Starting phenix.real_space_refine on Sun Mar 17 08:49:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr4_23956/03_2024/7mr4_23956.pdb" } resolution = 4.5 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 79 5.16 5 C 10785 2.51 5 N 3022 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 559": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1103": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17203 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6802 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 34, 'TRANS': 816} Chain breaks: 1 Chain: "C" Number of atoms: 8768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8768 Classifications: {'peptide': 1083} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1019} Chain breaks: 1 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 9.12, per 1000 atoms: 0.53 Number of scatterers: 17203 At special positions: 0 Unit cell: (125.4, 103.4, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 33 15.00 O 3284 8.00 N 3022 7.00 C 10785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.91 Conformation dependent library (CDL) restraints added in 2.9 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 16 sheets defined 59.0% alpha, 6.3% beta 9 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.518A pdb=" N ALA B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.824A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 155 through 173 removed outlier: 4.241A pdb=" N LEU B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.835A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 4.001A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 4.019A pdb=" N ARG B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.821A pdb=" N GLN B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.655A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.311A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.781A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.593A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 4.089A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.664A pdb=" N GLN B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.687A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.571A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 590 " --> pdb=" O VAL B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 634 through 656 Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.767A pdb=" N LEU B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 4.071A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 removed outlier: 4.130A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.590A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 808 Processing helix chain 'B' and resid 832 through 835 removed outlier: 4.200A pdb=" N GLN B 835 " --> pdb=" O ASP B 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 832 through 835' Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 849 through 861 removed outlier: 4.056A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.026A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 89 through 103 Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.273A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.847A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.622A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.750A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.752A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 460 through 463 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 500 removed outlier: 4.147A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.677A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 599 Proline residue: C 589 - end of helix removed outlier: 5.095A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 627 Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.985A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 647 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.565A pdb=" N ALA C 842 " --> pdb=" O GLN C 838 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 removed outlier: 3.612A pdb=" N MET C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 852 " --> pdb=" O PHE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 4.052A pdb=" N TYR C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.941A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.644A pdb=" N VAL C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.586A pdb=" N GLN C1022 " --> pdb=" O HIS C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1049 removed outlier: 3.528A pdb=" N GLY C1043 " --> pdb=" O PRO C1039 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 3.953A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 removed outlier: 3.555A pdb=" N ARG C1111 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C1112 " --> pdb=" O GLN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.789A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 54 through 61 removed outlier: 3.937A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.846A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 124 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.972A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.668A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.417A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 removed outlier: 3.511A pdb=" N MET B 541 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 547 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558 removed outlier: 6.325A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 751 through 754 removed outlier: 3.750A pdb=" N VAL B 752 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 814 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 754 " --> pdb=" O SER B 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.389A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 214 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 211 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 237 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 264 through 265 removed outlier: 3.673A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.558A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.520A pdb=" N CYS C 662 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS C 782 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.638A pdb=" N SER C 735 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 740 " --> pdb=" O SER C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.271A pdb=" N VAL C 832 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N TRP C 955 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 965 through 967 removed outlier: 6.669A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1050 through 1051 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 92 818 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.04 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5698 1.34 - 1.46: 3997 1.46 - 1.58: 7757 1.58 - 1.70: 64 1.70 - 1.82: 130 Bond restraints: 17646 Sorted by residual: bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.83e+01 bond pdb=" C TYR B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.77e+01 bond pdb=" C1' DG X 12 " pdb=" N9 DG X 12 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1' DA X 19 " pdb=" N9 DA X 19 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1' DA X 16 " pdb=" N9 DA X 16 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 17641 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.27: 491 105.27 - 112.53: 8790 112.53 - 119.80: 6455 119.80 - 127.06: 8027 127.06 - 134.32: 321 Bond angle restraints: 24084 Sorted by residual: angle pdb=" C PRO B 305 " pdb=" N ARG B 306 " pdb=" CA ARG B 306 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C SER B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.68 128.80 -8.12 1.52e+00 4.33e-01 2.86e+01 angle pdb=" N GLU B 696 " pdb=" CA GLU B 696 " pdb=" CB GLU B 696 " ideal model delta sigma weight residual 110.41 118.05 -7.64 1.68e+00 3.54e-01 2.07e+01 angle pdb=" CA MET C 396 " pdb=" CB MET C 396 " pdb=" CG MET C 396 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" C GLU C 273 " pdb=" N LEU C 274 " pdb=" CA LEU C 274 " ideal model delta sigma weight residual 120.39 126.17 -5.78 1.39e+00 5.18e-01 1.73e+01 ... (remaining 24079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.62: 9907 27.62 - 55.24: 585 55.24 - 82.86: 87 82.86 - 110.49: 11 110.49 - 138.11: 1 Dihedral angle restraints: 10591 sinusoidal: 4583 harmonic: 6008 Sorted by residual: dihedral pdb=" CA PRO B 405 " pdb=" C PRO B 405 " pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO B 755 " pdb=" C PRO B 755 " pdb=" N PHE B 756 " pdb=" CA PHE B 756 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER C 268 " pdb=" C SER C 268 " pdb=" N PHE C 269 " pdb=" CA PHE C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 10588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1930 0.047 - 0.094: 531 0.094 - 0.141: 160 0.141 - 0.188: 21 0.188 - 0.235: 4 Chirality restraints: 2646 Sorted by residual: chirality pdb=" CB THR B 304 " pdb=" CA THR B 304 " pdb=" OG1 THR B 304 " pdb=" CG2 THR B 304 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR B 445 " pdb=" CA THR B 445 " pdb=" OG1 THR B 445 " pdb=" CG2 THR B 445 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE C 506 " pdb=" CA ILE C 506 " pdb=" CG1 ILE C 506 " pdb=" CG2 ILE C 506 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2643 not shown) Planarity restraints: 3048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 598 " 0.024 2.00e-02 2.50e+03 3.10e-02 2.40e+01 pdb=" CG TRP B 598 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 598 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 598 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 598 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 598 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 598 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 598 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 598 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 598 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 658 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 96 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 97 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 97 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 97 " 0.037 5.00e-02 4.00e+02 ... (remaining 3045 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 151 2.59 - 3.17: 13741 3.17 - 3.75: 28243 3.75 - 4.32: 35325 4.32 - 4.90: 56853 Nonbonded interactions: 134313 Sorted by model distance: nonbonded pdb=" O6 DG X 11 " pdb=" O6 DG X 12 " model vdw 2.014 3.040 nonbonded pdb=" N1 DG X 11 " pdb=" N1 DG X 12 " model vdw 2.126 3.200 nonbonded pdb=" O TRP C 496 " pdb=" OG SER C 500 " model vdw 2.222 2.440 nonbonded pdb=" C2 DA X 16 " pdb=" N2 DG A 65 " model vdw 2.236 3.420 nonbonded pdb=" OE1 GLU C 499 " pdb=" OH TYR C 550 " model vdw 2.280 2.440 ... (remaining 134308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.350 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 49.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17646 Z= 0.276 Angle : 0.865 11.623 24084 Z= 0.467 Chirality : 0.048 0.235 2646 Planarity : 0.006 0.081 3048 Dihedral : 17.064 138.107 6685 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -1.71 (0.17), residues: 2047 helix: -0.34 (0.15), residues: 1086 sheet: -1.23 (0.43), residues: 143 loop : -2.16 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP B 598 HIS 0.011 0.001 HIS C 448 PHE 0.032 0.002 PHE B 378 TYR 0.027 0.002 TYR C 714 ARG 0.015 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8263 (tmm) cc_final: 0.7661 (tmm) REVERT: B 185 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 354 MET cc_start: 0.8881 (pmm) cc_final: 0.8361 (pmm) REVERT: B 390 ASP cc_start: 0.8932 (t70) cc_final: 0.8696 (t70) REVERT: B 453 MET cc_start: 0.8799 (mmm) cc_final: 0.8352 (mmm) REVERT: B 469 MET cc_start: 0.8160 (mtp) cc_final: 0.7703 (mpp) REVERT: B 501 MET cc_start: 0.6550 (mpp) cc_final: 0.6060 (mpp) REVERT: B 616 LEU cc_start: 0.9319 (mt) cc_final: 0.9114 (mt) REVERT: B 652 TRP cc_start: 0.7349 (t60) cc_final: 0.6816 (t60) REVERT: B 849 ASP cc_start: 0.8723 (p0) cc_final: 0.8498 (p0) REVERT: C 508 ASP cc_start: 0.7917 (p0) cc_final: 0.7531 (p0) REVERT: C 568 LEU cc_start: 0.9037 (mp) cc_final: 0.8655 (tt) REVERT: C 600 LEU cc_start: 0.7334 (tp) cc_final: 0.7120 (tp) REVERT: C 609 MET cc_start: 0.9026 (mmm) cc_final: 0.8296 (mmm) REVERT: C 678 LEU cc_start: 0.9299 (mt) cc_final: 0.8852 (mt) REVERT: C 738 ASP cc_start: 0.8714 (p0) cc_final: 0.8449 (p0) REVERT: D 5 LYS cc_start: 0.6292 (pptt) cc_final: 0.6068 (pptt) REVERT: D 121 ARG cc_start: 0.7467 (mmp-170) cc_final: 0.6420 (tpm170) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2633 time to fit residues: 74.1959 Evaluate side-chains 118 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 0.0060 chunk 83 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 17646 Z= 0.407 Angle : 0.734 11.001 24084 Z= 0.378 Chirality : 0.043 0.201 2646 Planarity : 0.005 0.064 3048 Dihedral : 13.808 131.200 2617 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.11 % Allowed : 8.54 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -1.04 (0.18), residues: 2047 helix: 0.40 (0.15), residues: 1110 sheet: -1.13 (0.43), residues: 158 loop : -2.20 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 184 HIS 0.007 0.002 HIS C 185 PHE 0.019 0.002 PHE B 127 TYR 0.046 0.003 TYR B 200 ARG 0.012 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8397 (tmm) cc_final: 0.8193 (tmm) REVERT: B 185 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8437 (mt-10) REVERT: B 200 TYR cc_start: 0.8496 (m-80) cc_final: 0.8213 (m-80) REVERT: B 354 MET cc_start: 0.8768 (pmm) cc_final: 0.8136 (pmm) REVERT: B 469 MET cc_start: 0.8286 (mtp) cc_final: 0.7773 (mpp) REVERT: B 501 MET cc_start: 0.6842 (mpp) cc_final: 0.5862 (mpp) REVERT: B 518 MET cc_start: 0.9060 (mpp) cc_final: 0.8766 (mpp) REVERT: B 665 MET cc_start: 0.8729 (mpp) cc_final: 0.8419 (mtt) REVERT: B 778 LEU cc_start: 0.9005 (tt) cc_final: 0.8337 (tt) REVERT: B 849 ASP cc_start: 0.8698 (p0) cc_final: 0.8435 (p0) REVERT: C 91 MET cc_start: 0.8808 (mtp) cc_final: 0.8299 (mmp) REVERT: C 240 PHE cc_start: 0.8874 (t80) cc_final: 0.8551 (t80) REVERT: C 271 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.5931 (t0) REVERT: C 396 MET cc_start: 0.8510 (pmm) cc_final: 0.8181 (pmm) REVERT: C 411 MET cc_start: 0.8485 (mmp) cc_final: 0.8042 (mmp) REVERT: C 448 HIS cc_start: 0.6286 (t-170) cc_final: 0.5939 (t-170) REVERT: C 508 ASP cc_start: 0.8004 (p0) cc_final: 0.7609 (p0) REVERT: C 600 LEU cc_start: 0.7479 (tp) cc_final: 0.7277 (tp) REVERT: C 678 LEU cc_start: 0.9200 (mt) cc_final: 0.8511 (mm) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.2589 time to fit residues: 60.9494 Evaluate side-chains 106 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 HIS B 458 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 380 HIS C 522 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17646 Z= 0.198 Angle : 0.573 9.142 24084 Z= 0.296 Chirality : 0.040 0.173 2646 Planarity : 0.004 0.064 3048 Dihedral : 13.733 130.263 2617 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.65 (0.18), residues: 2047 helix: 0.75 (0.16), residues: 1110 sheet: -1.01 (0.43), residues: 158 loop : -2.05 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 598 HIS 0.009 0.001 HIS C 113 PHE 0.016 0.001 PHE B 645 TYR 0.025 0.001 TYR B 514 ARG 0.006 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8517 (mt-10) REVERT: B 200 TYR cc_start: 0.8385 (m-80) cc_final: 0.7921 (m-80) REVERT: B 354 MET cc_start: 0.8871 (pmm) cc_final: 0.8625 (ptp) REVERT: B 469 MET cc_start: 0.8236 (mtp) cc_final: 0.7827 (mpp) REVERT: B 778 LEU cc_start: 0.9092 (tt) cc_final: 0.8173 (tt) REVERT: B 849 ASP cc_start: 0.8821 (p0) cc_final: 0.8544 (p0) REVERT: C 91 MET cc_start: 0.8636 (mtp) cc_final: 0.8174 (mmp) REVERT: C 240 PHE cc_start: 0.8800 (t80) cc_final: 0.8569 (t80) REVERT: C 396 MET cc_start: 0.8290 (pmm) cc_final: 0.7916 (pmm) REVERT: C 411 MET cc_start: 0.8623 (mmp) cc_final: 0.8065 (mmp) REVERT: C 508 ASP cc_start: 0.7894 (p0) cc_final: 0.7531 (p0) REVERT: C 516 LEU cc_start: 0.8909 (mt) cc_final: 0.8586 (mm) REVERT: C 594 MET cc_start: 0.8865 (tpp) cc_final: 0.8608 (tpp) REVERT: C 678 LEU cc_start: 0.9195 (mt) cc_final: 0.8620 (mm) REVERT: C 738 ASP cc_start: 0.8545 (p0) cc_final: 0.8317 (p0) REVERT: C 941 MET cc_start: 0.7733 (ptt) cc_final: 0.7361 (ptt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2659 time to fit residues: 65.4224 Evaluate side-chains 107 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 822 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17646 Z= 0.206 Angle : 0.561 8.715 24084 Z= 0.290 Chirality : 0.040 0.146 2646 Planarity : 0.004 0.061 3048 Dihedral : 13.624 128.951 2617 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.47 (0.19), residues: 2047 helix: 0.90 (0.16), residues: 1109 sheet: -1.11 (0.45), residues: 148 loop : -1.93 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 187 HIS 0.012 0.001 HIS D 65 PHE 0.019 0.001 PHE B 127 TYR 0.024 0.001 TYR B 514 ARG 0.006 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 200 TYR cc_start: 0.8442 (m-80) cc_final: 0.8188 (m-80) REVERT: B 354 MET cc_start: 0.8747 (pmm) cc_final: 0.7983 (pmm) REVERT: B 469 MET cc_start: 0.8262 (mtp) cc_final: 0.7619 (mpp) REVERT: B 501 MET cc_start: 0.7046 (mpp) cc_final: 0.6139 (mpp) REVERT: B 778 LEU cc_start: 0.9083 (tt) cc_final: 0.8639 (tt) REVERT: B 849 ASP cc_start: 0.8775 (p0) cc_final: 0.8465 (p0) REVERT: C 91 MET cc_start: 0.8652 (mtp) cc_final: 0.8162 (mmp) REVERT: C 240 PHE cc_start: 0.8821 (t80) cc_final: 0.8568 (t80) REVERT: C 396 MET cc_start: 0.8179 (pmm) cc_final: 0.7850 (pmm) REVERT: C 411 MET cc_start: 0.8663 (mmp) cc_final: 0.8118 (mmp) REVERT: C 508 ASP cc_start: 0.7940 (p0) cc_final: 0.7550 (p0) REVERT: C 537 MET cc_start: 0.6824 (mmt) cc_final: 0.6481 (mmp) REVERT: C 594 MET cc_start: 0.8918 (tpp) cc_final: 0.8677 (tpp) REVERT: C 678 LEU cc_start: 0.9219 (mt) cc_final: 0.8887 (mm) REVERT: C 738 ASP cc_start: 0.8521 (p0) cc_final: 0.8304 (p0) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2533 time to fit residues: 60.7592 Evaluate side-chains 109 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 17646 Z= 0.382 Angle : 0.707 11.632 24084 Z= 0.361 Chirality : 0.043 0.191 2646 Planarity : 0.005 0.067 3048 Dihedral : 13.720 128.775 2617 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.83 (0.18), residues: 2047 helix: 0.58 (0.16), residues: 1105 sheet: -1.23 (0.46), residues: 148 loop : -2.04 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 187 HIS 0.010 0.002 HIS B 714 PHE 0.023 0.002 PHE B 645 TYR 0.014 0.002 TYR B 394 ARG 0.006 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8472 (mt-10) REVERT: B 354 MET cc_start: 0.8795 (pmm) cc_final: 0.8206 (pmm) REVERT: B 453 MET cc_start: 0.9173 (mmm) cc_final: 0.8950 (mmm) REVERT: B 469 MET cc_start: 0.8160 (mtp) cc_final: 0.7953 (mtp) REVERT: B 501 MET cc_start: 0.7063 (mpp) cc_final: 0.6243 (mpp) REVERT: B 778 LEU cc_start: 0.9175 (tt) cc_final: 0.8690 (tt) REVERT: B 849 ASP cc_start: 0.8718 (p0) cc_final: 0.8401 (p0) REVERT: C 91 MET cc_start: 0.8712 (mtp) cc_final: 0.8257 (mmp) REVERT: C 240 PHE cc_start: 0.8841 (t80) cc_final: 0.8414 (t80) REVERT: C 396 MET cc_start: 0.8497 (pmm) cc_final: 0.8223 (pmm) REVERT: C 508 ASP cc_start: 0.7885 (p0) cc_final: 0.7511 (p0) REVERT: C 537 MET cc_start: 0.6931 (mmt) cc_final: 0.6680 (mmt) REVERT: C 594 MET cc_start: 0.9011 (tpp) cc_final: 0.8779 (tpp) REVERT: C 678 LEU cc_start: 0.9208 (mt) cc_final: 0.8694 (mm) REVERT: C 738 ASP cc_start: 0.8501 (p0) cc_final: 0.8037 (p0) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2772 time to fit residues: 61.8390 Evaluate side-chains 102 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 850 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17646 Z= 0.223 Angle : 0.597 9.869 24084 Z= 0.306 Chirality : 0.040 0.171 2646 Planarity : 0.004 0.066 3048 Dihedral : 13.669 129.043 2617 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.53 (0.19), residues: 2047 helix: 0.84 (0.16), residues: 1107 sheet: -1.14 (0.46), residues: 148 loop : -1.93 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 187 HIS 0.007 0.001 HIS B 714 PHE 0.016 0.001 PHE B 756 TYR 0.019 0.002 TYR B 514 ARG 0.005 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8470 (mt-10) REVERT: B 200 TYR cc_start: 0.8128 (m-80) cc_final: 0.7808 (m-80) REVERT: B 354 MET cc_start: 0.8725 (pmm) cc_final: 0.8173 (pmm) REVERT: B 453 MET cc_start: 0.9192 (mmm) cc_final: 0.8977 (mmm) REVERT: B 469 MET cc_start: 0.8178 (mtp) cc_final: 0.7591 (mpp) REVERT: B 501 MET cc_start: 0.6895 (mpp) cc_final: 0.6575 (mpp) REVERT: B 841 LEU cc_start: 0.9164 (mt) cc_final: 0.8808 (tt) REVERT: B 849 ASP cc_start: 0.8795 (p0) cc_final: 0.8478 (p0) REVERT: C 91 MET cc_start: 0.8635 (mtp) cc_final: 0.8193 (mmp) REVERT: C 240 PHE cc_start: 0.8785 (t80) cc_final: 0.8408 (t80) REVERT: C 411 MET cc_start: 0.8317 (mmm) cc_final: 0.8071 (mmp) REVERT: C 508 ASP cc_start: 0.7958 (p0) cc_final: 0.7544 (p0) REVERT: C 537 MET cc_start: 0.7078 (mmt) cc_final: 0.6485 (mmt) REVERT: C 594 MET cc_start: 0.9022 (tpp) cc_final: 0.8750 (tpp) REVERT: C 738 ASP cc_start: 0.8533 (p0) cc_final: 0.8307 (p0) REVERT: D 100 MET cc_start: 0.9225 (mmm) cc_final: 0.9002 (mmm) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2545 time to fit residues: 60.4260 Evaluate side-chains 107 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 850 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17646 Z= 0.272 Angle : 0.626 10.069 24084 Z= 0.321 Chirality : 0.041 0.144 2646 Planarity : 0.005 0.062 3048 Dihedral : 13.645 128.519 2617 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.53 (0.19), residues: 2047 helix: 0.81 (0.16), residues: 1112 sheet: -1.13 (0.46), residues: 148 loop : -1.89 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 187 HIS 0.008 0.001 HIS B 714 PHE 0.016 0.001 PHE B 756 TYR 0.033 0.002 TYR B 280 ARG 0.006 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8439 (mt-10) REVERT: B 354 MET cc_start: 0.8726 (pmm) cc_final: 0.8047 (pmm) REVERT: B 453 MET cc_start: 0.9171 (mmm) cc_final: 0.8966 (mmm) REVERT: B 469 MET cc_start: 0.8164 (mtp) cc_final: 0.7900 (mtp) REVERT: B 499 MET cc_start: 0.7711 (ttm) cc_final: 0.7452 (mtp) REVERT: B 501 MET cc_start: 0.6971 (mpp) cc_final: 0.6673 (mpp) REVERT: B 841 LEU cc_start: 0.9151 (mt) cc_final: 0.8849 (tt) REVERT: B 849 ASP cc_start: 0.8791 (p0) cc_final: 0.8417 (p0) REVERT: C 91 MET cc_start: 0.8686 (mtp) cc_final: 0.8224 (mmp) REVERT: C 240 PHE cc_start: 0.8768 (t80) cc_final: 0.8390 (t80) REVERT: C 411 MET cc_start: 0.8325 (mmm) cc_final: 0.8074 (mmp) REVERT: C 508 ASP cc_start: 0.8092 (p0) cc_final: 0.7652 (p0) REVERT: C 537 MET cc_start: 0.6553 (mmt) cc_final: 0.6289 (mmp) REVERT: C 594 MET cc_start: 0.9015 (tpp) cc_final: 0.8796 (tpp) REVERT: C 738 ASP cc_start: 0.8560 (p0) cc_final: 0.8346 (p0) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2537 time to fit residues: 60.5481 Evaluate side-chains 106 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.0020 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 GLN C 725 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17646 Z= 0.178 Angle : 0.584 8.034 24084 Z= 0.300 Chirality : 0.040 0.206 2646 Planarity : 0.004 0.065 3048 Dihedral : 13.574 127.972 2617 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 1.24 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.37 (0.19), residues: 2047 helix: 0.91 (0.16), residues: 1114 sheet: -1.00 (0.46), residues: 148 loop : -1.80 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 187 HIS 0.006 0.001 HIS B 714 PHE 0.017 0.001 PHE B 756 TYR 0.017 0.001 TYR B 514 ARG 0.004 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 453 MET cc_start: 0.9177 (mmm) cc_final: 0.8934 (mmm) REVERT: B 499 MET cc_start: 0.7666 (ttm) cc_final: 0.7434 (mtp) REVERT: B 501 MET cc_start: 0.7069 (mpp) cc_final: 0.6825 (mpp) REVERT: B 518 MET cc_start: 0.9039 (mpp) cc_final: 0.8719 (mpp) REVERT: B 778 LEU cc_start: 0.9112 (tt) cc_final: 0.8658 (tt) REVERT: B 841 LEU cc_start: 0.9121 (mt) cc_final: 0.8818 (tt) REVERT: B 849 ASP cc_start: 0.8836 (p0) cc_final: 0.8481 (p0) REVERT: C 91 MET cc_start: 0.8628 (mtp) cc_final: 0.8407 (mtt) REVERT: C 240 PHE cc_start: 0.8726 (t80) cc_final: 0.8408 (t80) REVERT: C 411 MET cc_start: 0.8331 (mmm) cc_final: 0.8063 (mmp) REVERT: C 465 PHE cc_start: 0.8480 (m-80) cc_final: 0.8143 (m-80) REVERT: C 504 TRP cc_start: 0.8723 (t-100) cc_final: 0.8351 (t-100) REVERT: C 508 ASP cc_start: 0.7865 (p0) cc_final: 0.7425 (p0) REVERT: C 594 MET cc_start: 0.9029 (tpp) cc_final: 0.8787 (tpp) REVERT: C 738 ASP cc_start: 0.8461 (p0) cc_final: 0.8143 (p0) REVERT: C 941 MET cc_start: 0.7570 (ptt) cc_final: 0.7264 (ptt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2666 time to fit residues: 65.3719 Evaluate side-chains 112 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 9.9990 chunk 191 optimal weight: 0.5980 chunk 174 optimal weight: 0.0970 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 chunk 175 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17646 Z= 0.153 Angle : 0.566 10.062 24084 Z= 0.288 Chirality : 0.040 0.163 2646 Planarity : 0.004 0.063 3048 Dihedral : 13.503 126.899 2617 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.06 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.22 (0.19), residues: 2047 helix: 1.04 (0.16), residues: 1114 sheet: -0.89 (0.46), residues: 148 loop : -1.74 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 187 HIS 0.006 0.001 HIS B 714 PHE 0.020 0.001 PHE B 64 TYR 0.017 0.001 TYR B 514 ARG 0.004 0.000 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 453 MET cc_start: 0.9179 (mmm) cc_final: 0.8938 (mmm) REVERT: B 469 MET cc_start: 0.8285 (mtp) cc_final: 0.7623 (mpp) REVERT: B 499 MET cc_start: 0.7629 (ttm) cc_final: 0.7423 (mtp) REVERT: B 501 MET cc_start: 0.6924 (mpp) cc_final: 0.6723 (mpp) REVERT: B 620 MET cc_start: 0.8157 (tmm) cc_final: 0.7885 (ppp) REVERT: B 738 ILE cc_start: 0.9608 (mp) cc_final: 0.9333 (tt) REVERT: B 778 LEU cc_start: 0.9194 (tt) cc_final: 0.8032 (tt) REVERT: B 841 LEU cc_start: 0.9156 (mt) cc_final: 0.8899 (tt) REVERT: B 849 ASP cc_start: 0.8819 (p0) cc_final: 0.8429 (p0) REVERT: C 91 MET cc_start: 0.8591 (mtp) cc_final: 0.8347 (mtt) REVERT: C 240 PHE cc_start: 0.8767 (t80) cc_final: 0.8486 (t80) REVERT: C 385 GLU cc_start: 0.8999 (tt0) cc_final: 0.8774 (tt0) REVERT: C 411 MET cc_start: 0.8279 (mmm) cc_final: 0.8063 (mmp) REVERT: C 465 PHE cc_start: 0.8453 (m-80) cc_final: 0.8110 (m-80) REVERT: C 504 TRP cc_start: 0.8635 (t-100) cc_final: 0.8370 (t-100) REVERT: C 508 ASP cc_start: 0.7864 (p0) cc_final: 0.7402 (p0) REVERT: C 594 MET cc_start: 0.9004 (tpp) cc_final: 0.8780 (tpp) REVERT: C 678 LEU cc_start: 0.9026 (mt) cc_final: 0.8579 (mt) REVERT: C 738 ASP cc_start: 0.8469 (p0) cc_final: 0.8126 (p0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2453 time to fit residues: 61.9902 Evaluate side-chains 113 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 850 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 17646 Z= 0.354 Angle : 0.696 10.649 24084 Z= 0.357 Chirality : 0.043 0.182 2646 Planarity : 0.005 0.058 3048 Dihedral : 13.619 126.799 2617 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.67 (0.19), residues: 2047 helix: 0.64 (0.16), residues: 1116 sheet: -1.03 (0.47), residues: 148 loop : -1.91 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 187 HIS 0.007 0.002 HIS B 714 PHE 0.023 0.002 PHE B 645 TYR 0.018 0.002 TYR B 514 ARG 0.006 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8496 (mt-10) REVERT: B 453 MET cc_start: 0.9200 (mmm) cc_final: 0.8980 (mmm) REVERT: B 499 MET cc_start: 0.7950 (ttm) cc_final: 0.7670 (mtp) REVERT: B 501 MET cc_start: 0.7087 (mpp) cc_final: 0.6876 (mpp) REVERT: B 778 LEU cc_start: 0.9306 (tt) cc_final: 0.8378 (tt) REVERT: B 841 LEU cc_start: 0.9146 (mt) cc_final: 0.8902 (tt) REVERT: B 849 ASP cc_start: 0.8788 (p0) cc_final: 0.8465 (p0) REVERT: C 91 MET cc_start: 0.8637 (mtp) cc_final: 0.8216 (mmp) REVERT: C 240 PHE cc_start: 0.8844 (t80) cc_final: 0.8381 (t80) REVERT: C 411 MET cc_start: 0.8370 (mmm) cc_final: 0.8009 (mmp) REVERT: C 508 ASP cc_start: 0.7990 (p0) cc_final: 0.7566 (p0) REVERT: C 678 LEU cc_start: 0.9006 (mt) cc_final: 0.8486 (mt) REVERT: C 738 ASP cc_start: 0.8309 (p0) cc_final: 0.7992 (p0) REVERT: C 941 MET cc_start: 0.7714 (ptt) cc_final: 0.7428 (ptt) REVERT: D 109 LEU cc_start: 0.8912 (tp) cc_final: 0.8711 (tp) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.2367 time to fit residues: 56.3393 Evaluate side-chains 105 residues out of total 1769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B 848 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052012 restraints weight = 95790.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.053345 restraints weight = 62330.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.054280 restraints weight = 45355.919| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17646 Z= 0.166 Angle : 0.583 8.201 24084 Z= 0.298 Chirality : 0.040 0.170 2646 Planarity : 0.004 0.065 3048 Dihedral : 13.563 125.691 2617 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.36 (0.19), residues: 2047 helix: 0.91 (0.16), residues: 1118 sheet: -0.94 (0.46), residues: 148 loop : -1.79 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 524 HIS 0.006 0.001 HIS B 714 PHE 0.019 0.001 PHE B 756 TYR 0.022 0.001 TYR B 514 ARG 0.004 0.000 ARG D 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.13 seconds wall clock time: 49 minutes 40.35 seconds (2980.35 seconds total)