Starting phenix.real_space_refine on Mon Nov 18 02:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p1i_17350/11_2024/8p1i_17350_trim.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 sd= 0.134 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 S 132 5.16 5 Cl 1 4.86 5 C 15157 2.51 5 N 3854 2.21 5 O 4361 1.98 5 H 23762 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 1.37s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47270 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 15689 Classifications: {'peptide': 1024} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 976} Chain breaks: 1 Chain: "B" Number of atoms: 15730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 15730 Classifications: {'peptide': 1026} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 978} Chain breaks: 1 Chain: "C" Number of atoms: 15711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 15711 Classifications: {'peptide': 1026} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 978} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'WQW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'WR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'PG8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.76, per 1000 atoms: 0.48 Number of scatterers: 47270 At special positions: 0 Unit cell: (115.506, 123.876, 143.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 132 16.00 P 3 15.00 O 4361 8.00 N 3854 7.00 C 15157 6.00 H 23762 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: 11.95 Conformation dependent library (CDL) restraints added in 3.9 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 24 sheets defined 60.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.835A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.838A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.695A pdb=" N GLN A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.540A pdb=" N ILE A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.575A pdb=" N PHE A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.705A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.865A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 4.715A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.612A pdb=" N ILE A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 4.073A pdb=" N ILE A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 removed outlier: 5.447A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 453 No H-bonds generated for 'chain 'A' and resid 452 through 453' Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 461 through 496 removed outlier: 3.671A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 537 Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.630A pdb=" N TYR A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 781 through 787 removed outlier: 4.048A pdb=" N GLY A 786 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 848 removed outlier: 3.572A pdb=" N GLY A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.811A pdb=" N GLN A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 892 removed outlier: 3.851A pdb=" N LEU A 875 " --> pdb=" O GLN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.699A pdb=" N VAL A 900 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 919 Processing helix chain 'A' and resid 923 through 953 removed outlier: 3.696A pdb=" N LEU A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 971 through 985 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 995 through 1016 removed outlier: 3.860A pdb=" N GLN A 999 " --> pdb=" O GLY A 995 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1032 Proline residue: A1022 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.721A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.502A pdb=" N ILE B 166 " --> pdb=" O MET B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.695A pdb=" N ALA B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 298 through 313 Processing helix chain 'B' and resid 314 through 317 Processing helix chain 'B' and resid 329 through 360 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.773A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.629A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.578A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.908A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 497 removed outlier: 3.602A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix removed outlier: 3.552A pdb=" N LEU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.643A pdb=" N ARG B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.761A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 638 through 641 removed outlier: 3.553A pdb=" N ASN B 641 " --> pdb=" O GLY B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 689 through 706 removed outlier: 4.213A pdb=" N LYS B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 741 through 754 Processing helix chain 'B' and resid 776 through 779 Processing helix chain 'B' and resid 781 through 787 removed outlier: 3.748A pdb=" N GLY B 786 " --> pdb=" O GLU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 848 Processing helix chain 'B' and resid 860 through 870 Processing helix chain 'B' and resid 871 through 892 removed outlier: 3.825A pdb=" N LEU B 875 " --> pdb=" O GLN B 871 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR B 876 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 Processing helix chain 'B' and resid 903 through 919 removed outlier: 4.006A pdb=" N GLY B 907 " --> pdb=" O VAL B 903 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 955 Processing helix chain 'B' and resid 958 through 991 removed outlier: 4.754A pdb=" N ARG B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Proline residue: B 973 - end of helix Proline residue: B 987 - end of helix Processing helix chain 'B' and resid 995 through 1032 removed outlier: 3.965A pdb=" N GLN B 999 " --> pdb=" O GLY B 995 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B1019 " --> pdb=" O ILE B1015 " (cutoff:3.500A) Proline residue: B1022 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.744A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.661A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.682A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.590A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.835A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 403 removed outlier: 4.376A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 Processing helix chain 'C' and resid 426 through 452 removed outlier: 5.749A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 460 through 496 removed outlier: 3.505A pdb=" N GLY C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 510 through 534 Processing helix chain 'C' and resid 537 through 558 removed outlier: 3.800A pdb=" N VAL C 542 " --> pdb=" O GLY C 538 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 638 through 641 removed outlier: 3.559A pdb=" N ASN C 641 " --> pdb=" O GLY C 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 638 through 641' Processing helix chain 'C' and resid 642 through 655 Processing helix chain 'C' and resid 690 through 706 Processing helix chain 'C' and resid 731 through 738 Processing helix chain 'C' and resid 741 through 754 Processing helix chain 'C' and resid 776 through 779 Processing helix chain 'C' and resid 781 through 787 Processing helix chain 'C' and resid 835 through 848 Processing helix chain 'C' and resid 860 through 892 Proline residue: C 873 - end of helix Processing helix chain 'C' and resid 895 through 902 Processing helix chain 'C' and resid 903 through 919 removed outlier: 3.648A pdb=" N GLY C 907 " --> pdb=" O VAL C 903 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 955 removed outlier: 3.828A pdb=" N ILE C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 985 removed outlier: 5.103A pdb=" N ARG C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Proline residue: C 973 - end of helix Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 995 through 1016 removed outlier: 4.182A pdb=" N GLN C 999 " --> pdb=" O GLY C 995 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1032 Proline residue: C1022 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.837A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN A 829 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY A 714 " --> pdb=" O GLN A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.837A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 77 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N ARG A 814 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU A 825 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 816 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.695A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 272 removed outlier: 7.569A pdb=" N TYR A 182 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR A 771 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N MET A 184 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET A 773 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE A 186 " --> pdb=" O MET A 773 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 759 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE A 772 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR A 757 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 219 removed outlier: 4.733A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER A 233 " --> pdb=" O PRO B 724 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.022A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 804 through 811 removed outlier: 8.594A pdb=" N ILE C 235 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 726 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 791 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.869A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 178 removed outlier: 3.776A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 322 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 178 removed outlier: 3.776A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER B 629 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 610 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.516A pdb=" N TYR B 182 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR B 771 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET B 184 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET B 773 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE B 186 " --> pdb=" O MET B 773 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN B 759 " --> pdb=" O VAL B 770 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 772 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR B 757 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.453A pdb=" N SER B 233 " --> pdb=" O PHE C 726 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 728 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 235 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 730 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.539A pdb=" N LYS B 252 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 717 removed outlier: 4.868A pdb=" N GLY B 714 " --> pdb=" O GLN B 829 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 829 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 828 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 789 through 791 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 131 removed outlier: 4.034A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.711A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.706A pdb=" N TYR C 182 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR C 771 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET C 184 " --> pdb=" O TYR C 771 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N MET C 773 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE C 186 " --> pdb=" O MET C 773 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN C 759 " --> pdb=" O VAL C 770 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE C 772 " --> pdb=" O TYR C 757 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 757 " --> pdb=" O ILE C 772 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 250 through 253 removed outlier: 3.610A pdb=" N LYS C 252 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 278 through 281 Processing sheet with id=AC5, first strand: chain 'C' and resid 712 through 717 removed outlier: 5.135A pdb=" N GLY C 714 " --> pdb=" O GLN C 829 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN C 829 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 828 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 791 1525 hydrogen bonds defined for protein. 4392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.44 Time building geometry restraints manager: 14.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 23756 1.02 - 1.22: 12 1.22 - 1.41: 9554 1.41 - 1.61: 14146 1.61 - 1.81: 261 Bond restraints: 47729 Sorted by residual: bond pdb=" CA VAL A 671 " pdb=" CB VAL A 671 " ideal model delta sigma weight residual 1.540 1.589 -0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" C23 WR6 B1101 " pdb=" O25 WR6 B1101 " ideal model delta sigma weight residual 1.333 1.404 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C29 WR6 B1101 " pdb=" O28 WR6 B1101 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" CA GLU A 672 " pdb=" C GLU A 672 " ideal model delta sigma weight residual 1.520 1.481 0.039 1.37e-02 5.33e+03 8.25e+00 bond pdb=" N GLU A 672 " pdb=" CA GLU A 672 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.42e-02 4.96e+03 5.24e+00 ... (remaining 47724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 86440 7.13 - 14.26: 10 14.26 - 21.39: 0 21.39 - 28.52: 0 28.52 - 35.65: 3 Bond angle restraints: 86453 Sorted by residual: angle pdb=" C LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 109.00 73.35 35.65 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 110.00 74.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB LYS B1034 " pdb=" CA LYS B1034 " pdb=" HA LYS B1034 " ideal model delta sigma weight residual 109.00 79.91 29.09 3.00e+00 1.11e-01 9.40e+01 angle pdb=" O44 WR6 B1101 " pdb=" P43 WR6 B1101 " pdb=" O45 WR6 B1101 " ideal model delta sigma weight residual 122.59 109.59 13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" N LYS B1034 " pdb=" CA LYS B1034 " pdb=" C LYS B1034 " ideal model delta sigma weight residual 111.00 121.86 -10.86 2.80e+00 1.28e-01 1.50e+01 ... (remaining 86448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 21472 27.72 - 55.45: 951 55.45 - 83.17: 87 83.17 - 110.90: 2 110.90 - 138.62: 2 Dihedral angle restraints: 22514 sinusoidal: 12385 harmonic: 10129 Sorted by residual: dihedral pdb=" CA VAL A 671 " pdb=" C VAL A 671 " pdb=" N GLU A 672 " pdb=" CA GLU A 672 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C14 WR6 B1101 " pdb=" C15 WR6 B1101 " pdb=" C16 WR6 B1101 " pdb=" C17 WR6 B1101 " ideal model delta sinusoidal sigma weight residual -60.93 77.69 -138.62 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C1 PG8 C1102 " pdb=" O3 PG8 C1102 " pdb=" P1 PG8 C1102 " pdb=" O6 PG8 C1102 " ideal model delta sinusoidal sigma weight residual 168.00 -74.84 -117.16 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 22511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3599 0.092 - 0.184: 197 0.184 - 0.275: 1 0.275 - 0.367: 0 0.367 - 0.459: 1 Chirality restraints: 3798 Sorted by residual: chirality pdb=" CA LYS B1034 " pdb=" N LYS B1034 " pdb=" C LYS B1034 " pdb=" CB LYS B1034 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C26 WR6 B1101 " pdb=" C27 WR6 B1101 " pdb=" C41 WR6 B1101 " pdb=" O25 WR6 B1101 " both_signs ideal model delta sigma weight residual False 2.22 2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL A 671 " pdb=" N VAL A 671 " pdb=" C VAL A 671 " pdb=" CB VAL A 671 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3795 not shown) Planarity restraints: 7079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 69 " 0.025 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" N ASN C 70 " -0.080 2.00e-02 2.50e+03 pdb=" CA ASN C 70 " 0.020 2.00e-02 2.50e+03 pdb=" H ASN C 70 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 671 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" N GLU A 672 " 0.079 2.00e-02 2.50e+03 pdb=" CA GLU A 672 " -0.020 2.00e-02 2.50e+03 pdb=" H GLU A 672 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 960 " -0.023 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" N GLU A 961 " 0.072 2.00e-02 2.50e+03 pdb=" CA GLU A 961 " -0.019 2.00e-02 2.50e+03 pdb=" H GLU A 961 " -0.031 2.00e-02 2.50e+03 ... (remaining 7076 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1594 2.17 - 2.78: 93905 2.78 - 3.38: 135609 3.38 - 3.99: 177517 3.99 - 4.60: 281493 Nonbonded interactions: 690118 Sorted by model distance: nonbonded pdb=" O VAL A 711 " pdb=" H ALA A 831 " model vdw 1.560 2.450 nonbonded pdb=" HH TYR A 757 " pdb=" OD1 ASP A 760 " model vdw 1.576 2.450 nonbonded pdb=" O ASN C 361 " pdb=" HG1 THR C 365 " model vdw 1.577 2.450 nonbonded pdb=" H GLY A 792 " pdb=" O GLN A 796 " model vdw 1.607 2.450 nonbonded pdb="HH21 ARG B 307 " pdb=" OD2 ASP B 328 " model vdw 1.607 2.450 ... (remaining 690113 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 1 through 1031 or (resid 1032 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or (resid 1033 and (name N or name CA or name C or name O or \ name CB or name OG )))) selection = (chain 'B' and (resid 1 through 499 or resid 509 through 1031 or (resid 1032 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name CE1 or name CE2 or name CZ )) or (resid 1033 and (name N or name C \ A or name C or name O or name CB or name OG )))) selection = (chain 'C' and (resid 1 through 499 or resid 509 through 1033)) } 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: 3.470 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: 0.820 Extract box with map and model: 1.730 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 97.530 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.130 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:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.071 23967 Z= 0.297 Angle : 0.549 12.998 32532 Z= 0.273 Chirality : 0.041 0.459 3798 Planarity : 0.003 0.047 4152 Dihedral : 13.759 138.623 8734 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3064 helix: 1.98 (0.13), residues: 1639 sheet: -0.54 (0.27), residues: 355 loop : -0.47 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 894 HIS 0.003 0.001 HIS A 338 PHE 0.028 0.001 PHE A 761 TYR 0.023 0.002 TYR B 49 ARG 0.002 0.000 ARG B 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 3.464 Fit side-chains revert: symmetry clash REVERT: A 917 PHE cc_start: 0.7112 (m-80) cc_final: 0.6630 (t80) REVERT: B 29 LYS cc_start: 0.7213 (mttt) cc_final: 0.5769 (pptt) REVERT: B 269 GLU cc_start: 0.8221 (pt0) cc_final: 0.7961 (pt0) REVERT: B 309 GLU cc_start: 0.7468 (tp30) cc_final: 0.7192 (mm-30) REVERT: B 574 MET cc_start: 0.7442 (ptt) cc_final: 0.7088 (ptm) REVERT: B 1015 ILE cc_start: 0.8589 (mm) cc_final: 0.8338 (mt) REVERT: C 29 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7132 (pptt) REVERT: C 267 LYS cc_start: 0.7652 (tttp) cc_final: 0.7391 (tttp) REVERT: C 312 LYS cc_start: 0.7101 (mttt) cc_final: 0.6764 (tmtt) REVERT: C 528 ASP cc_start: 0.7507 (t70) cc_final: 0.7229 (t0) REVERT: C 780 MET cc_start: 0.8860 (mmt) cc_final: 0.7911 (mmt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 2.8041 time to fit residues: 1126.0367 Evaluate side-chains 278 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23967 Z= 0.237 Angle : 0.532 10.615 32532 Z= 0.277 Chirality : 0.041 0.458 3798 Planarity : 0.004 0.034 4152 Dihedral : 6.113 96.052 3398 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.64 % Allowed : 7.44 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3064 helix: 2.02 (0.13), residues: 1662 sheet: -0.64 (0.27), residues: 349 loop : -0.47 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.003 0.001 HIS A 525 PHE 0.025 0.001 PHE C 616 TYR 0.014 0.001 TYR B 49 ARG 0.003 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 3.626 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7474 (mmmt) cc_final: 0.5638 (pptt) REVERT: A 69 MET cc_start: 0.8861 (mmt) cc_final: 0.8060 (mmt) REVERT: A 917 PHE cc_start: 0.7023 (m-80) cc_final: 0.6478 (t80) REVERT: B 29 LYS cc_start: 0.7187 (mttt) cc_final: 0.5750 (pptt) REVERT: B 167 SER cc_start: 0.8396 (t) cc_final: 0.7723 (p) REVERT: B 248 ASN cc_start: 0.8069 (t160) cc_final: 0.7801 (t0) REVERT: B 269 GLU cc_start: 0.8263 (pt0) cc_final: 0.7989 (pt0) REVERT: B 309 GLU cc_start: 0.7448 (tp30) cc_final: 0.7198 (mm-30) REVERT: B 423 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: B 644 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: B 1015 ILE cc_start: 0.8559 (mm) cc_final: 0.8324 (mt) REVERT: C 3 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7838 (m110) REVERT: C 29 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7129 (pptt) REVERT: C 267 LYS cc_start: 0.7604 (tttp) cc_final: 0.7346 (tttp) REVERT: C 312 LYS cc_start: 0.7219 (mttt) cc_final: 0.6806 (tmtt) REVERT: C 429 GLU cc_start: 0.7745 (mp0) cc_final: 0.7530 (mp0) REVERT: C 528 ASP cc_start: 0.7458 (t70) cc_final: 0.7203 (t0) REVERT: C 780 MET cc_start: 0.8850 (mmt) cc_final: 0.8100 (mmt) REVERT: C 840 MET cc_start: 0.8124 (mtp) cc_final: 0.7858 (mtm) outliers start: 16 outliers final: 8 residues processed: 303 average time/residue: 2.7514 time to fit residues: 974.0668 Evaluate side-chains 293 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 282 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 231 ASN A 922 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23967 Z= 0.322 Angle : 0.547 10.542 32532 Z= 0.283 Chirality : 0.042 0.456 3798 Planarity : 0.004 0.059 4152 Dihedral : 6.019 79.255 3398 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.00 % Allowed : 9.36 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3064 helix: 1.89 (0.12), residues: 1669 sheet: -0.77 (0.27), residues: 357 loop : -0.62 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 753 HIS 0.004 0.001 HIS A 525 PHE 0.017 0.001 PHE B 663 TYR 0.017 0.001 TYR B 49 ARG 0.006 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 294 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7692 (mmmt) cc_final: 0.5846 (pptt) REVERT: A 69 MET cc_start: 0.8847 (mmt) cc_final: 0.8153 (mmt) REVERT: A 917 PHE cc_start: 0.6980 (m-80) cc_final: 0.6421 (t80) REVERT: B 29 LYS cc_start: 0.7240 (mttt) cc_final: 0.5799 (pptt) REVERT: B 164 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: B 167 SER cc_start: 0.8400 (t) cc_final: 0.7726 (p) REVERT: B 248 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7579 (t0) REVERT: B 269 GLU cc_start: 0.8264 (pt0) cc_final: 0.7980 (pt0) REVERT: B 309 GLU cc_start: 0.7519 (tp30) cc_final: 0.7247 (mm-30) REVERT: B 423 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: B 644 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: B 1015 ILE cc_start: 0.8589 (mm) cc_final: 0.8332 (mt) REVERT: C 3 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7839 (m110) REVERT: C 29 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7130 (pptt) REVERT: C 151 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6728 (mt0) REVERT: C 267 LYS cc_start: 0.7616 (tttp) cc_final: 0.7332 (tttp) REVERT: C 312 LYS cc_start: 0.7309 (mttt) cc_final: 0.6826 (tmtt) REVERT: C 429 GLU cc_start: 0.7710 (mp0) cc_final: 0.7507 (mp0) REVERT: C 528 ASP cc_start: 0.7464 (t70) cc_final: 0.7210 (t0) REVERT: C 736 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: C 780 MET cc_start: 0.8807 (mmt) cc_final: 0.8112 (mmt) REVERT: C 840 MET cc_start: 0.8110 (mtp) cc_final: 0.7778 (mtm) outliers start: 25 outliers final: 13 residues processed: 306 average time/residue: 2.6929 time to fit residues: 965.9421 Evaluate side-chains 304 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 992 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 0.2980 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN C 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23967 Z= 0.233 Angle : 0.511 10.596 32532 Z= 0.263 Chirality : 0.041 0.457 3798 Planarity : 0.004 0.035 4152 Dihedral : 5.888 77.359 3398 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.04 % Allowed : 10.16 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3064 helix: 2.00 (0.13), residues: 1670 sheet: -0.77 (0.26), residues: 362 loop : -0.63 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 753 HIS 0.002 0.001 HIS A 525 PHE 0.015 0.001 PHE C 571 TYR 0.016 0.001 TYR B 49 ARG 0.003 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 3.466 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7477 (mmmt) cc_final: 0.5611 (pptt) REVERT: A 69 MET cc_start: 0.8831 (mmt) cc_final: 0.8222 (mmt) REVERT: A 79 SER cc_start: 0.8578 (p) cc_final: 0.8194 (t) REVERT: A 917 PHE cc_start: 0.6902 (m-80) cc_final: 0.6391 (t80) REVERT: B 29 LYS cc_start: 0.7208 (mttt) cc_final: 0.5783 (pptt) REVERT: B 164 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: B 167 SER cc_start: 0.8398 (t) cc_final: 0.7735 (p) REVERT: B 248 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 269 GLU cc_start: 0.8287 (pt0) cc_final: 0.8031 (pt0) REVERT: B 309 GLU cc_start: 0.7462 (tp30) cc_final: 0.7231 (mm-30) REVERT: B 423 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: B 644 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: B 1015 ILE cc_start: 0.8590 (mm) cc_final: 0.8331 (mt) REVERT: C 29 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7121 (pptt) REVERT: C 267 LYS cc_start: 0.7623 (tttp) cc_final: 0.7412 (tttp) REVERT: C 312 LYS cc_start: 0.7363 (mttt) cc_final: 0.6827 (tmtt) REVERT: C 429 GLU cc_start: 0.7728 (mp0) cc_final: 0.7440 (mp0) REVERT: C 528 ASP cc_start: 0.7417 (t70) cc_final: 0.7173 (t0) REVERT: C 780 MET cc_start: 0.8778 (mmt) cc_final: 0.8255 (mmt) REVERT: C 840 MET cc_start: 0.8088 (mtp) cc_final: 0.7709 (mtm) outliers start: 26 outliers final: 15 residues processed: 302 average time/residue: 2.7493 time to fit residues: 976.4228 Evaluate side-chains 303 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 284 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 965 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 0.0010 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23967 Z= 0.189 Angle : 0.494 10.664 32532 Z= 0.253 Chirality : 0.041 0.458 3798 Planarity : 0.004 0.057 4152 Dihedral : 5.717 69.282 3398 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 11.08 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3064 helix: 2.12 (0.13), residues: 1671 sheet: -0.78 (0.26), residues: 367 loop : -0.55 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.003 0.001 HIS A 525 PHE 0.014 0.001 PHE C 571 TYR 0.015 0.001 TYR B 49 ARG 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7537 (mmmt) cc_final: 0.5646 (pptt) REVERT: A 69 MET cc_start: 0.8832 (mmt) cc_final: 0.8309 (mmt) REVERT: A 79 SER cc_start: 0.8571 (p) cc_final: 0.8210 (t) REVERT: A 836 THR cc_start: 0.7920 (m) cc_final: 0.7254 (p) REVERT: A 917 PHE cc_start: 0.6922 (m-80) cc_final: 0.6399 (t80) REVERT: B 29 LYS cc_start: 0.7193 (mttt) cc_final: 0.5786 (pptt) REVERT: B 164 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6354 (m-30) REVERT: B 167 SER cc_start: 0.8344 (t) cc_final: 0.7695 (p) REVERT: B 269 GLU cc_start: 0.8274 (pt0) cc_final: 0.8021 (pt0) REVERT: B 309 GLU cc_start: 0.7439 (tp30) cc_final: 0.7199 (mm-30) REVERT: B 644 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: B 1015 ILE cc_start: 0.8514 (mm) cc_final: 0.8267 (mt) REVERT: C 29 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7142 (pptt) REVERT: C 123 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.5280 (mp10) REVERT: C 267 LYS cc_start: 0.7621 (tttp) cc_final: 0.7394 (tttp) REVERT: C 312 LYS cc_start: 0.7342 (mttt) cc_final: 0.6786 (tmtt) REVERT: C 429 GLU cc_start: 0.7719 (mp0) cc_final: 0.7406 (mp0) REVERT: C 528 ASP cc_start: 0.7391 (t70) cc_final: 0.7146 (t0) REVERT: C 736 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: C 780 MET cc_start: 0.8757 (mmt) cc_final: 0.8284 (mmt) REVERT: C 840 MET cc_start: 0.8057 (mtp) cc_final: 0.7750 (mtm) outliers start: 25 outliers final: 14 residues processed: 312 average time/residue: 2.7324 time to fit residues: 1022.7889 Evaluate side-chains 304 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 286 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 965 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 296 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23967 Z= 0.229 Angle : 0.503 10.689 32532 Z= 0.258 Chirality : 0.041 0.457 3798 Planarity : 0.004 0.047 4152 Dihedral : 5.636 70.224 3398 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.96 % Allowed : 11.36 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3064 helix: 2.10 (0.13), residues: 1672 sheet: -0.83 (0.25), residues: 401 loop : -0.50 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 894 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.001 PHE A 11 TYR 0.014 0.001 TYR B 49 ARG 0.007 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7570 (mmmt) cc_final: 0.5670 (pptt) REVERT: A 69 MET cc_start: 0.8819 (mmt) cc_final: 0.8273 (mmt) REVERT: A 79 SER cc_start: 0.8575 (p) cc_final: 0.8208 (t) REVERT: A 917 PHE cc_start: 0.6944 (m-80) cc_final: 0.6408 (t80) REVERT: B 29 LYS cc_start: 0.7200 (mttt) cc_final: 0.5801 (pptt) REVERT: B 164 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: B 167 SER cc_start: 0.8351 (t) cc_final: 0.7700 (p) REVERT: B 269 GLU cc_start: 0.8273 (pt0) cc_final: 0.8024 (pt0) REVERT: B 309 GLU cc_start: 0.7433 (tp30) cc_final: 0.7199 (mm-30) REVERT: B 644 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: B 1015 ILE cc_start: 0.8503 (mm) cc_final: 0.8259 (mt) REVERT: B 1027 VAL cc_start: 0.7664 (t) cc_final: 0.7464 (m) REVERT: C 29 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7169 (pptt) REVERT: C 123 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.5387 (mp10) REVERT: C 267 LYS cc_start: 0.7617 (tttp) cc_final: 0.7387 (tttp) REVERT: C 312 LYS cc_start: 0.7338 (mttt) cc_final: 0.6786 (tmtt) REVERT: C 429 GLU cc_start: 0.7729 (mp0) cc_final: 0.7415 (mp0) REVERT: C 528 ASP cc_start: 0.7402 (t70) cc_final: 0.7155 (t0) REVERT: C 780 MET cc_start: 0.8733 (mmt) cc_final: 0.8303 (mmt) REVERT: C 840 MET cc_start: 0.8072 (mtp) cc_final: 0.7767 (mtm) outliers start: 24 outliers final: 12 residues processed: 307 average time/residue: 2.6139 time to fit residues: 943.6288 Evaluate side-chains 306 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 291 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 448 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.0570 chunk 33 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 0.1980 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23967 Z= 0.145 Angle : 0.474 10.694 32532 Z= 0.242 Chirality : 0.040 0.458 3798 Planarity : 0.004 0.057 4152 Dihedral : 5.358 56.203 3398 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.72 % Allowed : 11.72 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 3064 helix: 2.27 (0.13), residues: 1674 sheet: -0.70 (0.26), residues: 378 loop : -0.40 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.002 0.000 HIS A 525 PHE 0.012 0.001 PHE A 380 TYR 0.010 0.001 TYR B 49 ARG 0.008 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7515 (mmmt) cc_final: 0.5639 (pptt) REVERT: A 79 SER cc_start: 0.8545 (p) cc_final: 0.8219 (t) REVERT: A 124 GLN cc_start: 0.7468 (tt0) cc_final: 0.7195 (tt0) REVERT: A 836 THR cc_start: 0.7929 (m) cc_final: 0.7249 (p) REVERT: A 917 PHE cc_start: 0.6951 (m-80) cc_final: 0.6375 (t80) REVERT: A 931 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7918 (mt) REVERT: B 29 LYS cc_start: 0.7145 (mttt) cc_final: 0.5787 (pptt) REVERT: B 167 SER cc_start: 0.8369 (t) cc_final: 0.7714 (p) REVERT: B 269 GLU cc_start: 0.8271 (pt0) cc_final: 0.8024 (pt0) REVERT: B 309 GLU cc_start: 0.7428 (tp30) cc_final: 0.7203 (mm-30) REVERT: B 644 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: C 29 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7174 (pptt) REVERT: C 123 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.5298 (mp10) REVERT: C 267 LYS cc_start: 0.7539 (tttp) cc_final: 0.7319 (tttp) REVERT: C 312 LYS cc_start: 0.7295 (mttt) cc_final: 0.6746 (tmtt) REVERT: C 429 GLU cc_start: 0.7685 (mp0) cc_final: 0.7406 (mp0) REVERT: C 528 ASP cc_start: 0.7347 (t70) cc_final: 0.7105 (t0) REVERT: C 680 ASP cc_start: 0.7964 (t0) cc_final: 0.7723 (t0) REVERT: C 780 MET cc_start: 0.8705 (mmt) cc_final: 0.8406 (mmt) REVERT: C 840 MET cc_start: 0.8031 (mtp) cc_final: 0.7716 (mtm) outliers start: 18 outliers final: 8 residues processed: 310 average time/residue: 2.5727 time to fit residues: 948.0863 Evaluate side-chains 300 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 289 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 231 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23967 Z= 0.169 Angle : 0.483 10.747 32532 Z= 0.245 Chirality : 0.040 0.458 3798 Planarity : 0.003 0.049 4152 Dihedral : 5.296 54.349 3398 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.48 % Allowed : 12.48 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 3064 helix: 2.30 (0.13), residues: 1674 sheet: -0.74 (0.25), residues: 402 loop : -0.33 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 788 HIS 0.002 0.000 HIS A 525 PHE 0.014 0.001 PHE B 627 TYR 0.011 0.001 TYR B 49 ARG 0.004 0.000 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 299 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7539 (mmmt) cc_final: 0.5654 (pptt) REVERT: A 79 SER cc_start: 0.8549 (p) cc_final: 0.8215 (t) REVERT: A 824 LEU cc_start: 0.7988 (mt) cc_final: 0.7783 (mt) REVERT: A 836 THR cc_start: 0.7920 (m) cc_final: 0.7232 (p) REVERT: A 917 PHE cc_start: 0.6951 (m-80) cc_final: 0.6379 (t80) REVERT: B 29 LYS cc_start: 0.7165 (mttt) cc_final: 0.5809 (pptt) REVERT: B 164 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6314 (m-30) REVERT: B 167 SER cc_start: 0.8358 (t) cc_final: 0.7716 (p) REVERT: B 269 GLU cc_start: 0.8280 (pt0) cc_final: 0.8038 (pt0) REVERT: B 309 GLU cc_start: 0.7428 (tp30) cc_final: 0.7198 (mm-30) REVERT: B 644 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: C 29 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7201 (pptt) REVERT: C 123 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.5326 (mp10) REVERT: C 267 LYS cc_start: 0.7557 (tttp) cc_final: 0.7341 (tttp) REVERT: C 312 LYS cc_start: 0.7282 (mttt) cc_final: 0.6733 (tmtt) REVERT: C 429 GLU cc_start: 0.7693 (mp0) cc_final: 0.7422 (mp0) REVERT: C 528 ASP cc_start: 0.7354 (t70) cc_final: 0.7100 (t0) REVERT: C 780 MET cc_start: 0.8674 (mmt) cc_final: 0.8376 (mmt) REVERT: C 840 MET cc_start: 0.8029 (mtp) cc_final: 0.7715 (mtm) outliers start: 12 outliers final: 7 residues processed: 303 average time/residue: 2.6304 time to fit residues: 939.4604 Evaluate side-chains 301 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 291 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 0.3980 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23967 Z= 0.145 Angle : 0.475 10.730 32532 Z= 0.240 Chirality : 0.040 0.458 3798 Planarity : 0.004 0.069 4152 Dihedral : 5.209 54.634 3398 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 12.76 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 3064 helix: 2.36 (0.13), residues: 1676 sheet: -0.65 (0.26), residues: 406 loop : -0.30 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 753 HIS 0.001 0.000 HIS A 338 PHE 0.012 0.001 PHE A 380 TYR 0.021 0.001 TYR B 653 ARG 0.011 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 301 time to evaluate : 3.473 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7527 (mmmt) cc_final: 0.5643 (pptt) REVERT: A 79 SER cc_start: 0.8543 (p) cc_final: 0.8208 (t) REVERT: A 124 GLN cc_start: 0.7472 (tt0) cc_final: 0.7194 (tt0) REVERT: A 836 THR cc_start: 0.7874 (m) cc_final: 0.7173 (p) REVERT: A 917 PHE cc_start: 0.6965 (m-80) cc_final: 0.6376 (t80) REVERT: B 29 LYS cc_start: 0.7161 (mttt) cc_final: 0.5816 (pptt) REVERT: B 164 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6292 (m-30) REVERT: B 167 SER cc_start: 0.8340 (t) cc_final: 0.7692 (p) REVERT: B 269 GLU cc_start: 0.8275 (pt0) cc_final: 0.8034 (pt0) REVERT: B 309 GLU cc_start: 0.7420 (tp30) cc_final: 0.7188 (mm-30) REVERT: B 644 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: C 29 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7198 (pptt) REVERT: C 123 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.5407 (mp10) REVERT: C 267 LYS cc_start: 0.7512 (tttp) cc_final: 0.7302 (tttp) REVERT: C 312 LYS cc_start: 0.7265 (mttt) cc_final: 0.6729 (tmtt) REVERT: C 429 GLU cc_start: 0.7696 (mp0) cc_final: 0.7432 (mp0) REVERT: C 528 ASP cc_start: 0.7328 (t70) cc_final: 0.7071 (t0) REVERT: C 680 ASP cc_start: 0.7910 (t0) cc_final: 0.7691 (t0) REVERT: C 780 MET cc_start: 0.8641 (mmt) cc_final: 0.8416 (mmt) REVERT: C 840 MET cc_start: 0.8016 (mtp) cc_final: 0.7700 (mtm) outliers start: 14 outliers final: 7 residues processed: 307 average time/residue: 2.6562 time to fit residues: 966.6973 Evaluate side-chains 307 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 297 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23967 Z= 0.289 Angle : 0.528 10.726 32532 Z= 0.270 Chirality : 0.042 0.458 3798 Planarity : 0.004 0.049 4152 Dihedral : 5.490 68.591 3398 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.44 % Allowed : 12.88 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3064 helix: 2.15 (0.13), residues: 1675 sheet: -0.78 (0.26), residues: 402 loop : -0.43 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 894 HIS 0.003 0.001 HIS A 525 PHE 0.023 0.001 PHE A 11 TYR 0.021 0.001 TYR B 653 ARG 0.003 0.000 ARG C 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 291 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7650 (mmmt) cc_final: 0.5741 (pptt) REVERT: A 69 MET cc_start: 0.8780 (mmt) cc_final: 0.8249 (mmt) REVERT: A 79 SER cc_start: 0.8543 (p) cc_final: 0.8192 (t) REVERT: A 836 THR cc_start: 0.7992 (m) cc_final: 0.7294 (p) REVERT: A 917 PHE cc_start: 0.6962 (m-80) cc_final: 0.6384 (t80) REVERT: B 29 LYS cc_start: 0.7229 (mttt) cc_final: 0.5851 (pptt) REVERT: B 164 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6319 (m-30) REVERT: B 167 SER cc_start: 0.8415 (t) cc_final: 0.7744 (p) REVERT: B 269 GLU cc_start: 0.8271 (pt0) cc_final: 0.8029 (pt0) REVERT: B 309 GLU cc_start: 0.7439 (tp30) cc_final: 0.7177 (mm-30) REVERT: B 644 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: B 1010 MET cc_start: 0.7232 (mmm) cc_final: 0.7015 (mmm) REVERT: C 29 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7144 (pptt) REVERT: C 123 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.5641 (mp10) REVERT: C 312 LYS cc_start: 0.7268 (mttt) cc_final: 0.6759 (tmtt) REVERT: C 429 GLU cc_start: 0.7720 (mp0) cc_final: 0.7436 (mp0) REVERT: C 528 ASP cc_start: 0.7398 (t70) cc_final: 0.7114 (t0) REVERT: C 780 MET cc_start: 0.8661 (mmt) cc_final: 0.8353 (mmt) REVERT: C 840 MET cc_start: 0.8075 (mtp) cc_final: 0.7768 (mtm) outliers start: 11 outliers final: 7 residues processed: 295 average time/residue: 2.6776 time to fit residues: 928.4261 Evaluate side-chains 299 residues out of total 2500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 289 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 213 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: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098953 restraints weight = 81930.386| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.91 r_work: 0.3029 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23967 Z= 0.233 Angle : 0.508 10.614 32532 Z= 0.259 Chirality : 0.041 0.456 3798 Planarity : 0.004 0.064 4152 Dihedral : 5.484 70.274 3398 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 12.76 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3064 helix: 2.15 (0.12), residues: 1674 sheet: -0.78 (0.26), residues: 402 loop : -0.42 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 894 HIS 0.003 0.001 HIS A 525 PHE 0.019 0.001 PHE C 11 TYR 0.021 0.001 TYR B 653 ARG 0.007 0.000 ARG C 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15479.33 seconds wall clock time: 268 minutes 33.25 seconds (16113.25 seconds total)