Starting phenix.real_space_refine on Thu Feb 5 19:23:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nh6_49403/02_2026/9nh6_49403.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 1.077 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 Zn 2 6.06 5 P 49 5.49 5 S 115 5.16 5 C 12151 2.51 5 N 3365 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19390 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "E" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 670 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 858 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 865 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 2 Chain: "H" Number of atoms: 4917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4917 Classifications: {'peptide': 616} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 590} Chain breaks: 8 Chain: "I" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4705 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 564} Chain breaks: 2 Chain: "J" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3825 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 12, 'TRANS': 468} Chain breaks: 4 Chain: "K" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "Z" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 630 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 23} Chain: "Y" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain breaks: 1 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.72, per 1000 atoms: 0.24 Number of scatterers: 19390 At special positions: 0 Unit cell: (122.925, 122.925, 188.1, 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) Zn 2 29.99 S 115 16.00 P 49 15.00 O 3708 8.00 N 3365 7.00 C 12151 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: 1.26 Conformation dependent library (CDL) restraints added in 905.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 73 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 158 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 71 " pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 76 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 418 " 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 14 sheets defined 42.3% alpha, 21.3% beta 13 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.847A pdb=" N LYS A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.573A pdb=" N GLN B 11 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 28 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.850A pdb=" N LEU C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 107 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.995A pdb=" N GLU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.547A pdb=" N ASP H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 52 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 53 " --> pdb=" O MET H 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 53' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 96 through 114 removed outlier: 4.260A pdb=" N TRP H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 215 through 232 removed outlier: 3.813A pdb=" N GLU H 219 " --> pdb=" O ARG H 215 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 260 Processing helix chain 'H' and resid 261 through 264 Processing helix chain 'H' and resid 272 through 285 removed outlier: 4.545A pdb=" N ALA H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 289 Processing helix chain 'H' and resid 290 through 295 removed outlier: 3.637A pdb=" N ARG H 294 " --> pdb=" O ASN H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 317 removed outlier: 3.526A pdb=" N PHE H 317 " --> pdb=" O MET H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 345 removed outlier: 3.711A pdb=" N ARG H 338 " --> pdb=" O SER H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 Processing helix chain 'H' and resid 368 through 370 No H-bonds generated for 'chain 'H' and resid 368 through 370' Processing helix chain 'H' and resid 398 through 410 removed outlier: 4.829A pdb=" N GLU H 404 " --> pdb=" O GLN H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 436 removed outlier: 3.694A pdb=" N LEU H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 498 No H-bonds generated for 'chain 'H' and resid 496 through 498' Processing helix chain 'H' and resid 499 through 504 removed outlier: 4.180A pdb=" N TYR H 503 " --> pdb=" O ASP H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 534 removed outlier: 3.780A pdb=" N LEU H 526 " --> pdb=" O PRO H 522 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS H 532 " --> pdb=" O TYR H 528 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 533 " --> pdb=" O GLN H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 590 Processing helix chain 'H' and resid 607 through 622 Processing helix chain 'H' and resid 664 through 681 Processing helix chain 'I' and resid 42 through 50 removed outlier: 4.074A pdb=" N LYS I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 88 through 107 Processing helix chain 'I' and resid 115 through 125 removed outlier: 3.734A pdb=" N LYS I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 229 Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 260 through 264 Processing helix chain 'I' and resid 272 through 281 Processing helix chain 'I' and resid 283 through 287 removed outlier: 3.524A pdb=" N TRP I 286 " --> pdb=" O GLN I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 297 Processing helix chain 'I' and resid 313 through 318 Processing helix chain 'I' and resid 335 through 346 removed outlier: 4.144A pdb=" N ARG I 339 " --> pdb=" O CYS I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 371 Processing helix chain 'I' and resid 545 through 556 Processing helix chain 'I' and resid 567 through 583 removed outlier: 3.639A pdb=" N PHE I 581 " --> pdb=" O CYS I 577 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 617 Processing helix chain 'I' and resid 721 through 726 removed outlier: 4.101A pdb=" N GLN I 726 " --> pdb=" O SER I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 726 through 732 Processing helix chain 'I' and resid 765 through 777 removed outlier: 3.902A pdb=" N TYR I 769 " --> pdb=" O CYS I 765 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 45 removed outlier: 3.651A pdb=" N LEU J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 64 removed outlier: 3.884A pdb=" N VAL J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 70 Processing helix chain 'J' and resid 73 through 79 removed outlier: 3.517A pdb=" N ILE J 77 " --> pdb=" O PHE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 83 Processing helix chain 'J' and resid 85 through 103 Processing helix chain 'J' and resid 106 through 119 removed outlier: 3.557A pdb=" N ILE J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU J 117 " --> pdb=" O ASN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 147 removed outlier: 3.551A pdb=" N VAL J 126 " --> pdb=" O ASN J 122 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL J 139 " --> pdb=" O GLN J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 176 through 194 Processing helix chain 'J' and resid 224 through 244 removed outlier: 3.569A pdb=" N MET J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL J 244 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.596A pdb=" N ILE J 275 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN J 276 " --> pdb=" O SER J 272 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS J 282 " --> pdb=" O TYR J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 311 removed outlier: 3.679A pdb=" N HIS J 311 " --> pdb=" O SER J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 316 removed outlier: 3.970A pdb=" N LEU J 315 " --> pdb=" O PRO J 312 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU J 316 " --> pdb=" O ALA J 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 312 through 316' Processing helix chain 'J' and resid 317 through 327 removed outlier: 3.738A pdb=" N THR J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU J 324 " --> pdb=" O GLN J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 550 removed outlier: 4.161A pdb=" N LEU J 550 " --> pdb=" O SER J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 572 removed outlier: 3.543A pdb=" N ALA J 560 " --> pdb=" O ALA J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 579 removed outlier: 3.552A pdb=" N SER J 579 " --> pdb=" O ALA J 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 594 removed outlier: 4.138A pdb=" N THR J 594 " --> pdb=" O ALA J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 600 through 611 removed outlier: 4.178A pdb=" N VAL J 604 " --> pdb=" O LEU J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 634 removed outlier: 3.586A pdb=" N ALA J 619 " --> pdb=" O ARG J 615 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 633 " --> pdb=" O ALA J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 635 through 637 No H-bonds generated for 'chain 'J' and resid 635 through 637' Processing helix chain 'J' and resid 639 through 656 Processing helix chain 'J' and resid 662 through 670 removed outlier: 3.512A pdb=" N LYS J 666 " --> pdb=" O GLY J 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL J 668 " --> pdb=" O PHE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 686 Processing helix chain 'J' and resid 691 through 706 removed outlier: 3.955A pdb=" N GLY J 695 " --> pdb=" O ARG J 691 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE J 703 " --> pdb=" O LEU J 699 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE J 704 " --> pdb=" O ARG J 700 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 719 removed outlier: 3.587A pdb=" N TYR J 713 " --> pdb=" O ARG J 709 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 737 Processing helix chain 'K' and resid 716 through 722 removed outlier: 3.734A pdb=" N ARG K 721 " --> pdb=" O ILE K 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 54 through 58 removed outlier: 6.599A pdb=" N GLU F 49 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS F 58 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 47 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN F 43 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR F 47 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS F 30 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU F 49 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU F 28 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N MET F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 74 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG E 76 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG E 71 " --> pdb=" O HIS E 65 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS E 65 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN E 73 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU E 63 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE E 77 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP E 59 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU E 79 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL E 57 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 49 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP E 59 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE E 47 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA E 61 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E 45 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU E 63 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE E 43 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS E 65 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET E 41 " --> pdb=" O HIS E 65 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET E 41 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU E 35 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 86 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER E 89 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET G 59 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS G 45 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET G 59 " --> pdb=" O ASP G 43 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP G 43 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL G 61 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL G 41 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL G 41 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N CYS G 45 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN G 28 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU G 47 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N HIS G 26 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET G 69 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN A 60 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 60 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 44 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR A 62 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN A 42 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS A 41 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA A 35 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N MET A 43 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 33 " --> pdb=" O MET A 43 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN A 45 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 31 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 69 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS B 64 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 48 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 66 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP B 46 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY B 68 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 41 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS B 45 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 28 " --> pdb=" O CYS B 45 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 47 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 26 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG B 16 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL B 82 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP C 71 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 12.341A pdb=" N GLY B 84 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 13.875A pdb=" N LEU C 69 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 66 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 60 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS C 68 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR C 58 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP C 70 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE C 52 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 46 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 54 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP C 44 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS C 56 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C 42 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR C 30 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL C 82 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP C 32 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 181 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG D 180 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 54 through 58 removed outlier: 6.599A pdb=" N GLU F 49 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS F 58 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 47 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU F 61 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS D 172 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D 356 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN D 170 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU D 358 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LYS D 168 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 181 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG D 180 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.474A pdb=" N THR H 93 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 67 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS H 36 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU H 68 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET H 38 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N CYS H 27 " --> pdb=" O LEU H 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 144 through 146 removed outlier: 8.460A pdb=" N ALA H 163 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY H 178 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU H 204 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU H 201 " --> pdb=" O ILE H 415 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL H 417 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE H 203 " --> pdb=" O VAL H 417 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 414 " --> pdb=" O HIS H 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.420A pdb=" N ILE H 268 " --> pdb=" O SER H 309 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY H 236 " --> pdb=" O VAL H 325 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA H 327 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG H 235 " --> pdb=" O GLY H 351 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE H 353 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 237 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'I' and resid 606 through 610 removed outlier: 4.752A pdb=" N LYS H 462 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR H 492 " --> pdb=" O LEU H 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 480 through 481 removed outlier: 3.607A pdb=" N VAL H 481 " --> pdb=" O GLY I 633 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY I 633 " --> pdb=" O VAL H 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 537 through 542 removed outlier: 3.666A pdb=" N GLY I 762 " --> pdb=" O THR H 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 127 through 129 removed outlier: 6.656A pdb=" N ILE I 84 " --> pdb=" O GLN I 127 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU I 129 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA I 86 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL I 58 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR I 87 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU I 59 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU I 31 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N CYS I 20 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AB3, first strand: chain 'I' and resid 172 through 173 removed outlier: 6.690A pdb=" N LEU I 198 " --> pdb=" O ILE I 562 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU I 561 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 308 through 311 removed outlier: 6.876A pdb=" N LEU I 266 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N CYS I 311 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU I 268 " --> pdb=" O CYS I 311 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU I 234 " --> pdb=" O ILE I 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 377 through 384 845 hydrogen bonds defined for protein. 2367 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5426 1.33 - 1.46: 3661 1.46 - 1.58: 10447 1.58 - 1.70: 95 1.70 - 1.82: 190 Bond restraints: 19819 Sorted by residual: bond pdb=" N GLU H 544 " pdb=" CA GLU H 544 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.87e+00 bond pdb=" CG LEU H 160 " pdb=" CD1 LEU H 160 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.12e+00 bond pdb=" C PRO I 704 " pdb=" N PRO I 705 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" CA GLU H 544 " pdb=" C GLU H 544 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.74e+00 bond pdb=" CG GLU J 626 " pdb=" CD GLU J 626 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.22e+00 ... (remaining 19814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26122 2.08 - 4.16: 725 4.16 - 6.24: 100 6.24 - 8.32: 25 8.32 - 10.41: 8 Bond angle restraints: 26980 Sorted by residual: angle pdb=" C HIS I 711 " pdb=" CA HIS I 711 " pdb=" CB HIS I 711 " ideal model delta sigma weight residual 116.54 110.14 6.40 1.15e+00 7.56e-01 3.10e+01 angle pdb=" C LYS H 545 " pdb=" N PRO H 546 " pdb=" CA PRO H 546 " ideal model delta sigma weight residual 119.85 124.93 -5.08 1.01e+00 9.80e-01 2.53e+01 angle pdb=" CB LYS I 624 " pdb=" CG LYS I 624 " pdb=" CD LYS I 624 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" CA HIS I 711 " pdb=" C HIS I 711 " pdb=" N GLN I 712 " ideal model delta sigma weight residual 119.52 116.39 3.13 7.90e-01 1.60e+00 1.57e+01 angle pdb=" N ASP I 33 " pdb=" CA ASP I 33 " pdb=" C ASP I 33 " ideal model delta sigma weight residual 110.80 119.19 -8.39 2.13e+00 2.20e-01 1.55e+01 ... (remaining 26975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 11254 23.09 - 46.17: 726 46.17 - 69.26: 121 69.26 - 92.35: 29 92.35 - 115.43: 1 Dihedral angle restraints: 12131 sinusoidal: 5455 harmonic: 6676 Sorted by residual: dihedral pdb=" CA GLU I 627 " pdb=" C GLU I 627 " pdb=" N LEU I 628 " pdb=" CA LEU I 628 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU H 39 " pdb=" C LEU H 39 " pdb=" N ASP H 40 " pdb=" CA ASP H 40 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CA GLU H 544 " pdb=" CB GLU H 544 " ideal model delta harmonic sigma weight residual 122.80 133.46 -10.66 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 12128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2694 0.075 - 0.150: 401 0.150 - 0.225: 45 0.225 - 0.299: 4 0.299 - 0.374: 1 Chirality restraints: 3145 Sorted by residual: chirality pdb=" CA GLU H 544 " pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CB GLU H 544 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB VAL I 564 " pdb=" CA VAL I 564 " pdb=" CG1 VAL I 564 " pdb=" CG2 VAL I 564 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE I 170 " pdb=" CA ILE I 170 " pdb=" CG1 ILE I 170 " pdb=" CG2 ILE I 170 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3142 not shown) Planarity restraints: 3254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 345 " -0.032 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP I 345 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP I 345 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP I 345 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 345 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 345 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 345 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 345 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 345 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 345 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS H 260 " -0.061 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO H 261 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO H 261 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 261 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 559 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO H 560 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO H 560 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 560 " -0.046 5.00e-02 4.00e+02 ... (remaining 3251 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 281 2.70 - 3.25: 18451 3.25 - 3.80: 30950 3.80 - 4.35: 42711 4.35 - 4.90: 68952 Nonbonded interactions: 161345 Sorted by model distance: nonbonded pdb=" OD2 ASP H 179 " pdb="ZN ZN H 701 " model vdw 2.146 2.230 nonbonded pdb=" OD2 ASP H 179 " pdb="ZN ZN H 702 " model vdw 2.385 2.230 nonbonded pdb=" CE LYS I 290 " pdb=" OP1 G Y 46 " model vdw 2.527 3.440 nonbonded pdb=" NZ LYS I 290 " pdb=" OP1 G Y 46 " model vdw 2.531 3.120 nonbonded pdb=" OD2 ASP I 33 " pdb=" CB SER I 61 " model vdw 2.547 3.440 ... (remaining 161340 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: 4.510 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19824 Z= 0.191 Angle : 0.824 10.405 26980 Z= 0.447 Chirality : 0.053 0.374 3145 Planarity : 0.006 0.093 3254 Dihedral : 15.133 115.432 7793 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2241 helix: -0.32 (0.17), residues: 821 sheet: -0.62 (0.24), residues: 441 loop : -0.71 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 218 TYR 0.017 0.002 TYR H 103 PHE 0.030 0.002 PHE H 551 TRP 0.068 0.004 TRP I 345 HIS 0.009 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00416 (19819) covalent geometry : angle 0.82378 (26980) hydrogen bonds : bond 0.13898 ( 863) hydrogen bonds : angle 6.77438 ( 2425) metal coordination : bond 0.00161 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8382 (ppp) cc_final: 0.8156 (pp-130) REVERT: G 20 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7746 (mmmt) REVERT: G 35 ASP cc_start: 0.7915 (p0) cc_final: 0.7570 (p0) REVERT: C 7 VAL cc_start: 0.8565 (p) cc_final: 0.8350 (m) REVERT: C 47 ASP cc_start: 0.8262 (p0) cc_final: 0.7924 (p0) REVERT: D 142 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6585 (ttp-170) REVERT: H 400 GLN cc_start: 0.7110 (mt0) cc_final: 0.6415 (tm130) REVERT: I 124 ASP cc_start: 0.8116 (m-30) cc_final: 0.7909 (m-30) REVERT: I 217 GLU cc_start: 0.8041 (pt0) cc_final: 0.7800 (mt-10) REVERT: J 649 LEU cc_start: 0.6698 (mm) cc_final: 0.6425 (mm) outliers start: 2 outliers final: 1 residues processed: 325 average time/residue: 0.5445 time to fit residues: 200.2568 Evaluate side-chains 253 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 379 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS G 5 HIS D 357 HIS H 366 HIS ** H 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 553 ASN H 588 GLN I 572 GLN J 81 GLN J 557 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.198803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160645 restraints weight = 23268.746| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.72 r_work: 0.3691 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19824 Z= 0.158 Angle : 0.625 7.906 26980 Z= 0.325 Chirality : 0.045 0.161 3145 Planarity : 0.005 0.065 3254 Dihedral : 12.132 114.394 3214 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.77 % Allowed : 9.03 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2241 helix: 0.42 (0.18), residues: 819 sheet: -0.50 (0.24), residues: 437 loop : -0.64 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 28 TYR 0.035 0.002 TYR J 642 PHE 0.020 0.002 PHE J 664 TRP 0.045 0.002 TRP I 345 HIS 0.007 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00372 (19819) covalent geometry : angle 0.62489 (26980) hydrogen bonds : bond 0.04137 ( 863) hydrogen bonds : angle 5.20986 ( 2425) metal coordination : bond 0.00133 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7441 (mt-10) REVERT: B 2 THR cc_start: 0.8764 (t) cc_final: 0.8543 (m) REVERT: B 9 MET cc_start: 0.8088 (mmm) cc_final: 0.7882 (mmp) REVERT: F 61 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: G 20 LYS cc_start: 0.8691 (ttpt) cc_final: 0.7849 (mmmt) REVERT: G 35 ASP cc_start: 0.8148 (p0) cc_final: 0.7731 (p0) REVERT: C 7 VAL cc_start: 0.8574 (p) cc_final: 0.8182 (m) REVERT: C 47 ASP cc_start: 0.8566 (p0) cc_final: 0.8296 (p0) REVERT: D 142 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.6695 (ttt180) REVERT: H 248 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: H 295 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7256 (mmtm) REVERT: H 400 GLN cc_start: 0.7335 (mt0) cc_final: 0.6496 (tm130) REVERT: I 581 PHE cc_start: 0.8583 (t80) cc_final: 0.8358 (t80) REVERT: J 620 PHE cc_start: 0.6803 (m-10) cc_final: 0.6217 (m-10) REVERT: J 649 LEU cc_start: 0.7044 (mm) cc_final: 0.6826 (mm) REVERT: J 658 ASP cc_start: 0.5868 (p0) cc_final: 0.4918 (t0) outliers start: 36 outliers final: 19 residues processed: 297 average time/residue: 0.5524 time to fit residues: 185.8274 Evaluate side-chains 273 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 494 ILE Chi-restraints excluded: chain H residue 500 LEU Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 191 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN H 366 HIS ** H 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 GLN ** H 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 572 GLN J 81 GLN J 122 ASN J 245 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.190626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152317 restraints weight = 23236.353| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.73 r_work: 0.3580 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 19824 Z= 0.278 Angle : 0.752 19.576 26980 Z= 0.387 Chirality : 0.050 0.256 3145 Planarity : 0.006 0.073 3254 Dihedral : 12.443 127.531 3214 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.50 % Allowed : 12.17 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2241 helix: 0.37 (0.18), residues: 819 sheet: -0.55 (0.24), residues: 428 loop : -0.72 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 382 TYR 0.023 0.002 TYR H 103 PHE 0.024 0.002 PHE H 523 TRP 0.047 0.003 TRP I 345 HIS 0.011 0.002 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00672 (19819) covalent geometry : angle 0.75232 (26980) hydrogen bonds : bond 0.04794 ( 863) hydrogen bonds : angle 5.44826 ( 2425) metal coordination : bond 0.00470 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 0.770 Fit side-chains REVERT: A 12 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7369 (mt-10) REVERT: B 9 MET cc_start: 0.8209 (mmm) cc_final: 0.7943 (mmp) REVERT: F 61 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: G 20 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8024 (mptp) REVERT: H 158 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7585 (t70) REVERT: H 400 GLN cc_start: 0.7368 (mt0) cc_final: 0.6725 (tm130) REVERT: I 764 LEU cc_start: 0.7259 (mt) cc_final: 0.7054 (pp) REVERT: J 203 ILE cc_start: 0.8519 (mp) cc_final: 0.8208 (mt) REVERT: J 628 ASN cc_start: 0.7932 (t0) cc_final: 0.7143 (t0) REVERT: J 646 LEU cc_start: 0.7601 (mp) cc_final: 0.7196 (pt) outliers start: 51 outliers final: 27 residues processed: 305 average time/residue: 0.5574 time to fit residues: 192.2591 Evaluate side-chains 272 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 494 ILE Chi-restraints excluded: chain H residue 500 LEU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 207 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 366 HIS H 493 HIS H 502 ASN H 513 GLN I 312 HIS J 81 GLN J 122 ASN J 245 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.195975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157766 restraints weight = 23300.795| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.72 r_work: 0.3660 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19824 Z= 0.119 Angle : 0.590 14.013 26980 Z= 0.301 Chirality : 0.043 0.187 3145 Planarity : 0.004 0.054 3254 Dihedral : 12.062 111.407 3214 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.21 % Allowed : 14.47 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2241 helix: 0.86 (0.18), residues: 815 sheet: -0.41 (0.25), residues: 418 loop : -0.64 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 382 TYR 0.019 0.001 TYR J 642 PHE 0.042 0.002 PHE J 620 TRP 0.024 0.002 TRP I 345 HIS 0.005 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00272 (19819) covalent geometry : angle 0.58985 (26980) hydrogen bonds : bond 0.03562 ( 863) hydrogen bonds : angle 4.95784 ( 2425) metal coordination : bond 0.00071 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7215 (mt-10) REVERT: B 2 THR cc_start: 0.8828 (t) cc_final: 0.8485 (m) REVERT: B 9 MET cc_start: 0.8129 (mmm) cc_final: 0.7855 (mmp) REVERT: B 75 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7731 (mt-10) REVERT: F 42 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8148 (mtt) REVERT: G 20 LYS cc_start: 0.8714 (ttpt) cc_final: 0.7920 (mmmt) REVERT: G 35 ASP cc_start: 0.8068 (p0) cc_final: 0.7813 (p0) REVERT: D 142 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.6696 (ttt180) REVERT: H 158 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7228 (t70) REVERT: H 400 GLN cc_start: 0.7197 (mt0) cc_final: 0.6586 (tm130) REVERT: H 540 LEU cc_start: 0.7489 (pt) cc_final: 0.6917 (pp) REVERT: J 197 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6828 (ttt-90) REVERT: J 208 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6974 (mm-30) REVERT: J 628 ASN cc_start: 0.7877 (t0) cc_final: 0.7138 (t0) outliers start: 45 outliers final: 19 residues processed: 296 average time/residue: 0.5428 time to fit residues: 182.7586 Evaluate side-chains 270 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 HIS H 502 ASN ** H 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN J 81 GLN J 245 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.194262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156287 restraints weight = 23329.922| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.73 r_work: 0.3640 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19824 Z= 0.141 Angle : 0.615 16.309 26980 Z= 0.310 Chirality : 0.044 0.163 3145 Planarity : 0.004 0.056 3254 Dihedral : 11.980 116.262 3212 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.80 % Allowed : 15.21 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2241 helix: 0.97 (0.18), residues: 816 sheet: -0.47 (0.24), residues: 428 loop : -0.53 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 382 TYR 0.019 0.001 TYR H 103 PHE 0.022 0.001 PHE H 551 TRP 0.025 0.002 TRP I 345 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00332 (19819) covalent geometry : angle 0.61517 (26980) hydrogen bonds : bond 0.03621 ( 863) hydrogen bonds : angle 4.90214 ( 2425) metal coordination : bond 0.00145 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7387 (mt-10) REVERT: A 34 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: B 2 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8436 (m) REVERT: B 9 MET cc_start: 0.8131 (mmm) cc_final: 0.7859 (mmp) REVERT: B 75 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7618 (mt-10) REVERT: F 42 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8196 (mtt) REVERT: G 20 LYS cc_start: 0.8737 (ttpt) cc_final: 0.7904 (mmmt) REVERT: G 32 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7997 (mmp80) REVERT: G 35 ASP cc_start: 0.8152 (p0) cc_final: 0.7883 (p0) REVERT: H 158 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7230 (t70) REVERT: H 400 GLN cc_start: 0.7219 (mt0) cc_final: 0.6544 (tm130) REVERT: H 540 LEU cc_start: 0.7461 (pt) cc_final: 0.6900 (pp) REVERT: J 197 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6861 (ttt-90) REVERT: J 207 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: J 620 PHE cc_start: 0.7614 (m-80) cc_final: 0.6837 (m-80) REVERT: J 627 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: J 628 ASN cc_start: 0.7872 (t0) cc_final: 0.7212 (t0) outliers start: 57 outliers final: 30 residues processed: 291 average time/residue: 0.5366 time to fit residues: 177.3701 Evaluate side-chains 286 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 197 ARG Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 223 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 HIS I 344 GLN J 81 GLN J 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.195744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158435 restraints weight = 23255.114| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.64 r_work: 0.3673 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19824 Z= 0.118 Angle : 0.573 14.592 26980 Z= 0.292 Chirality : 0.043 0.155 3145 Planarity : 0.004 0.055 3254 Dihedral : 11.827 112.930 3212 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.80 % Allowed : 15.80 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2241 helix: 1.16 (0.18), residues: 817 sheet: -0.36 (0.25), residues: 409 loop : -0.49 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 382 TYR 0.017 0.001 TYR H 103 PHE 0.021 0.001 PHE H 551 TRP 0.022 0.002 TRP I 345 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00272 (19819) covalent geometry : angle 0.57344 (26980) hydrogen bonds : bond 0.03349 ( 863) hydrogen bonds : angle 4.75211 ( 2425) metal coordination : bond 0.00091 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.766 Fit side-chains REVERT: A 12 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7184 (mt-10) REVERT: A 34 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: B 2 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8413 (m) REVERT: B 9 MET cc_start: 0.8082 (mmm) cc_final: 0.7796 (mmp) REVERT: B 75 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7603 (mt-10) REVERT: F 42 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: G 20 LYS cc_start: 0.8717 (ttpt) cc_final: 0.7898 (mmmt) REVERT: G 35 ASP cc_start: 0.8101 (p0) cc_final: 0.7768 (p0) REVERT: D 142 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.6727 (ttt180) REVERT: H 158 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7153 (t70) REVERT: H 400 GLN cc_start: 0.7259 (mt0) cc_final: 0.6603 (tm130) REVERT: J 135 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: J 197 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6838 (ttt-90) REVERT: J 627 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: J 628 ASN cc_start: 0.7888 (t0) cc_final: 0.7300 (t0) outliers start: 57 outliers final: 32 residues processed: 294 average time/residue: 0.5723 time to fit residues: 190.2351 Evaluate side-chains 289 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 575 MET Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 197 ARG Chi-restraints excluded: chain J residue 627 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN D 357 HIS H 307 HIS H 366 HIS I 344 GLN J 81 GLN J 122 ASN J 628 ASN J 654 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149858 restraints weight = 23329.747| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.68 r_work: 0.3552 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 19824 Z= 0.309 Angle : 0.762 14.871 26980 Z= 0.390 Chirality : 0.051 0.274 3145 Planarity : 0.006 0.063 3254 Dihedral : 12.317 131.087 3212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.39 % Allowed : 16.54 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2241 helix: 0.66 (0.18), residues: 821 sheet: -0.41 (0.24), residues: 431 loop : -0.62 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 105 TYR 0.025 0.002 TYR H 103 PHE 0.026 0.002 PHE I 303 TRP 0.037 0.003 TRP I 345 HIS 0.009 0.002 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00746 (19819) covalent geometry : angle 0.76223 (26980) hydrogen bonds : bond 0.04571 ( 863) hydrogen bonds : angle 5.34762 ( 2425) metal coordination : bond 0.00389 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 0.785 Fit side-chains REVERT: A 12 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7378 (mt-10) REVERT: B 9 MET cc_start: 0.8239 (mmm) cc_final: 0.8000 (mmp) REVERT: F 42 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: G 20 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8008 (mptp) REVERT: G 32 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8235 (mmp80) REVERT: H 158 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7500 (t70) REVERT: H 400 GLN cc_start: 0.7360 (mt0) cc_final: 0.6520 (tm130) REVERT: H 540 LEU cc_start: 0.7690 (pt) cc_final: 0.7054 (pp) REVERT: J 135 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: J 197 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7554 (ttm-80) REVERT: J 207 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.5887 (mt0) REVERT: J 241 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7822 (ttpt) REVERT: J 627 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: J 628 ASN cc_start: 0.8061 (t160) cc_final: 0.7512 (t0) outliers start: 69 outliers final: 34 residues processed: 303 average time/residue: 0.5686 time to fit residues: 195.1607 Evaluate side-chains 292 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 494 ILE Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 564 VAL Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 197 ARG Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 627 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN C 96 GLN D 357 HIS H 366 HIS I 344 GLN J 81 GLN J 122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157360 restraints weight = 24143.734| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.71 r_work: 0.3704 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 19824 Z= 0.131 Angle : 0.619 14.901 26980 Z= 0.313 Chirality : 0.044 0.186 3145 Planarity : 0.004 0.054 3254 Dihedral : 12.001 112.687 3212 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.85 % Allowed : 17.76 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2241 helix: 1.01 (0.18), residues: 822 sheet: -0.39 (0.25), residues: 416 loop : -0.57 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 382 TYR 0.020 0.001 TYR J 642 PHE 0.020 0.002 PHE I 581 TRP 0.023 0.002 TRP I 345 HIS 0.004 0.001 HIS I 312 Details of bonding type rmsd covalent geometry : bond 0.00310 (19819) covalent geometry : angle 0.61861 (26980) hydrogen bonds : bond 0.03558 ( 863) hydrogen bonds : angle 4.96927 ( 2425) metal coordination : bond 0.00089 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 0.668 Fit side-chains REVERT: B 2 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8404 (m) REVERT: B 9 MET cc_start: 0.8276 (mmm) cc_final: 0.8022 (mmp) REVERT: B 75 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7618 (mt-10) REVERT: F 42 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: G 20 LYS cc_start: 0.8765 (ttpt) cc_final: 0.7839 (mmmt) REVERT: G 35 ASP cc_start: 0.8294 (p0) cc_final: 0.8054 (p0) REVERT: H 10 ASP cc_start: 0.6913 (t70) cc_final: 0.6686 (OUTLIER) REVERT: H 158 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7217 (t70) REVERT: H 400 GLN cc_start: 0.7286 (mt0) cc_final: 0.6498 (tm130) REVERT: H 540 LEU cc_start: 0.7556 (pt) cc_final: 0.6823 (pp) REVERT: J 135 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: J 203 ILE cc_start: 0.8530 (mp) cc_final: 0.8274 (mt) REVERT: J 207 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5826 (mt0) REVERT: J 241 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7616 (ttpt) REVERT: J 598 SER cc_start: 0.6777 (t) cc_final: 0.6433 (m) REVERT: J 616 LEU cc_start: 0.7787 (pt) cc_final: 0.7391 (pp) REVERT: J 627 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7207 (m-80) outliers start: 58 outliers final: 32 residues processed: 306 average time/residue: 0.5566 time to fit residues: 193.2810 Evaluate side-chains 293 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 676 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 627 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 57 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN C 96 GLN H 366 HIS ** H 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 276 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.194536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157407 restraints weight = 24015.098| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.72 r_work: 0.3701 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19824 Z= 0.134 Angle : 0.622 13.473 26980 Z= 0.314 Chirality : 0.044 0.187 3145 Planarity : 0.004 0.056 3254 Dihedral : 11.900 115.955 3212 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.60 % Allowed : 18.79 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2241 helix: 1.10 (0.18), residues: 829 sheet: -0.39 (0.25), residues: 412 loop : -0.50 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 382 TYR 0.019 0.001 TYR J 642 PHE 0.028 0.002 PHE J 664 TRP 0.022 0.002 TRP I 345 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00318 (19819) covalent geometry : angle 0.62151 (26980) hydrogen bonds : bond 0.03510 ( 863) hydrogen bonds : angle 4.86167 ( 2425) metal coordination : bond 0.00111 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 0.592 Fit side-chains REVERT: A 34 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 2 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8384 (m) REVERT: B 9 MET cc_start: 0.8257 (mmm) cc_final: 0.8006 (mmp) REVERT: B 75 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7613 (mt-10) REVERT: F 42 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8323 (mtt) REVERT: G 20 LYS cc_start: 0.8780 (ttpt) cc_final: 0.7833 (mmmt) REVERT: G 35 ASP cc_start: 0.8259 (p0) cc_final: 0.8026 (p0) REVERT: H 10 ASP cc_start: 0.6930 (t70) cc_final: 0.6705 (OUTLIER) REVERT: H 158 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7189 (t70) REVERT: H 400 GLN cc_start: 0.7155 (mt0) cc_final: 0.6404 (tm130) REVERT: J 135 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: J 207 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.5773 (mt0) REVERT: J 241 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7552 (ttpt) REVERT: J 598 SER cc_start: 0.6729 (t) cc_final: 0.6433 (m) REVERT: J 616 LEU cc_start: 0.7787 (pt) cc_final: 0.7469 (pp) REVERT: J 627 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7228 (m-80) outliers start: 53 outliers final: 33 residues processed: 296 average time/residue: 0.4887 time to fit residues: 165.0180 Evaluate side-chains 292 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 627 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 48 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN D 143 ASN H 366 HIS ** H 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.192981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155741 restraints weight = 24163.892| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.78 r_work: 0.3674 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19824 Z= 0.175 Angle : 0.662 13.392 26980 Z= 0.334 Chirality : 0.045 0.199 3145 Planarity : 0.004 0.057 3254 Dihedral : 11.951 117.720 3212 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.36 % Allowed : 19.53 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2241 helix: 1.08 (0.18), residues: 826 sheet: -0.29 (0.25), residues: 403 loop : -0.53 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 382 TYR 0.021 0.002 TYR H 103 PHE 0.025 0.002 PHE I 581 TRP 0.026 0.002 TRP I 345 HIS 0.006 0.001 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00424 (19819) covalent geometry : angle 0.66156 (26980) hydrogen bonds : bond 0.03769 ( 863) hydrogen bonds : angle 4.97920 ( 2425) metal coordination : bond 0.00159 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4482 Ramachandran restraints generated. 2241 Oldfield, 0 Emsley, 2241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.739 Fit side-chains REVERT: A 34 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: B 2 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8387 (m) REVERT: B 9 MET cc_start: 0.8311 (mmm) cc_final: 0.8064 (mmp) REVERT: B 75 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7588 (mt-10) REVERT: F 42 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8383 (mtt) REVERT: F 61 GLU cc_start: 0.8358 (tt0) cc_final: 0.8027 (tp30) REVERT: G 20 LYS cc_start: 0.8805 (ttpt) cc_final: 0.7849 (mmmt) REVERT: G 35 ASP cc_start: 0.8380 (p0) cc_final: 0.8151 (p0) REVERT: H 158 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7315 (t70) REVERT: H 400 GLN cc_start: 0.7325 (mt0) cc_final: 0.6577 (tm130) REVERT: J 83 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7896 (t70) REVERT: J 135 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: J 207 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.5832 (mt0) REVERT: J 241 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7593 (ttpt) REVERT: J 598 SER cc_start: 0.6972 (t) cc_final: 0.6632 (m) REVERT: J 616 LEU cc_start: 0.7833 (pt) cc_final: 0.7524 (pp) REVERT: J 627 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: J 639 LEU cc_start: 0.7557 (mt) cc_final: 0.7104 (tp) REVERT: J 675 THR cc_start: 0.6889 (p) cc_final: 0.6365 (p) outliers start: 48 outliers final: 33 residues processed: 293 average time/residue: 0.5352 time to fit residues: 178.5134 Evaluate side-chains 295 residues out of total 2038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 352 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 158 HIS Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 382 LEU Chi-restraints excluded: chain H residue 466 VAL Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 628 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 627 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 126 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 205 optimal weight: 0.0770 chunk 78 optimal weight: 0.5980 chunk 138 optimal weight: 0.0010 chunk 94 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN C 96 GLN D 160 HIS H 366 HIS J 81 GLN J 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.196789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160093 restraints weight = 24306.860| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.71 r_work: 0.3747 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19824 Z= 0.112 Angle : 0.605 13.614 26980 Z= 0.305 Chirality : 0.043 0.219 3145 Planarity : 0.004 0.055 3254 Dihedral : 11.759 111.081 3212 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.01 % Allowed : 19.87 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2241 helix: 1.25 (0.18), residues: 821 sheet: -0.18 (0.26), residues: 387 loop : -0.50 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 382 TYR 0.021 0.001 TYR J 642 PHE 0.025 0.001 PHE I 581 TRP 0.020 0.002 TRP J 229 HIS 0.004 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00259 (19819) covalent geometry : angle 0.60500 (26980) hydrogen bonds : bond 0.03312 ( 863) hydrogen bonds : angle 4.77706 ( 2425) metal coordination : bond 0.00054 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7131.01 seconds wall clock time: 122 minutes 4.99 seconds (7324.99 seconds total)