdb=" CD1 LEU B 386 " pdb=" CD2 LEU B 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA VAL B 455 " pdb=" N VAL B 455 " pdb=" C VAL B 455 " pdb=" CB VAL B 455 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.36e-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: 3.070 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: 0.190 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.090 Find NCS groups from input model: 0.460 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20689 Z= 0.150 Angle : 0.546 9.209 29108 Z= 0.313 Chirality : 0.038 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 covalent geometry : bond 0.00317 (20689) covalent geometry : angle 0.54580 (29108) hydrogen bonds : bond 0.13095 ( 894) hydrogen bonds : angle 6.70530 ( 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 : 0.883 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: 1.3210 time to fit residues: 177.2638 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 : 0.845 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.097806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061256 restraints weight = 121455.792| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.65 r_work: 0.2827 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20689 Z= 0.168 Angle : 0.499 7.456 29108 Z= 0.281 Chirality : 0.037 0.144 3405 Planarity : 0.004 0.044 2709 Dihedral : 21.933 176.397 5660 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 0.38 % Allowed : 4.41 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1726 helix: 1.24 (0.18), residues: 810 sheet: 0.19 (0.41), residues: 182 loop : -1.05 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.020 0.001 TYR B 273 PHE 0.011 0.001 PHE C 495 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00357 (20689) covalent geometry : angle 0.49944 (29108) hydrogen bonds : bond 0.04793 ( 894) hydrogen bonds : angle 4.84159 ( 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 98 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.863 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: 0.9489 (mmp) cc_final: 0.9222 (mmm) REVERT: C 414 LYS cc_start: 0.9002 (tttp) cc_final: 0.8578 (ttmm) REVERT: C 514 MET cc_start: 0.8652 (ttp) cc_final: 0.8098 (ttp) REVERT: A 489 MET cc_start: 0.8149 (mtp) cc_final: 0.7799 (mtp) REVERT: A 551 MET cc_start: 0.8872 (ptm) cc_final: 0.8609 (ptm) REVERT: B 325 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8437 (ttpp) REVERT: B 551 MET cc_start: 0.7052 (ptm) cc_final: 0.6573 (ptm) REVERT: B 560 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8445 (tptp) outliers start: 6 outliers final: 0 residues processed: 95 average time/residue: 1.2981 time to fit residues: 139.0804 Evaluate side-chains 82 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN A 255 GLN B 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057631 restraints weight = 120685.189| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.61 r_work: 0.2729 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20689 Z= 0.269 Angle : 0.522 5.820 29108 Z= 0.296 Chirality : 0.039 0.152 3405 Planarity : 0.004 0.054 2709 Dihedral : 22.117 177.276 5660 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 0.77 % Allowed : 5.43 % Favored : 93.80 % 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: 0.69 (0.21), residues: 1726 helix: 1.59 (0.18), residues: 810 sheet: 0.16 (0.40), residues: 185 loop : -0.73 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 473 TYR 0.018 0.001 TYR A 273 PHE 0.013 0.001 PHE B 124 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00582 (20689) covalent geometry : angle 0.52151 (29108) hydrogen bonds : bond 0.05161 ( 894) hydrogen bonds : angle 4.71580 ( 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 95 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.889 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 414 LYS cc_start: 0.9125 (tttp) cc_final: 0.8701 (ttpp) REVERT: A 317 ASP cc_start: 0.8900 (m-30) cc_final: 0.8689 (m-30) REVERT: A 551 MET cc_start: 0.8792 (ptm) cc_final: 0.8565 (ptm) REVERT: B 551 MET cc_start: 0.7114 (ptm) cc_final: 0.6707 (ptm) REVERT: B 560 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8438 (tptp) outliers start: 12 outliers final: 2 residues processed: 88 average time/residue: 1.2261 time to fit residues: 122.7328 Evaluate side-chains 77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain A residue 486 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 147 optimal weight: 0.0470 chunk 192 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058708 restraints weight = 120230.768| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.59 r_work: 0.2770 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20689 Z= 0.175 Angle : 0.480 4.844 29108 Z= 0.270 Chirality : 0.037 0.139 3405 Planarity : 0.003 0.059 2709 Dihedral : 22.067 177.421 5660 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 0.32 % Allowed : 7.16 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1726 helix: 1.77 (0.18), residues: 810 sheet: 0.06 (0.39), residues: 185 loop : -0.55 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.017 0.001 TYR B 273 PHE 0.009 0.001 PHE A 97 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00371 (20689) covalent geometry : angle 0.47954 (29108) hydrogen bonds : bond 0.04525 ( 894) hydrogen bonds : angle 4.47936 ( 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 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 256 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 317 ASP cc_start: 0.8978 (m-30) cc_final: 0.8769 (m-30) REVERT: C 414 LYS cc_start: 0.9119 (tttp) cc_final: 0.8682 (ttpp) REVERT: C 514 MET cc_start: 0.8702 (ttp) cc_final: 0.8231 (ttp) REVERT: A 551 MET cc_start: 0.8817 (ptm) cc_final: 0.8584 (ptm) REVERT: B 270 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8299 (ttm-80) REVERT: B 551 MET cc_start: 0.7132 (ptm) cc_final: 0.6732 (ptm) REVERT: B 560 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8426 (tptp) outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 1.2234 time to fit residues: 119.0415 Evaluate side-chains 79 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 372 ILE 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: 8.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056970 restraints weight = 120528.346| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.53 r_work: 0.2733 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20689 Z= 0.232 Angle : 0.499 6.115 29108 Z= 0.281 Chirality : 0.038 0.140 3405 Planarity : 0.004 0.049 2709 Dihedral : 22.091 177.504 5660 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 0.38 % Allowed : 7.93 % 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: 0.96 (0.21), residues: 1726 helix: 1.80 (0.18), residues: 810 sheet: -0.11 (0.39), residues: 185 loop : -0.44 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 332 TYR 0.017 0.001 TYR B 273 PHE 0.012 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00496 (20689) covalent geometry : angle 0.49854 (29108) hydrogen bonds : bond 0.04687 ( 894) hydrogen bonds : angle 4.49248 ( 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 81 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.898 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 256 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 414 LYS cc_start: 0.9213 (tttp) cc_final: 0.8758 (ttpp) REVERT: C 514 MET cc_start: 0.8767 (ttp) cc_final: 0.8325 (ttp) REVERT: A 489 MET cc_start: 0.8188 (mtp) cc_final: 0.7765 (mtp) REVERT: A 551 MET cc_start: 0.8649 (ptm) cc_final: 0.8074 (ptm) REVERT: B 560 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8495 (tmtt) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 1.1751 time to fit residues: 105.1395 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 : 0.700 ------------------------------------------------------------------------------- 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 383 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 187 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 547 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060089 restraints weight = 122056.438| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.52 r_work: 0.2690 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20689 Z= 0.210 Angle : 0.487 7.819 29108 Z= 0.274 Chirality : 0.038 0.143 3405 Planarity : 0.003 0.037 2709 Dihedral : 22.077 177.886 5660 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 0.45 % Allowed : 8.25 % 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: 1.03 (0.21), residues: 1726 helix: 1.84 (0.18), residues: 810 sheet: -0.10 (0.39), residues: 185 loop : -0.38 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.018 0.001 TYR B 273 PHE 0.011 0.001 PHE A 97 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00447 (20689) covalent geometry : angle 0.48673 (29108) hydrogen bonds : bond 0.04537 ( 894) hydrogen bonds : angle 4.43195 ( 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 81 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.866 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: 0.9165 (tttp) cc_final: 0.8716 (ttpp) REVERT: A 62 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7275 (p) REVERT: A 551 MET cc_start: 0.8742 (ptm) cc_final: 0.8357 (ptm) REVERT: B 560 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8489 (tmtt) outliers start: 7 outliers final: 3 residues processed: 79 average time/residue: 1.1762 time to fit residues: 106.3163 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 : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056987 restraints weight = 122000.571| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.58 r_work: 0.2682 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20689 Z= 0.222 Angle : 0.494 7.360 29108 Z= 0.278 Chirality : 0.038 0.142 3405 Planarity : 0.003 0.037 2709 Dihedral : 22.092 178.281 5660 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 0.45 % Allowed : 8.63 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1726 helix: 1.72 (0.18), residues: 823 sheet: -0.22 (0.38), residues: 187 loop : -0.49 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 332 TYR 0.018 0.001 TYR A 273 PHE 0.011 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00474 (20689) covalent geometry : angle 0.49436 (29108) hydrogen bonds : bond 0.04579 ( 894) hydrogen bonds : angle 4.42107 ( 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 82 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 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: symmetry clash REVERT: C 414 LYS cc_start: 0.9150 (tttp) cc_final: 0.8672 (ttpp) REVERT: A 489 MET cc_start: 0.8091 (mtp) cc_final: 0.7797 (mtp) REVERT: A 551 MET cc_start: 0.8685 (ptm) cc_final: 0.8302 (ptm) REVERT: B 62 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 560 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8490 (tmtt) outliers start: 7 outliers final: 3 residues processed: 79 average time/residue: 1.1609 time to fit residues: 106.0722 Evaluate side-chains 77 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 3 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.093884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057921 restraints weight = 120891.381| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.55 r_work: 0.2678 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2641 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= 0.179 Angle : 0.484 7.161 29108 Z= 0.271 Chirality : 0.037 0.147 3405 Planarity : 0.003 0.035 2709 Dihedral : 22.072 178.393 5660 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 0.58 % Allowed : 8.50 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.21), residues: 1726 helix: 1.88 (0.18), residues: 811 sheet: -0.10 (0.39), residues: 181 loop : -0.29 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 332 TYR 0.017 0.001 TYR B 273 PHE 0.009 0.001 PHE A 97 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00380 (20689) covalent geometry : angle 0.48399 (29108) hydrogen bonds : bond 0.04402 ( 894) hydrogen bonds : angle 4.33943 ( 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 86 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.830 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 45 GLN cc_start: 0.9076 (mt0) cc_final: 0.8479 (mp10) REVERT: C 414 LYS cc_start: 0.9109 (tttp) cc_final: 0.8632 (ttpp) REVERT: C 514 MET cc_start: 0.8728 (ttp) cc_final: 0.8216 (ttp) REVERT: A 62 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7120 (p) REVERT: A 489 MET cc_start: 0.8029 (mtp) cc_final: 0.7742 (mtp) REVERT: A 514 MET cc_start: 0.9165 (mtp) cc_final: 0.8909 (ttm) REVERT: A 524 ASP cc_start: 0.8968 (m-30) cc_final: 0.8724 (p0) REVERT: A 551 MET cc_start: 0.8708 (ptm) cc_final: 0.8335 (ptm) REVERT: B 62 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7627 (p) REVERT: B 560 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8481 (tmtt) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 1.1401 time to fit residues: 109.3603 Evaluate side-chains 81 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 194 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.093979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057612 restraints weight = 122854.726| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.60 r_work: 0.2677 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2720 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= 0.175 Angle : 0.481 6.960 29108 Z= 0.269 Chirality : 0.037 0.144 3405 Planarity : 0.003 0.033 2709 Dihedral : 22.049 178.355 5660 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.64 % Allowed : 8.38 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1726 helix: 1.92 (0.18), residues: 811 sheet: -0.14 (0.39), residues: 187 loop : -0.29 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 332 TYR 0.016 0.001 TYR B 273 PHE 0.009 0.001 PHE A 97 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00372 (20689) covalent geometry : angle 0.48139 (29108) hydrogen bonds : bond 0.04366 ( 894) hydrogen bonds : angle 4.30644 ( 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 88 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.878 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 414 LYS cc_start: 0.9092 (tttp) cc_final: 0.8618 (ttpp) REVERT: C 549 PHE cc_start: 0.9099 (t80) cc_final: 0.8821 (t80) REVERT: A 62 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7086 (p) REVERT: A 489 MET cc_start: 0.8105 (mtp) cc_final: 0.7773 (mtp) REVERT: A 551 MET cc_start: 0.8710 (ptm) cc_final: 0.8339 (ptm) REVERT: B 62 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 560 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8591 (mppt) outliers start: 10 outliers final: 4 residues processed: 84 average time/residue: 1.0366 time to fit residues: 101.6412 Evaluate side-chains 81 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 62 THR 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: 8.9990 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.093235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056975 restraints weight = 122047.674| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.58 r_work: 0.2681 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20689 Z= 0.218 Angle : 0.501 11.523 29108 Z= 0.280 Chirality : 0.038 0.144 3405 Planarity : 0.003 0.036 2709 Dihedral : 22.082 178.734 5660 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 0.51 % Allowed : 8.70 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1726 helix: 1.87 (0.18), residues: 811 sheet: -0.17 (0.39), residues: 187 loop : -0.28 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.018 0.001 TYR A 273 PHE 0.013 0.001 PHE B 570 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00468 (20689) covalent geometry : angle 0.50110 (29108) hydrogen bonds : bond 0.04540 ( 894) hydrogen bonds : angle 4.37113 ( 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 82 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.611 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 45 GLN cc_start: 0.9078 (mt0) cc_final: 0.8518 (mp10) REVERT: C 514 MET cc_start: 0.8762 (ttp) cc_final: 0.8257 (ttp) REVERT: C 549 PHE cc_start: 0.9133 (t80) cc_final: 0.8843 (t80) REVERT: A 62 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 489 MET cc_start: 0.8102 (mtp) cc_final: 0.7817 (mtp) REVERT: A 551 MET cc_start: 0.8721 (ptm) cc_final: 0.8354 (ptm) REVERT: B 62 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7728 (p) REVERT: B 514 MET cc_start: 0.8029 (tpp) cc_final: 0.7552 (tpt) REVERT: B 560 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8611 (mppt) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 1.0251 time to fit residues: 93.9968 Evaluate side-chains 79 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 62 THR 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 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.0870 chunk 193 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN 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 = 0.094899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058719 restraints weight = 122034.376| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.61 r_work: 0.2724 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20689 Z= 0.125 Angle : 0.475 9.806 29108 Z= 0.263 Chirality : 0.036 0.147 3405 Planarity : 0.003 0.033 2709 Dihedral : 22.024 178.520 5660 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 0.64 % Allowed : 8.57 % Favored : 90.79 % 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: 1.30 (0.21), residues: 1726 helix: 2.04 (0.18), residues: 813 sheet: -0.11 (0.39), residues: 186 loop : -0.16 (0.26), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.015 0.001 TYR B 273 PHE 0.007 0.001 PHE B 46 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00266 (20689) covalent geometry : angle 0.47529 (29108) hydrogen bonds : bond 0.04145 ( 894) hydrogen bonds : angle 4.18787 ( 2425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9678.90 seconds wall clock time: 164 minutes 54.86 seconds (9894.86 seconds total)