Starting phenix.real_space_refine on Fri Jun 20 16:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.map" model { file = "/net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1t_15804/06_2025/8b1t_15804.cif" } resolution = 3.4 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: 6 Type Number sf(0) Gaussians P 53 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 15000 2.51 5 N 4224 2.21 5 O 4604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23986 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 9145 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 1 Chain: "C" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8738 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1014} Chain breaks: 1 Chain: "D" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4644 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 25, 'TRANS': 575} Chain breaks: 1 Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.82, per 1000 atoms: 0.58 Number of scatterers: 23986 At special positions: 0 Unit cell: (154.76, 152.64, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 53 15.00 Mg 1 11.99 O 4604 8.00 N 4224 7.00 C 15000 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 - 3.00 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: 6.64 Conformation dependent library (CDL) restraints added in 3.1 seconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 18 sheets defined 56.3% alpha, 10.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 8.55 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.732A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' 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 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.612A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.519A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 241 through 250 removed outlier: 4.151A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.851A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.943A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.634A pdb=" N ARG B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.850A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.708A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.532A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.064A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.593A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.595A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 701 removed outlier: 3.969A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.896A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.609A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.561A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 905 through 911 Processing helix chain 'B' and resid 948 through 961 removed outlier: 3.605A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 4.434A pdb=" N VAL B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 4.732A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1050 Processing helix chain 'B' and resid 1089 through 1093 Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.039A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1161 through 1174 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.005A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.693A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) 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: 3.859A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.717A 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: 4.909A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.703A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.539A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.610A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.635A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) 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 414 through 429 removed outlier: 3.674A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix removed outlier: 3.809A pdb=" N ALA C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.630A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.716A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.865A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 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: 3.750A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.537A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.411A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.731A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.607A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 3.599A pdb=" N GLN C 795 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.002A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.744A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.935A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 935 removed outlier: 3.800A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 removed outlier: 3.577A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1077 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 3.722A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.769A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 48 removed outlier: 3.538A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 4.884A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.637A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.514A pdb=" N CYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 223 removed outlier: 3.644A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.605A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.823A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.559A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 365 through 377 removed outlier: 3.519A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 400 through 424 removed outlier: 4.853A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.668A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.731A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.619A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 606 removed outlier: 3.835A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.723A pdb=" N ASN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 40 through 52 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.260A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE B 127 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.393A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.543A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.400A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.400A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.201A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS C 6 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.930A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.294A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.293A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.692A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 963 through 968 removed outlier: 6.415A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.541A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.461A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 238 through 239 removed outlier: 8.978A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 171 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.891A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER D 578 " --> pdb=" O HIS D 548 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 550 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR D 580 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE D 552 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.716A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 10.29 Time building geometry restraints manager: 7.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7353 1.33 - 1.45: 3755 1.45 - 1.57: 13221 1.57 - 1.69: 105 1.69 - 1.81: 173 Bond restraints: 24607 Sorted by residual: bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.528 1.580 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" O2G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.530 1.576 -0.046 2.00e-02 2.50e+03 5.39e+00 ... (remaining 24602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 33557 3.65 - 7.29: 39 7.29 - 10.94: 5 10.94 - 14.59: 0 14.59 - 18.24: 1 Bond angle restraints: 33602 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 108.71 18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " pdb=" O2B ANP B1501 " ideal model delta sigma weight residual 120.08 109.58 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C SER B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.60 125.29 -4.69 1.53e+00 4.27e-01 9.39e+00 angle pdb=" CA LEU C 323 " pdb=" CB LEU C 323 " pdb=" CG LEU C 323 " ideal model delta sigma weight residual 116.30 126.89 -10.59 3.50e+00 8.16e-02 9.15e+00 angle pdb=" N LEU B 175 " pdb=" CA LEU B 175 " pdb=" C LEU B 175 " ideal model delta sigma weight residual 109.60 113.05 -3.45 1.15e+00 7.56e-01 8.99e+00 ... (remaining 33597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 13619 16.89 - 33.78: 737 33.78 - 50.67: 272 50.67 - 67.57: 99 67.57 - 84.46: 13 Dihedral angle restraints: 14740 sinusoidal: 6390 harmonic: 8350 Sorted by residual: dihedral pdb=" CA ASN B1003 " pdb=" C ASN B1003 " pdb=" N GLU B1004 " pdb=" CA GLU B1004 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 127 " pdb=" C PHE B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3181 0.050 - 0.101: 419 0.101 - 0.151: 87 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 3689 Sorted by residual: chirality pdb=" C3' ANP B1501 " pdb=" C2' ANP B1501 " pdb=" C4' ANP B1501 " pdb=" O3' ANP B1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU C 323 " pdb=" CB LEU C 323 " pdb=" CD1 LEU C 323 " pdb=" CD2 LEU C 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 3686 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 658 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 382 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 658 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO B 659 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 659 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 659 " -0.020 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 184 2.63 - 3.20: 21007 3.20 - 3.77: 36354 3.77 - 4.33: 49805 4.33 - 4.90: 82512 Nonbonded interactions: 189862 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.065 2.170 nonbonded pdb=" NH1 ARG B 682 " pdb=" O ARG B 728 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP B1044 " pdb=" NE2 GLN B1112 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP B 388 " pdb=" NZ LYS B 745 " model vdw 2.232 3.120 ... (remaining 189857 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 ========== 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 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: 0.820 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: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 62.490 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 24607 Z= 0.155 Angle : 0.540 18.237 33602 Z= 0.320 Chirality : 0.036 0.252 3689 Planarity : 0.004 0.045 4231 Dihedral : 13.043 84.457 9328 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Rotamer: Outliers : 1.44 % Allowed : 3.90 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.96 (0.14), residues: 2855 helix: -0.22 (0.12), residues: 1481 sheet: -0.71 (0.27), residues: 311 loop : -1.03 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 652 HIS 0.003 0.001 HIS B 171 PHE 0.010 0.001 PHE C 857 TYR 0.018 0.001 TYR B1111 ARG 0.004 0.000 ARG C 433 Details of bonding type rmsd hydrogen bonds : bond 0.14878 ( 1180) hydrogen bonds : angle 5.76785 ( 3414) covalent geometry : bond 0.00313 (24607) covalent geometry : angle 0.53977 (33602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 452 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 PHE cc_start: 0.8704 (m-80) cc_final: 0.8383 (m-80) REVERT: B 604 MET cc_start: 0.8116 (tpt) cc_final: 0.7771 (tpt) REVERT: B 672 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 709 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7327 (mtm-85) REVERT: B 1079 LEU cc_start: 0.9360 (tp) cc_final: 0.9143 (tt) REVERT: C 42 MET cc_start: 0.8972 (tpt) cc_final: 0.8596 (tpt) REVERT: C 556 LEU cc_start: 0.8817 (mt) cc_final: 0.8537 (mt) REVERT: C 617 GLN cc_start: 0.8214 (tp40) cc_final: 0.7989 (tp40) REVERT: C 924 MET cc_start: 0.8470 (mmp) cc_final: 0.8232 (mmp) REVERT: D 78 LEU cc_start: 0.6377 (mm) cc_final: 0.6129 (tp) REVERT: D 136 LEU cc_start: 0.8316 (tp) cc_final: 0.7905 (tt) outliers start: 35 outliers final: 5 residues processed: 480 average time/residue: 0.4323 time to fit residues: 303.2431 Evaluate side-chains 189 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 0.0010 chunk 75 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 181 GLN B 440 HIS B 458 ASN B 484 ASN B 594 GLN B 650 GLN B 769 HIS B 835 GLN B 843 GLN B 848 GLN B1018 GLN B1057 GLN B1072 HIS B1103 GLN B1134 HIS B1161 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 336 HIS C 510 ASN C 749 GLN C 979 GLN D 22 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 523 GLN D 556 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081690 restraints weight = 46147.571| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.43 r_work: 0.2977 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24607 Z= 0.205 Angle : 0.586 11.327 33602 Z= 0.304 Chirality : 0.041 0.212 3689 Planarity : 0.005 0.048 4231 Dihedral : 13.760 87.820 3741 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.34 % Allowed : 8.82 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.38 (0.15), residues: 2855 helix: 1.00 (0.13), residues: 1510 sheet: -0.11 (0.28), residues: 301 loop : -0.64 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 265 HIS 0.006 0.001 HIS C 6 PHE 0.017 0.002 PHE B 461 TYR 0.020 0.002 TYR B1111 ARG 0.007 0.001 ARG D 376 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 1180) hydrogen bonds : angle 4.45256 ( 3414) covalent geometry : bond 0.00487 (24607) covalent geometry : angle 0.58649 (33602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 505 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 655 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7747 (mpp80) REVERT: B 709 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7700 (mtm-85) REVERT: B 968 VAL cc_start: 0.7211 (t) cc_final: 0.6959 (t) REVERT: B 1078 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 1079 LEU cc_start: 0.9378 (tp) cc_final: 0.9174 (tt) REVERT: C 30 PHE cc_start: 0.8752 (m-10) cc_final: 0.8532 (m-10) REVERT: C 556 LEU cc_start: 0.8951 (mt) cc_final: 0.8666 (mt) REVERT: C 559 GLU cc_start: 0.8084 (tt0) cc_final: 0.7867 (mt-10) REVERT: C 835 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 924 MET cc_start: 0.8821 (mmp) cc_final: 0.8488 (mmp) REVERT: D 78 LEU cc_start: 0.6447 (mm) cc_final: 0.6190 (tp) REVERT: D 239 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8807 (p) REVERT: D 384 THR cc_start: 0.8303 (p) cc_final: 0.8044 (t) REVERT: D 407 MET cc_start: 0.8006 (ttp) cc_final: 0.7684 (tmm) REVERT: D 462 MET cc_start: 0.7490 (mmm) cc_final: 0.6910 (mmp) REVERT: D 470 ARG cc_start: 0.7987 (ttt180) cc_final: 0.7408 (mtm110) outliers start: 57 outliers final: 28 residues processed: 243 average time/residue: 0.3286 time to fit residues: 131.5106 Evaluate side-chains 188 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 705 HIS B 834 HIS C1108 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080022 restraints weight = 46214.308| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.59 r_work: 0.2941 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24607 Z= 0.218 Angle : 0.570 10.468 33602 Z= 0.296 Chirality : 0.040 0.176 3689 Planarity : 0.004 0.046 4231 Dihedral : 13.700 86.384 3738 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.59 % Allowed : 9.97 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.70 (0.15), residues: 2855 helix: 1.30 (0.13), residues: 1503 sheet: -0.00 (0.28), residues: 305 loop : -0.54 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 265 HIS 0.006 0.001 HIS C 6 PHE 0.020 0.002 PHE B 461 TYR 0.018 0.002 TYR B1111 ARG 0.005 0.001 ARG D 445 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1180) hydrogen bonds : angle 4.32904 ( 3414) covalent geometry : bond 0.00521 (24607) covalent geometry : angle 0.57000 (33602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7898 (m-10) cc_final: 0.7636 (m-10) REVERT: B 332 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (mt) REVERT: B 431 MET cc_start: 0.8467 (mpp) cc_final: 0.8213 (mpp) REVERT: B 655 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8058 (mpp80) REVERT: B 709 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7693 (mtm-85) REVERT: B 968 VAL cc_start: 0.7315 (t) cc_final: 0.7106 (t) REVERT: B 1078 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8605 (tt) REVERT: C 30 PHE cc_start: 0.8855 (m-10) cc_final: 0.8637 (m-10) REVERT: C 95 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8946 (mt) REVERT: C 646 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: C 835 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 924 MET cc_start: 0.8840 (mmp) cc_final: 0.8496 (mmp) REVERT: D 78 LEU cc_start: 0.6509 (mm) cc_final: 0.6195 (tp) REVERT: D 462 MET cc_start: 0.7666 (mmm) cc_final: 0.7079 (mmp) REVERT: D 470 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7315 (mtm110) outliers start: 63 outliers final: 37 residues processed: 230 average time/residue: 0.3901 time to fit residues: 146.0406 Evaluate side-chains 196 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1150 HIS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 244 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1057 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 HIS D 65 HIS ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084207 restraints weight = 46570.885| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.52 r_work: 0.3031 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24607 Z= 0.124 Angle : 0.492 10.378 33602 Z= 0.257 Chirality : 0.038 0.158 3689 Planarity : 0.003 0.048 4231 Dihedral : 13.595 88.440 3736 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.30 % Allowed : 11.00 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 1.11 (0.16), residues: 2855 helix: 1.67 (0.13), residues: 1504 sheet: 0.17 (0.29), residues: 303 loop : -0.41 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.004 0.001 HIS C 336 PHE 0.017 0.001 PHE C 193 TYR 0.018 0.001 TYR B1111 ARG 0.017 0.000 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1180) hydrogen bonds : angle 4.05441 ( 3414) covalent geometry : bond 0.00285 (24607) covalent geometry : angle 0.49185 (33602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 2.556 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7921 (m-10) cc_final: 0.7679 (m-10) REVERT: B 354 MET cc_start: 0.8347 (mtt) cc_final: 0.8097 (mtt) REVERT: B 431 MET cc_start: 0.8577 (mpp) cc_final: 0.8321 (mpp) REVERT: B 568 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7334 (tpp80) REVERT: B 655 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8157 (mpp80) REVERT: B 709 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7848 (mtm-85) REVERT: B 901 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7917 (t60) REVERT: B 968 VAL cc_start: 0.7232 (t) cc_final: 0.7002 (t) REVERT: B 1078 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8666 (tt) REVERT: C 30 PHE cc_start: 0.8802 (m-10) cc_final: 0.8518 (m-10) REVERT: C 661 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8958 (mt) REVERT: C 924 MET cc_start: 0.8738 (mmp) cc_final: 0.8469 (mmp) REVERT: D 78 LEU cc_start: 0.6381 (mm) cc_final: 0.6101 (tp) REVERT: D 462 MET cc_start: 0.7833 (mmm) cc_final: 0.7186 (mmp) REVERT: D 470 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7249 (mtm110) REVERT: D 520 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8141 (mtpt) outliers start: 56 outliers final: 29 residues processed: 222 average time/residue: 0.3637 time to fit residues: 131.4148 Evaluate side-chains 193 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 520 LYS Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082310 restraints weight = 46735.054| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.44 r_work: 0.2998 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24607 Z= 0.150 Angle : 0.501 10.198 33602 Z= 0.260 Chirality : 0.038 0.153 3689 Planarity : 0.004 0.049 4231 Dihedral : 13.536 88.199 3734 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.59 % Allowed : 11.49 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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 (0.16), residues: 2855 helix: 1.80 (0.13), residues: 1497 sheet: 0.18 (0.28), residues: 303 loop : -0.35 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.004 0.001 HIS C 6 PHE 0.016 0.001 PHE B 257 TYR 0.017 0.001 TYR B1111 ARG 0.006 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1180) hydrogen bonds : angle 4.04550 ( 3414) covalent geometry : bond 0.00355 (24607) covalent geometry : angle 0.50067 (33602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7985 (m-10) cc_final: 0.7780 (m-10) REVERT: B 332 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8557 (mt) REVERT: B 354 MET cc_start: 0.8169 (mtt) cc_final: 0.7940 (mtt) REVERT: B 431 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: B 655 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8137 (mpp80) REVERT: B 709 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7649 (mtm-85) REVERT: B 968 VAL cc_start: 0.7145 (t) cc_final: 0.6921 (t) REVERT: B 1078 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (tt) REVERT: C 661 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8960 (mt) REVERT: C 924 MET cc_start: 0.8647 (mmp) cc_final: 0.8339 (mmp) REVERT: D 78 LEU cc_start: 0.6422 (mm) cc_final: 0.6208 (tp) REVERT: D 407 MET cc_start: 0.8117 (tmm) cc_final: 0.7736 (tmm) REVERT: D 462 MET cc_start: 0.7799 (mmm) cc_final: 0.7147 (mmp) REVERT: D 470 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7284 (mtm110) outliers start: 63 outliers final: 41 residues processed: 216 average time/residue: 0.4280 time to fit residues: 156.2234 Evaluate side-chains 206 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 247 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 184 optimal weight: 0.2980 chunk 249 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 255 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.083243 restraints weight = 46316.379| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.34 r_work: 0.3025 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24607 Z= 0.120 Angle : 0.474 10.133 33602 Z= 0.247 Chirality : 0.037 0.151 3689 Planarity : 0.003 0.050 4231 Dihedral : 13.453 88.556 3734 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.34 % Allowed : 12.02 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 1.40 (0.16), residues: 2855 helix: 1.95 (0.13), residues: 1499 sheet: 0.25 (0.29), residues: 301 loop : -0.32 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.005 0.001 HIS B 769 PHE 0.016 0.001 PHE C 193 TYR 0.017 0.001 TYR B1111 ARG 0.003 0.000 ARG D 575 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1180) hydrogen bonds : angle 3.93983 ( 3414) covalent geometry : bond 0.00277 (24607) covalent geometry : angle 0.47368 (33602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: B 156 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: B 310 PHE cc_start: 0.7978 (m-10) cc_final: 0.7778 (m-10) REVERT: B 332 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8577 (mt) REVERT: B 354 MET cc_start: 0.8190 (mtt) cc_final: 0.7972 (mtt) REVERT: B 431 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (mpp) REVERT: B 568 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7330 (tpp80) REVERT: B 655 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8149 (mpp80) REVERT: B 709 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7607 (mtm-85) REVERT: B 968 VAL cc_start: 0.7116 (t) cc_final: 0.6888 (t) REVERT: B 1050 CYS cc_start: 0.5005 (OUTLIER) cc_final: 0.4318 (t) REVERT: B 1078 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8626 (tt) REVERT: B 1140 TYR cc_start: 0.8411 (m-10) cc_final: 0.8156 (m-80) REVERT: C 95 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8989 (mt) REVERT: C 924 MET cc_start: 0.8604 (mmp) cc_final: 0.8307 (mmp) REVERT: D 407 MET cc_start: 0.8120 (tmm) cc_final: 0.7725 (tmm) REVERT: D 462 MET cc_start: 0.7726 (mmm) cc_final: 0.7121 (mmp) REVERT: D 470 ARG cc_start: 0.7652 (ttt180) cc_final: 0.7244 (mtm110) outliers start: 57 outliers final: 36 residues processed: 216 average time/residue: 0.3557 time to fit residues: 126.0948 Evaluate side-chains 202 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 251 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 206 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.112167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083994 restraints weight = 46605.675| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.48 r_work: 0.3024 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24607 Z= 0.116 Angle : 0.475 10.145 33602 Z= 0.246 Chirality : 0.037 0.149 3689 Planarity : 0.003 0.049 4231 Dihedral : 13.377 88.716 3734 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.26 % Allowed : 12.47 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 1.49 (0.16), residues: 2855 helix: 2.04 (0.13), residues: 1497 sheet: 0.36 (0.29), residues: 291 loop : -0.31 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 993 HIS 0.003 0.001 HIS C 6 PHE 0.016 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.003 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 1180) hydrogen bonds : angle 3.89807 ( 3414) covalent geometry : bond 0.00269 (24607) covalent geometry : angle 0.47483 (33602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: B 332 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 354 MET cc_start: 0.8117 (mtt) cc_final: 0.7914 (mtt) REVERT: B 431 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8134 (mpp) REVERT: B 568 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7337 (tpp80) REVERT: B 655 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8200 (mpp80) REVERT: B 709 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7616 (mtm-85) REVERT: B 968 VAL cc_start: 0.7102 (t) cc_final: 0.6876 (t) REVERT: B 1050 CYS cc_start: 0.4888 (OUTLIER) cc_final: 0.4330 (t) REVERT: B 1078 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8644 (tt) REVERT: C 924 MET cc_start: 0.8605 (mmp) cc_final: 0.8301 (mmp) REVERT: D 407 MET cc_start: 0.8104 (tmm) cc_final: 0.7720 (tmm) REVERT: D 462 MET cc_start: 0.7712 (mmm) cc_final: 0.7123 (mmp) REVERT: D 470 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7247 (mtm110) REVERT: A 18 SER cc_start: 0.8744 (t) cc_final: 0.8053 (p) outliers start: 55 outliers final: 37 residues processed: 213 average time/residue: 0.3423 time to fit residues: 118.7843 Evaluate side-chains 204 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 242 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 848 GLN D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081787 restraints weight = 46661.864| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.48 r_work: 0.2982 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24607 Z= 0.197 Angle : 0.535 10.221 33602 Z= 0.277 Chirality : 0.039 0.173 3689 Planarity : 0.004 0.048 4231 Dihedral : 13.409 87.901 3734 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.59 % Allowed : 12.68 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 1.26 (0.16), residues: 2855 helix: 1.84 (0.13), residues: 1499 sheet: 0.25 (0.29), residues: 300 loop : -0.40 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 248 HIS 0.005 0.001 HIS C 6 PHE 0.016 0.002 PHE B 461 TYR 0.016 0.002 TYR B1111 ARG 0.003 0.000 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1180) hydrogen bonds : angle 4.07776 ( 3414) covalent geometry : bond 0.00467 (24607) covalent geometry : angle 0.53484 (33602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 2.936 Fit side-chains REVERT: B 156 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 310 PHE cc_start: 0.8060 (m-10) cc_final: 0.7827 (m-10) REVERT: B 332 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 354 MET cc_start: 0.8267 (mtt) cc_final: 0.8034 (mtt) REVERT: B 431 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8168 (mpp) REVERT: B 655 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8241 (mpp80) REVERT: B 658 MET cc_start: 0.8736 (tpp) cc_final: 0.8522 (tpp) REVERT: B 709 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7604 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4200 (t) REVERT: B 1078 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8606 (tt) REVERT: B 1140 TYR cc_start: 0.8483 (m-10) cc_final: 0.8202 (m-10) REVERT: C 835 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 924 MET cc_start: 0.8628 (mmp) cc_final: 0.8325 (mmp) REVERT: D 462 MET cc_start: 0.7739 (mmm) cc_final: 0.7143 (mmp) REVERT: D 470 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7275 (mtm110) outliers start: 63 outliers final: 41 residues processed: 207 average time/residue: 0.3303 time to fit residues: 112.1822 Evaluate side-chains 201 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1150 HIS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 873 GLU Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 203 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN D 518 ASN D 542 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080286 restraints weight = 47173.154| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.48 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24607 Z= 0.244 Angle : 0.590 10.240 33602 Z= 0.303 Chirality : 0.041 0.182 3689 Planarity : 0.004 0.047 4231 Dihedral : 13.447 87.950 3734 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.50 % Allowed : 12.64 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.96 (0.16), residues: 2855 helix: 1.58 (0.13), residues: 1510 sheet: 0.08 (0.29), residues: 300 loop : -0.52 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 248 HIS 0.006 0.001 HIS C 6 PHE 0.020 0.002 PHE B 461 TYR 0.016 0.002 TYR B1111 ARG 0.006 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 1180) hydrogen bonds : angle 4.23823 ( 3414) covalent geometry : bond 0.00583 (24607) covalent geometry : angle 0.58959 (33602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: B 156 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: B 310 PHE cc_start: 0.8065 (m-10) cc_final: 0.7845 (m-10) REVERT: B 332 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 354 MET cc_start: 0.8512 (mtt) cc_final: 0.8270 (mtt) REVERT: B 431 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: B 655 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8356 (mpp80) REVERT: B 658 MET cc_start: 0.8993 (tpp) cc_final: 0.8774 (tpp) REVERT: B 1078 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (tt) REVERT: B 1171 MET cc_start: 0.7856 (tmm) cc_final: 0.7622 (tmm) REVERT: C 835 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 924 MET cc_start: 0.8791 (mmp) cc_final: 0.8522 (mmp) REVERT: D 462 MET cc_start: 0.7780 (mmm) cc_final: 0.7202 (mmp) REVERT: D 470 ARG cc_start: 0.7938 (ttt180) cc_final: 0.7366 (mtm110) outliers start: 61 outliers final: 47 residues processed: 202 average time/residue: 0.3247 time to fit residues: 108.5755 Evaluate side-chains 202 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1150 HIS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 873 GLU Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 141 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN D 300 GLN D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080455 restraints weight = 47056.011| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.51 r_work: 0.2962 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24607 Z= 0.213 Angle : 0.565 9.901 33602 Z= 0.291 Chirality : 0.040 0.168 3689 Planarity : 0.004 0.044 4231 Dihedral : 13.435 88.580 3734 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.30 % Allowed : 12.72 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.99 (0.16), residues: 2855 helix: 1.63 (0.13), residues: 1503 sheet: 0.04 (0.29), residues: 304 loop : -0.54 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 248 HIS 0.005 0.001 HIS C 6 PHE 0.017 0.002 PHE B 461 TYR 0.016 0.002 TYR B1111 ARG 0.006 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1180) hydrogen bonds : angle 4.20180 ( 3414) covalent geometry : bond 0.00511 (24607) covalent geometry : angle 0.56497 (33602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 2.892 Fit side-chains revert: symmetry clash REVERT: B 156 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: B 310 PHE cc_start: 0.8037 (m-10) cc_final: 0.7824 (m-10) REVERT: B 332 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 354 MET cc_start: 0.8246 (mtt) cc_final: 0.8028 (mtt) REVERT: B 431 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8168 (mpp) REVERT: B 655 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8210 (mpp80) REVERT: B 658 MET cc_start: 0.8788 (tpp) cc_final: 0.8576 (tpp) REVERT: B 709 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7608 (mtm-85) REVERT: B 1078 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 1140 TYR cc_start: 0.8486 (m-80) cc_final: 0.8181 (m-10) REVERT: C 835 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 924 MET cc_start: 0.8638 (mmp) cc_final: 0.8338 (mmp) REVERT: D 462 MET cc_start: 0.7797 (mmm) cc_final: 0.7256 (mmp) REVERT: D 470 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7322 (mtm110) outliers start: 56 outliers final: 40 residues processed: 200 average time/residue: 0.3343 time to fit residues: 111.2737 Evaluate side-chains 194 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 873 GLU Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 84 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 283 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082540 restraints weight = 46496.179| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.50 r_work: 0.3002 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24607 Z= 0.129 Angle : 0.511 10.069 33602 Z= 0.265 Chirality : 0.038 0.156 3689 Planarity : 0.004 0.044 4231 Dihedral : 13.355 89.536 3733 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.81 % Allowed : 13.17 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 1.27 (0.16), residues: 2855 helix: 1.89 (0.13), residues: 1499 sheet: 0.15 (0.29), residues: 304 loop : -0.44 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 710 HIS 0.003 0.001 HIS C 6 PHE 0.015 0.001 PHE C 193 TYR 0.026 0.001 TYR B 173 ARG 0.007 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1180) hydrogen bonds : angle 4.03264 ( 3414) covalent geometry : bond 0.00301 (24607) covalent geometry : angle 0.51108 (33602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10988.14 seconds wall clock time: 193 minutes 8.37 seconds (11588.37 seconds total)