Starting phenix.real_space_refine on Mon Sep 30 00:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_15804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_15804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_15804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_15804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1t_15804/09_2024/8b1t_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-5461/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: 13.77, per 1000 atoms: 0.57 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: 5.91 Conformation dependent library (CDL) restraints added in 3.0 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: 7.78 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: 10.00 Time building geometry restraints manager: 7.00 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: 1.030 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: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 58.380 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.930 ------------------------------------------------------------------------------- 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= 0.197 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 2.883 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: 0.4275 time to fit residues: 299.5317 Evaluate side-chains 189 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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= 0.322 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 *********************** 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 fitting. rotamer outliers: 57 poor density : 199 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 655 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7612 (mpp80) REVERT: B 709 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7352 (mtm-85) REVERT: B 968 VAL cc_start: 0.7070 (t) cc_final: 0.6845 (t) REVERT: B 1078 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 1079 LEU cc_start: 0.9351 (tp) cc_final: 0.9136 (tt) REVERT: C 556 LEU cc_start: 0.8876 (mt) cc_final: 0.8628 (mt) REVERT: C 835 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6736 (tm-30) REVERT: C 924 MET cc_start: 0.8533 (mmp) cc_final: 0.8228 (mmp) REVERT: D 78 LEU cc_start: 0.6412 (mm) cc_final: 0.6212 (tp) REVERT: D 239 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8708 (p) REVERT: D 384 THR cc_start: 0.8325 (p) cc_final: 0.8025 (t) REVERT: D 407 MET cc_start: 0.7841 (ttp) cc_final: 0.7575 (tmm) REVERT: D 462 MET cc_start: 0.7386 (mmm) cc_final: 0.6842 (mmp) REVERT: D 470 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7419 (mtm110) outliers start: 57 outliers final: 28 residues processed: 243 average time/residue: 0.3211 time to fit residues: 128.2879 Evaluate side-chains 188 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 705 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 GLN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24607 Z= 0.209 Angle : 0.502 10.255 33602 Z= 0.262 Chirality : 0.038 0.161 3689 Planarity : 0.004 0.047 4231 Dihedral : 13.566 87.244 3738 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.89 % Allowed : 10.01 % Favored : 88.10 % 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: 0.97 (0.15), residues: 2855 helix: 1.53 (0.13), residues: 1507 sheet: 0.20 (0.28), residues: 305 loop : -0.46 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 265 HIS 0.004 0.001 HIS B 171 PHE 0.018 0.001 PHE B 257 TYR 0.018 0.001 TYR B1111 ARG 0.005 0.000 ARG D 445 *********************** 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 225 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7792 (m-10) cc_final: 0.7547 (m-10) REVERT: B 332 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 354 MET cc_start: 0.7729 (mtt) cc_final: 0.7521 (mtt) REVERT: B 568 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7153 (tpp80) REVERT: B 655 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7655 (mpp80) REVERT: B 709 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7400 (mtm-85) REVERT: B 901 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.7778 (t60) REVERT: B 1078 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 835 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6783 (tm-30) REVERT: C 924 MET cc_start: 0.8511 (mmp) cc_final: 0.8206 (mmp) REVERT: D 78 LEU cc_start: 0.6444 (mm) cc_final: 0.6234 (tp) REVERT: D 239 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8694 (p) REVERT: D 462 MET cc_start: 0.7482 (mmm) cc_final: 0.6926 (mmp) REVERT: D 470 ARG cc_start: 0.7748 (ttt180) cc_final: 0.7333 (mtm110) outliers start: 46 outliers final: 23 residues processed: 215 average time/residue: 0.3333 time to fit residues: 115.2610 Evaluate side-chains 184 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 2.625 ------------------------------------------------------------------------------- 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 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 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP 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 350 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 136 LEU 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 263 LEU Chi-restraints excluded: chain D residue 367 ILE 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 261 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 281 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 834 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24607 Z= 0.270 Angle : 0.524 10.231 33602 Z= 0.272 Chirality : 0.039 0.156 3689 Planarity : 0.004 0.049 4231 Dihedral : 13.576 87.809 3736 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.54 % Allowed : 10.42 % Favored : 87.03 % 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: 1.07 (0.15), residues: 2855 helix: 1.62 (0.13), residues: 1503 sheet: 0.20 (0.28), residues: 305 loop : -0.39 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 710 HIS 0.005 0.001 HIS C 6 PHE 0.017 0.001 PHE B 461 TYR 0.016 0.002 TYR B1111 ARG 0.003 0.000 ARG A 13 *********************** 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 228 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 166 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 604 MET cc_start: 0.8144 (mmm) cc_final: 0.7907 (mmm) REVERT: B 655 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7891 (mpp80) REVERT: B 709 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7343 (mtm-85) REVERT: B 1078 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 95 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8755 (mt) REVERT: C 835 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6869 (tm-30) REVERT: C 924 MET cc_start: 0.8521 (mmp) cc_final: 0.8214 (mmp) REVERT: D 78 LEU cc_start: 0.6405 (mm) cc_final: 0.6124 (tp) REVERT: D 239 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (p) REVERT: D 462 MET cc_start: 0.7676 (mmm) cc_final: 0.7095 (mmp) REVERT: D 470 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7375 (mtm110) outliers start: 62 outliers final: 41 residues processed: 215 average time/residue: 0.3391 time to fit residues: 117.1639 Evaluate side-chains 200 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 154 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 407 THR 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 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 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 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 665 MET Chi-restraints excluded: chain C residue 740 SER 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 239 THR Chi-restraints excluded: chain D residue 250 SER 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 493 LEU Chi-restraints excluded: chain D residue 523 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** C 759 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24607 Z= 0.219 Angle : 0.496 10.234 33602 Z= 0.258 Chirality : 0.038 0.153 3689 Planarity : 0.003 0.047 4231 Dihedral : 13.517 87.811 3734 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.75 % Allowed : 10.79 % Favored : 86.46 % 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: 1.81 (0.13), residues: 1497 sheet: 0.27 (0.28), residues: 303 loop : -0.33 (0.19), 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 C 193 TYR 0.017 0.001 TYR B1111 ARG 0.003 0.000 ARG D 325 *********************** 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 236 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 169 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 332 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 568 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7368 (tpp80) REVERT: B 655 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7961 (mpp80) REVERT: B 658 MET cc_start: 0.8391 (tpp) cc_final: 0.8184 (tpp) REVERT: B 709 ARG cc_start: 0.7691 (tpp80) cc_final: 0.7314 (mtm-85) REVERT: B 1078 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8601 (tt) REVERT: C 95 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8782 (mt) REVERT: C 661 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 924 MET cc_start: 0.8471 (mmp) cc_final: 0.8157 (mmp) REVERT: D 78 LEU cc_start: 0.6395 (mm) cc_final: 0.6168 (tp) REVERT: D 239 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 407 MET cc_start: 0.8070 (tmm) cc_final: 0.7658 (tmm) REVERT: D 462 MET cc_start: 0.7687 (mmm) cc_final: 0.7062 (mmp) REVERT: D 470 ARG cc_start: 0.7603 (ttt180) cc_final: 0.7372 (mtm110) outliers start: 67 outliers final: 42 residues processed: 223 average time/residue: 0.3282 time to fit residues: 120.0006 Evaluate side-chains 206 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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 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 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 1002 LEU Chi-restraints excluded: chain B residue 1005 THR 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 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 661 ILE 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 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 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 D residue 520 LYS Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain D residue 577 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 165 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 147 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** C 660 ASN D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3089 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= 0.180 Angle : 0.475 10.095 33602 Z= 0.248 Chirality : 0.037 0.149 3689 Planarity : 0.003 0.048 4231 Dihedral : 13.441 88.472 3734 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.54 % Allowed : 11.24 % Favored : 86.21 % 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: 1.94 (0.13), residues: 1507 sheet: 0.31 (0.28), residues: 303 loop : -0.33 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 445 *********************** 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 228 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 166 time to evaluate : 2.759 Fit side-chains revert: symmetry clash REVERT: B 431 MET cc_start: 0.7867 (mpp) cc_final: 0.7638 (mpp) REVERT: B 568 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7401 (tpp80) REVERT: B 655 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.7968 (mpp80) REVERT: B 709 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7269 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4150 (t) REVERT: B 1078 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 1140 TYR cc_start: 0.8375 (m-10) cc_final: 0.8123 (m-80) REVERT: C 924 MET cc_start: 0.8454 (mmp) cc_final: 0.8148 (mmp) REVERT: D 239 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8554 (p) REVERT: D 462 MET cc_start: 0.7613 (mmm) cc_final: 0.7028 (mmp) REVERT: D 470 ARG cc_start: 0.7560 (ttt180) cc_final: 0.7244 (mtm110) outliers start: 62 outliers final: 42 residues processed: 215 average time/residue: 0.3185 time to fit residues: 112.5045 Evaluate side-chains 201 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 154 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 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 540 LEU 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 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 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 641 LEU 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 79 GLN 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 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 D residue 518 ASN Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain D residue 577 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 271 optimal weight: 9.9990 chunk 31 optimal weight: 0.0670 chunk 160 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 overall best weight: 2.7322 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24607 Z= 0.260 Angle : 0.507 10.144 33602 Z= 0.262 Chirality : 0.038 0.149 3689 Planarity : 0.004 0.043 4231 Dihedral : 13.442 87.996 3734 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.54 % Allowed : 11.86 % Favored : 85.60 % 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: 1.36 (0.16), residues: 2855 helix: 1.91 (0.13), residues: 1500 sheet: 0.28 (0.29), residues: 301 loop : -0.34 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 993 HIS 0.004 0.001 HIS C 6 PHE 0.015 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.002 0.000 ARG B 655 *********************** 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 219 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 157 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 655 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8066 (mpp80) REVERT: B 658 MET cc_start: 0.8430 (tpp) cc_final: 0.8218 (tpp) REVERT: B 709 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7224 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4858 (OUTLIER) cc_final: 0.4241 (t) REVERT: B 1078 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8555 (tt) REVERT: C 924 MET cc_start: 0.8459 (mmp) cc_final: 0.8158 (mmp) REVERT: D 239 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 462 MET cc_start: 0.7629 (mmm) cc_final: 0.7049 (mmp) REVERT: D 470 ARG cc_start: 0.7607 (ttt180) cc_final: 0.7250 (mtm110) outliers start: 62 outliers final: 48 residues processed: 205 average time/residue: 0.3332 time to fit residues: 111.9965 Evaluate side-chains 202 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU 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 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 540 LEU 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 990 LEU 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 B residue 1150 HIS 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 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 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 239 THR 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 D residue 518 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN B 848 GLN D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24607 Z= 0.236 Angle : 0.502 10.167 33602 Z= 0.260 Chirality : 0.038 0.188 3689 Planarity : 0.004 0.045 4231 Dihedral : 13.426 88.165 3734 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.26 % Allowed : 12.35 % Favored : 85.39 % 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: 1.37 (0.16), residues: 2855 helix: 1.93 (0.13), residues: 1501 sheet: 0.28 (0.29), residues: 301 loop : -0.35 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 993 HIS 0.004 0.001 HIS C 6 PHE 0.015 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.002 0.000 ARG B 655 *********************** 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 212 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 157 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 655 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8048 (mpp80) REVERT: B 658 MET cc_start: 0.8430 (tpp) cc_final: 0.8213 (tpp) REVERT: B 709 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7215 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4713 (OUTLIER) cc_final: 0.4128 (t) REVERT: B 1078 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 1140 TYR cc_start: 0.8388 (m-10) cc_final: 0.8117 (m-80) REVERT: C 924 MET cc_start: 0.8457 (mmp) cc_final: 0.8142 (mmp) REVERT: D 239 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8560 (p) REVERT: D 462 MET cc_start: 0.7601 (mmm) cc_final: 0.7018 (mmp) REVERT: D 470 ARG cc_start: 0.7599 (ttt180) cc_final: 0.7265 (mtm110) outliers start: 55 outliers final: 47 residues processed: 200 average time/residue: 0.3311 time to fit residues: 109.0216 Evaluate side-chains 200 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 2.633 ------------------------------------------------------------------------------- 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 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 540 LEU 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 990 LEU 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 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 867 THR 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 239 THR 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 D residue 518 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.0040 chunk 268 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24607 Z= 0.253 Angle : 0.511 10.184 33602 Z= 0.264 Chirality : 0.038 0.171 3689 Planarity : 0.004 0.044 4231 Dihedral : 13.404 88.340 3734 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.50 % Allowed : 12.15 % Favored : 85.35 % 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: 1.33 (0.16), residues: 2855 helix: 1.90 (0.13), residues: 1505 sheet: 0.28 (0.29), residues: 301 loop : -0.38 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 993 HIS 0.004 0.001 HIS C 6 PHE 0.015 0.001 PHE C 193 TYR 0.016 0.001 TYR B1111 ARG 0.002 0.000 ARG B 655 *********************** 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 212 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 151 time to evaluate : 2.848 Fit side-chains revert: symmetry clash REVERT: B 655 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8019 (mpp80) REVERT: B 658 MET cc_start: 0.8437 (tpp) cc_final: 0.8224 (tpp) REVERT: B 709 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7261 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4845 (OUTLIER) cc_final: 0.4317 (t) REVERT: B 1078 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8548 (tt) REVERT: C 924 MET cc_start: 0.8461 (mmp) cc_final: 0.8148 (mmp) REVERT: D 239 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8567 (p) REVERT: D 462 MET cc_start: 0.7604 (mmm) cc_final: 0.7028 (mmp) REVERT: D 470 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7263 (mtm110) outliers start: 61 outliers final: 49 residues processed: 199 average time/residue: 0.3260 time to fit residues: 107.1049 Evaluate side-chains 200 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 147 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 382 MET Chi-restraints excluded: chain B residue 407 THR 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 540 LEU 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 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 740 SER Chi-restraints excluded: chain C residue 867 THR 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 239 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 5.9990 chunk 276 optimal weight: 0.0270 chunk 168 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 289 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24607 Z= 0.168 Angle : 0.491 10.132 33602 Z= 0.254 Chirality : 0.037 0.160 3689 Planarity : 0.003 0.046 4231 Dihedral : 13.331 89.073 3734 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.05 % Allowed : 12.68 % 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: 1.52 (0.16), residues: 2855 helix: 2.05 (0.13), residues: 1507 sheet: 0.42 (0.29), residues: 298 loop : -0.31 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 710 HIS 0.002 0.001 HIS C 6 PHE 0.016 0.001 PHE C 193 TYR 0.017 0.001 TYR B1111 ARG 0.009 0.000 ARG D 466 ********************** 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 fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 568 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7397 (tpp80) REVERT: B 655 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7950 (mpp80) REVERT: B 709 ARG cc_start: 0.7700 (tpp80) cc_final: 0.7277 (mtm-85) REVERT: B 1050 CYS cc_start: 0.4785 (OUTLIER) cc_final: 0.4392 (t) REVERT: B 1078 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 1140 TYR cc_start: 0.8406 (m-80) cc_final: 0.8119 (m-10) REVERT: C 924 MET cc_start: 0.8440 (mmp) cc_final: 0.8135 (mmp) REVERT: D 239 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 462 MET cc_start: 0.7534 (mmm) cc_final: 0.7006 (mmp) REVERT: D 470 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7208 (mtm110) REVERT: A 18 SER cc_start: 0.8708 (t) cc_final: 0.8055 (p) outliers start: 50 outliers final: 41 residues processed: 199 average time/residue: 0.3241 time to fit residues: 106.4236 Evaluate side-chains 198 residues out of total 2437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR 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 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 540 LEU 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 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 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 867 THR 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 239 THR 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 D residue 518 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.083972 restraints weight = 46589.041| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.44 r_work: 0.3027 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 24607 Z= 0.272 Angle : 0.648 59.200 33602 Z= 0.372 Chirality : 0.040 0.545 3689 Planarity : 0.003 0.045 4231 Dihedral : 13.342 89.027 3734 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.89 % Allowed : 12.93 % Favored : 85.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.48 (0.16), residues: 2855 helix: 2.01 (0.13), residues: 1507 sheet: 0.40 (0.29), residues: 298 loop : -0.32 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 710 HIS 0.009 0.001 HIS C 377 PHE 0.016 0.001 PHE C 193 TYR 0.017 0.001 TYR B1111 ARG 0.005 0.000 ARG C 706 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4295.82 seconds wall clock time: 77 minutes 39.86 seconds (4659.86 seconds total)