Starting phenix.real_space_refine on Sat Aug 8 13:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.cif Found real_map, /net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28op_56683/08_2026/28op_56683.map" } resolution = 2.7 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= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 120 5.49 5 S 136 5.16 5 C 17502 2.51 5 N 4794 2.21 5 O 5421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27973 Number of models: 1 Model: "" Number of chains: 18 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "U" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1369 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1220 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "W" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "Y" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1239 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5096 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 607} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1926 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2509 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2629 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 25} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.56, per 1000 atoms: 0.20 Number of scatterers: 27973 At special positions: 0 Unit cell: (116.848, 202.608, 205.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 120 15.00 O 5421 8.00 N 4794 7.00 C 17502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 202 " distance=2.05 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6140 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 15 sheets defined 66.4% alpha, 9.8% beta 54 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'M' and resid 24 through 38 removed outlier: 4.560A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.623A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.827A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 155 Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.632A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 39 removed outlier: 4.466A pdb=" N ASP S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 72 removed outlier: 4.109A pdb=" N GLU S 59 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN S 60 " --> pdb=" O ARG S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.503A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'T' and resid 454 through 472 removed outlier: 3.599A pdb=" N ALA T 458 " --> pdb=" O ASP T 454 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 477 through 506 Processing helix chain 'T' and resid 511 through 523 Processing helix chain 'T' and resid 530 through 539 Processing helix chain 'T' and resid 540 through 545 Processing helix chain 'U' and resid 254 through 269 removed outlier: 3.777A pdb=" N PHE U 258 " --> pdb=" O VAL U 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 375 Proline residue: U 332 - end of helix removed outlier: 4.346A pdb=" N ASP U 370 " --> pdb=" O GLN U 366 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL U 371 " --> pdb=" O ASP U 367 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN U 372 " --> pdb=" O TYR U 368 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA U 373 " --> pdb=" O SER U 369 " (cutoff:3.500A) Processing helix chain 'U' and resid 386 through 399 removed outlier: 4.134A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 417 removed outlier: 3.529A pdb=" N LYS U 413 " --> pdb=" O HIS U 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.643A pdb=" N LEU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 86 removed outlier: 3.673A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 15 Processing helix chain 'X' and resid 24 through 54 Processing helix chain 'X' and resid 59 through 74 removed outlier: 3.577A pdb=" N LEU X 63 " --> pdb=" O ASP X 59 " (cutoff:3.500A) Proline residue: X 68 - end of helix Processing helix chain 'H' and resid 37 through 66 removed outlier: 4.097A pdb=" N THR H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 119 removed outlier: 3.629A pdb=" N LYS H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 189 removed outlier: 4.512A pdb=" N MET H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 223 Processing helix chain 'H' and resid 226 through 229 Processing helix chain 'H' and resid 230 through 238 Processing helix chain 'I' and resid 62 through 76 removed outlier: 3.666A pdb=" N GLY I 76 " --> pdb=" O TYR I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.523A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 119 removed outlier: 3.603A pdb=" N ILE I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY I 119 " --> pdb=" O ILE I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 140 through 154 removed outlier: 3.896A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 178 through 184 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 197 through 209 Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 Processing helix chain 'I' and resid 269 through 282 Processing helix chain 'I' and resid 340 through 344 removed outlier: 3.637A pdb=" N GLN I 343 " --> pdb=" O PRO I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.526A pdb=" N SER I 365 " --> pdb=" O GLN I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 378 removed outlier: 4.007A pdb=" N CYS I 378 " --> pdb=" O HIS I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 400 removed outlier: 3.598A pdb=" N CYS I 400 " --> pdb=" O LEU I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 410 removed outlier: 3.948A pdb=" N HIS I 410 " --> pdb=" O ASN I 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 407 through 410' Processing helix chain 'I' and resid 411 through 427 removed outlier: 4.103A pdb=" N THR I 415 " --> pdb=" O GLY I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 443 Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.740A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 474 Proline residue: I 472 - end of helix Processing helix chain 'I' and resid 474 through 483 Processing helix chain 'I' and resid 486 through 513 removed outlier: 3.726A pdb=" N HIS I 513 " --> pdb=" O SER I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 551 Processing helix chain 'I' and resid 554 through 570 removed outlier: 3.553A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 568 " --> pdb=" O PHE I 564 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP I 570 " --> pdb=" O GLU I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 584 through 593 Processing helix chain 'I' and resid 596 through 625 removed outlier: 4.231A pdb=" N LEU I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 653 removed outlier: 3.848A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 removed outlier: 3.516A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 700 Processing helix chain 'I' and resid 707 through 712 removed outlier: 4.555A pdb=" N ARG I 712 " --> pdb=" O SER I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 713 through 726 removed outlier: 3.671A pdb=" N SER I 717 " --> pdb=" O GLY I 713 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 739 Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 54 through 76 Processing helix chain 'K' and resid 85 through 149 removed outlier: 3.841A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 188 Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.543A pdb=" N VAL K 226 " --> pdb=" O ARG K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 Processing helix chain 'L' and resid 26 through 38 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 87 through 105 Processing helix chain 'L' and resid 167 through 172 Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.670A pdb=" N ASP L 205 " --> pdb=" O GLN L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 269 Processing helix chain 'L' and resid 276 through 296 Processing helix chain 'L' and resid 324 through 326 No H-bonds generated for 'chain 'L' and resid 324 through 326' Processing helix chain 'L' and resid 327 through 344 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 17 through 29 removed outlier: 4.689A pdb=" N THR N 22 " --> pdb=" O MET N 18 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.566A pdb=" N LYS N 59 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 Processing helix chain 'N' and resid 77 through 81 removed outlier: 3.807A pdb=" N LYS N 81 " --> pdb=" O GLN N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 114 Processing helix chain 'N' and resid 166 through 170 removed outlier: 4.045A pdb=" N ARG N 169 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 184 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 removed outlier: 3.767A pdb=" N GLN N 253 " --> pdb=" O GLN N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 309 Processing helix chain 'N' and resid 320 through 325 removed outlier: 3.536A pdb=" N THR N 324 " --> pdb=" O SER N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 110 through 112 No H-bonds generated for 'chain 'O' and resid 110 through 112' Processing helix chain 'O' and resid 160 through 169 removed outlier: 3.703A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 201 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.711A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 287 Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 160 removed outlier: 3.526A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 removed outlier: 3.539A pdb=" N TYR P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.788A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP P 250 " --> pdb=" O ALA P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 256 No H-bonds generated for 'chain 'P' and resid 254 through 256' Processing helix chain 'P' and resid 257 through 270 removed outlier: 3.650A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 4.033A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 124 Processing helix chain 'Q' and resid 136 through 201 removed outlier: 3.624A pdb=" N SER Q 188 " --> pdb=" O GLN Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 221 removed outlier: 4.164A pdb=" N LEU Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 229 Processing helix chain 'Q' and resid 234 through 248 removed outlier: 4.482A pdb=" N LEU Q 238 " --> pdb=" O ASN Q 234 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Q 242 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 267 removed outlier: 4.024A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 107 removed outlier: 4.673A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 114 removed outlier: 4.235A pdb=" N GLN R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 4.209A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 4.097A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 removed outlier: 3.650A pdb=" N ILE R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 Processing sheet with id=AA1, first strand: chain 'M' and resid 128 through 130 removed outlier: 8.697A pdb=" N LEU M 129 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE M 99 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 76 through 77 Processing sheet with id=AA3, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AA4, first strand: chain 'T' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA7, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.846A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.846A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU L 240 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL L 307 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU L 238 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU L 250 " --> pdb=" O VAL L 243 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS L 245 " --> pdb=" O GLN L 248 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER L 249 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR N 273 " --> pdb=" O LEU N 291 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU N 265 " --> pdb=" O SER N 299 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASP N 338 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLU N 272 " --> pdb=" O ASP N 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AB2, first strand: chain 'N' and resid 119 through 125 removed outlier: 4.970A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 121 through 130 removed outlier: 3.826A pdb=" N THR O 128 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL O 143 " --> pdb=" O ILE O 150 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE O 150 " --> pdb=" O VAL O 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 210 through 211 removed outlier: 3.553A pdb=" N SER O 219 " --> pdb=" O GLN O 210 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 76 through 87 removed outlier: 5.009A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU P 123 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL P 135 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE P 125 " --> pdb=" O SER P 133 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER P 133 " --> pdb=" O ILE P 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 205 through 209 1691 hydrogen bonds defined for protein. 4956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8703 1.34 - 1.48: 7185 1.48 - 1.61: 12551 1.61 - 1.74: 79 1.74 - 1.87: 211 Bond restraints: 28729 Sorted by residual: bond pdb=" C3' DT Y-134 " pdb=" C2' DT Y-134 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.52e+01 bond pdb=" C3' DC Y-135 " pdb=" C2' DC Y-135 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DG Y-144 " pdb=" C2' DG Y-144 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG Y-163 " pdb=" C2' DG Y-163 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT Y-133 " pdb=" C2' DT Y-133 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 28724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 38668 3.04 - 6.08: 498 6.08 - 9.13: 64 9.13 - 12.17: 15 12.17 - 15.21: 8 Bond angle restraints: 39253 Sorted by residual: angle pdb=" N MET Q 254 " pdb=" CA MET Q 254 " pdb=" CB MET Q 254 " ideal model delta sigma weight residual 110.28 120.53 -10.25 1.55e+00 4.16e-01 4.38e+01 angle pdb=" CA MET Q 254 " pdb=" CB MET Q 254 " pdb=" CG MET Q 254 " ideal model delta sigma weight residual 114.10 126.69 -12.59 2.00e+00 2.50e-01 3.96e+01 angle pdb=" CA LYS L 229 " pdb=" CB LYS L 229 " pdb=" CG LYS L 229 " ideal model delta sigma weight residual 114.10 126.50 -12.40 2.00e+00 2.50e-01 3.84e+01 angle pdb=" CA MET R 136 " pdb=" CB MET R 136 " pdb=" CG MET R 136 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.48e+01 angle pdb=" N MET R 136 " pdb=" CA MET R 136 " pdb=" CB MET R 136 " ideal model delta sigma weight residual 110.28 119.31 -9.03 1.55e+00 4.16e-01 3.39e+01 ... (remaining 39248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 16271 35.33 - 70.67: 994 70.67 - 106.00: 26 106.00 - 141.34: 1 141.34 - 176.67: 1 Dihedral angle restraints: 17293 sinusoidal: 7940 harmonic: 9353 Sorted by residual: dihedral pdb=" CA LYS O 146 " pdb=" C LYS O 146 " pdb=" N PRO O 147 " pdb=" CA PRO O 147 " ideal model delta harmonic sigma weight residual 0.00 -31.56 31.56 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CD ARG N 44 " pdb=" NE ARG N 44 " pdb=" CZ ARG N 44 " pdb=" NH1 ARG N 44 " ideal model delta sinusoidal sigma weight residual 0.00 -44.30 44.30 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CA LEU M 52 " pdb=" C LEU M 52 " pdb=" N PRO M 53 " pdb=" CA PRO M 53 " ideal model delta harmonic sigma weight residual 0.00 25.71 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 17290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3374 0.054 - 0.108: 914 0.108 - 0.162: 168 0.162 - 0.216: 30 0.216 - 0.269: 9 Chirality restraints: 4495 Sorted by residual: chirality pdb=" CA MET R 136 " pdb=" N MET R 136 " pdb=" C MET R 136 " pdb=" CB MET R 136 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA MET Q 88 " pdb=" N MET Q 88 " pdb=" C MET Q 88 " pdb=" CB MET Q 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB THR L 316 " pdb=" CA THR L 316 " pdb=" OG1 THR L 316 " pdb=" CG2 THR L 316 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4492 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 44 " 0.604 9.50e-02 1.11e+02 2.72e-01 5.45e+01 pdb=" NE ARG N 44 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG N 44 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG N 44 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG N 44 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 544 " -0.574 9.50e-02 1.11e+02 2.59e-01 4.91e+01 pdb=" NE ARG T 544 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG T 544 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG T 544 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG T 544 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 220 " -0.564 9.50e-02 1.11e+02 2.54e-01 4.85e+01 pdb=" NE ARG I 220 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG I 220 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG I 220 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG I 220 " -0.001 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6732 2.80 - 3.33: 27623 3.33 - 3.85: 48925 3.85 - 4.38: 56983 4.38 - 4.90: 91970 Nonbonded interactions: 232233 Sorted by model distance: nonbonded pdb=" O ASP N 29 " pdb=" OD1 ASP N 29 " model vdw 2.279 3.040 nonbonded pdb=" O THR K 164 " pdb=" OD1 ASN K 168 " model vdw 2.417 3.040 nonbonded pdb=" O GLU O 131 " pdb=" OE1 GLU O 131 " model vdw 2.433 3.040 nonbonded pdb=" O ASP C 306 " pdb=" OD1 ASP C 306 " model vdw 2.441 3.040 nonbonded pdb=" O THR I 653 " pdb=" OG SER I 654 " model vdw 2.453 3.040 ... (remaining 232228 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 28.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.006 0.081 28730 Z= 0.333 Angle : 0.940 15.211 39255 Z= 0.553 Chirality : 0.052 0.269 4495 Planarity : 0.016 0.272 4524 Dihedral : 18.555 176.671 11150 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.33 % Favored : 96.38 % Rotamer: Outliers : 2.17 % Allowed : 15.21 % Favored : 82.62 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -0.32 (0.14), residues: 3096 helix: 0.59 (0.11), residues: 1951 sheet: -0.62 (0.28), residues: 280 loop : -1.80 (0.18), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.007 ARG H 107 TYR 0.033 0.003 TYR S 15 PHE 0.042 0.003 PHE O 287 TRP 0.020 0.003 TRP N 132 HIS 0.014 0.002 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.33 (28729) covalent geometry : angle 0.93935 / 0.55 (39253) SS BOND : bond 0.01634 / 0.86 ( 1) SS BOND : angle 6.23105 / 3.45 ( 2) hydrogen bonds : bond 0.11314 / 7.89 ( 1806) hydrogen bonds : angle 5.50975 / 4.00 ( 5226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 92 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8138 (t80) REVERT: S 87 ARG cc_start: 0.7361 (mmm-85) cc_final: 0.7072 (mtp85) REVERT: I 168 LEU cc_start: 0.8433 (tt) cc_final: 0.8040 (tp) REVERT: I 443 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8352 (mp) REVERT: K 222 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6715 (tmt170) REVERT: L 177 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7818 (p0) REVERT: L 190 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7423 (tp30) REVERT: L 238 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: N 82 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8620 (t) REVERT: N 128 GLU cc_start: 0.7291 (pt0) cc_final: 0.7037 (pt0) REVERT: N 157 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: N 337 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6996 (mtp180) outliers start: 62 outliers final: 39 residues processed: 326 average time/residue: 0.7767 time to fit residues: 291.7164 Evaluate side-chains 310 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 109 HIS Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain T residue 461 SER Chi-restraints excluded: chain U residue 296 SER Chi-restraints excluded: chain U residue 361 LEU Chi-restraints excluded: chain U residue 402 SER Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 156 CYS Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain L residue 26 PRO Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 171 ASN Chi-restraints excluded: chain N residue 337 ARG Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain Q residue 163 ASP Chi-restraints excluded: chain C residue 303 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 453 GLN T 492 GLN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 368 ASN I 638 GLN N 129 ASN ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.249439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.214371 restraints weight = 31822.563| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.79 r_work: 0.4113 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28730 Z= 0.158 Angle : 0.666 10.566 39255 Z= 0.352 Chirality : 0.041 0.235 4495 Planarity : 0.004 0.050 4524 Dihedral : 18.844 172.443 4764 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.71 % Rotamer: Outliers : 2.98 % Allowed : 13.70 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.26 (0.15), residues: 3096 helix: 1.83 (0.11), residues: 1988 sheet: -0.32 (0.28), residues: 279 loop : -1.22 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 220 TYR 0.026 0.002 TYR L 207 PHE 0.028 0.002 PHE O 287 TRP 0.017 0.002 TRP I 652 HIS 0.008 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (28729) covalent geometry : angle 0.66538 / 0.35 (39253) SS BOND : bond 0.01833 / 0.96 ( 1) SS BOND : angle 4.86269 / 2.75 ( 2) hydrogen bonds : bond 0.05944 / 3.97 ( 1806) hydrogen bonds : angle 4.32784 / 3.17 ( 5226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 286 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 38 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: M 136 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: H 189 MET cc_start: 0.6235 (tmm) cc_final: 0.5992 (ttt) REVERT: I 168 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8103 (tp) REVERT: I 394 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: L 177 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7734 (p0) REVERT: L 238 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: N 2 ASP cc_start: 0.6649 (t0) cc_final: 0.6429 (t0) REVERT: N 82 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8705 (t) REVERT: N 97 ASP cc_start: 0.7047 (t0) cc_final: 0.6649 (t0) REVERT: N 128 GLU cc_start: 0.7225 (pt0) cc_final: 0.6960 (pt0) REVERT: N 157 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7511 (mt0) outliers start: 85 outliers final: 30 residues processed: 353 average time/residue: 0.7702 time to fit residues: 313.2867 Evaluate side-chains 291 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 136 GLU Chi-restraints excluded: chain T residue 488 ASP Chi-restraints excluded: chain T residue 514 ASP Chi-restraints excluded: chain U residue 361 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 736 ARG Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 112 optimal weight: 2.9990 chunk 268 optimal weight: 0.0270 chunk 311 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 205 optimal weight: 0.5980 chunk 293 optimal weight: 9.9990 chunk 270 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 620 ASN I 638 GLN N 268 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.248759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.214901 restraints weight = 31769.479| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.62 r_work: 0.4122 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4083 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28730 Z= 0.165 Angle : 0.643 11.364 39255 Z= 0.338 Chirality : 0.040 0.223 4495 Planarity : 0.004 0.070 4524 Dihedral : 18.692 177.658 4722 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 15.14 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.54 (0.15), residues: 3096 helix: 2.07 (0.11), residues: 1988 sheet: -0.33 (0.29), residues: 269 loop : -1.11 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 101 TYR 0.027 0.002 TYR L 207 PHE 0.024 0.002 PHE O 287 TRP 0.017 0.002 TRP I 652 HIS 0.007 0.001 HIS N 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (28729) covalent geometry : angle 0.64165 / 0.34 (39253) SS BOND : bond 0.01780 / 0.94 ( 1) SS BOND : angle 5.06634 / 2.88 ( 2) hydrogen bonds : bond 0.05685 / 3.79 ( 1806) hydrogen bonds : angle 4.14175 / 3.04 ( 5226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 272 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 38 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: I 168 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8145 (tp) REVERT: I 394 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: L 177 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7807 (p0) REVERT: L 238 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: N 82 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (t) REVERT: N 157 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7635 (mt0) outliers start: 82 outliers final: 40 residues processed: 337 average time/residue: 0.7755 time to fit residues: 300.8610 Evaluate side-chains 309 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain T residue 514 ASP Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 275 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN H 176 GLN H 239 GLN I 638 GLN K 269 GLN N 34 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.247956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.212716 restraints weight = 31478.392| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.72 r_work: 0.4105 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28730 Z= 0.199 Angle : 0.659 11.482 39255 Z= 0.346 Chirality : 0.042 0.229 4495 Planarity : 0.005 0.068 4524 Dihedral : 18.715 177.853 4716 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 3.50 % Allowed : 15.14 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.52 (0.15), residues: 3096 helix: 2.03 (0.11), residues: 1987 sheet: -0.22 (0.28), residues: 279 loop : -1.09 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 423 TYR 0.035 0.002 TYR L 207 PHE 0.022 0.002 PHE O 287 TRP 0.018 0.002 TRP L 265 HIS 0.008 0.001 HIS N 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (28729) covalent geometry : angle 0.65795 / 0.35 (39253) SS BOND : bond 0.01947 / 1.02 ( 1) SS BOND : angle 5.81441 / 3.30 ( 2) hydrogen bonds : bond 0.05785 / 3.86 ( 1806) hydrogen bonds : angle 4.08599 / 3.01 ( 5226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 271 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 38 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: W 83 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8242 (mp) REVERT: I 168 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8176 (tp) REVERT: I 394 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: K 257 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: L 107 LEU cc_start: 0.8298 (mt) cc_final: 0.7940 (mt) REVERT: L 177 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (p0) REVERT: L 238 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: N 82 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8585 (t) REVERT: N 157 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7988 (mt0) outliers start: 100 outliers final: 48 residues processed: 353 average time/residue: 0.7611 time to fit residues: 310.3168 Evaluate side-chains 305 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain T residue 514 ASP Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 233 LYS Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 242 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 293 optimal weight: 50.0000 chunk 229 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 17 GLN ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 362 GLN I 638 GLN L 232 HIS ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.248027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.212441 restraints weight = 31475.226| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.79 r_work: 0.4088 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28730 Z= 0.182 Angle : 0.653 12.740 39255 Z= 0.339 Chirality : 0.041 0.231 4495 Planarity : 0.005 0.075 4524 Dihedral : 18.681 178.517 4713 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 3.15 % Allowed : 16.15 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.62 (0.15), residues: 3096 helix: 2.09 (0.11), residues: 1989 sheet: -0.21 (0.29), residues: 279 loop : -1.00 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 30 TYR 0.033 0.002 TYR L 207 PHE 0.021 0.002 PHE O 287 TRP 0.017 0.002 TRP L 265 HIS 0.008 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (28729) covalent geometry : angle 0.65163 / 0.34 (39253) SS BOND : bond 0.01944 / 1.02 ( 1) SS BOND : angle 5.49085 / 3.12 ( 2) hydrogen bonds : bond 0.05559 / 3.70 ( 1806) hydrogen bonds : angle 4.00771 / 2.95 ( 5226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 271 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 38 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: W 83 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8273 (mp) REVERT: I 168 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8325 (tt) REVERT: I 394 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: K 257 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: L 107 LEU cc_start: 0.8262 (mt) cc_final: 0.7891 (mt) REVERT: L 177 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7807 (p0) REVERT: L 238 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: N 82 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8607 (t) REVERT: N 114 ARG cc_start: 0.7831 (tmm160) cc_final: 0.7496 (tmm160) REVERT: N 157 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8100 (mt0) outliers start: 90 outliers final: 50 residues processed: 340 average time/residue: 0.7507 time to fit residues: 294.6136 Evaluate side-chains 322 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 514 ASP Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 496 SER Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 650 CYS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 233 LYS Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 267 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 58 optimal weight: 50.0000 chunk 152 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 492 GLN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 638 GLN K 102 GLN L 277 GLN N 50 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.248064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.213672 restraints weight = 31507.239| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.65 r_work: 0.4103 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28730 Z= 0.181 Angle : 0.646 12.339 39255 Z= 0.337 Chirality : 0.041 0.232 4495 Planarity : 0.004 0.068 4524 Dihedral : 18.674 178.698 4712 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 3.29 % Allowed : 16.78 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.68 (0.15), residues: 3096 helix: 2.15 (0.11), residues: 1982 sheet: -0.21 (0.29), residues: 279 loop : -0.97 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 70 TYR 0.034 0.002 TYR L 207 PHE 0.021 0.002 PHE O 287 TRP 0.017 0.002 TRP L 265 HIS 0.008 0.001 HIS N 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (28729) covalent geometry : angle 0.64446 / 0.34 (39253) SS BOND : bond 0.01961 / 1.03 ( 1) SS BOND : angle 5.48226 / 3.11 ( 2) hydrogen bonds : bond 0.05473 / 3.65 ( 1806) hydrogen bonds : angle 3.97848 / 2.93 ( 5226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 272 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 74 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7232 (mtm-85) REVERT: W 83 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8259 (mp) REVERT: I 168 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8290 (tt) REVERT: I 394 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6802 (mp10) REVERT: K 257 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6620 (mm-30) REVERT: L 177 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7790 (p0) REVERT: L 238 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: N 82 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8595 (t) REVERT: N 97 ASP cc_start: 0.7174 (t0) cc_final: 0.6897 (t0) REVERT: N 114 ARG cc_start: 0.7821 (tmm160) cc_final: 0.7453 (tmm160) REVERT: N 157 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8159 (mt0) outliers start: 94 outliers final: 54 residues processed: 345 average time/residue: 0.7289 time to fit residues: 289.4770 Evaluate side-chains 325 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 487 ILE Chi-restraints excluded: chain I residue 496 SER Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 650 CYS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 88 MET Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 214 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 204 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 638 GLN K 102 GLN K 269 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.248052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.212723 restraints weight = 31358.226| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 2.73 r_work: 0.4091 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28730 Z= 0.183 Angle : 0.652 12.680 39255 Z= 0.339 Chirality : 0.041 0.233 4495 Planarity : 0.004 0.067 4524 Dihedral : 18.670 178.856 4710 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 3.26 % Allowed : 17.03 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.68 (0.15), residues: 3096 helix: 2.13 (0.11), residues: 1989 sheet: -0.18 (0.29), residues: 279 loop : -0.95 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 70 TYR 0.035 0.002 TYR L 207 PHE 0.021 0.002 PHE O 287 TRP 0.016 0.002 TRP L 265 HIS 0.009 0.001 HIS N 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (28729) covalent geometry : angle 0.65130 / 0.34 (39253) SS BOND : bond 0.01964 / 1.03 ( 1) SS BOND : angle 5.49884 / 3.12 ( 2) hydrogen bonds : bond 0.05447 / 3.63 ( 1806) hydrogen bonds : angle 3.97397 / 2.93 ( 5226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 271 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 92 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.7937 (OUTLIER) REVERT: S 74 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7261 (mtm-85) REVERT: U 329 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6889 (mmp-170) REVERT: W 83 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (mp) REVERT: I 168 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8296 (tt) REVERT: I 394 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6777 (mp10) REVERT: K 257 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: L 107 LEU cc_start: 0.8239 (mt) cc_final: 0.7923 (mt) REVERT: L 177 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7837 (p0) REVERT: L 238 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: N 82 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8595 (t) REVERT: N 157 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8203 (mt0) outliers start: 93 outliers final: 54 residues processed: 340 average time/residue: 0.7536 time to fit residues: 295.8715 Evaluate side-chains 327 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 487 ILE Chi-restraints excluded: chain I residue 496 SER Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 650 CYS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 106 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 270 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 492 GLN ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN H 201 ASN I 638 GLN K 102 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.246785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.211441 restraints weight = 31604.853| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.71 r_work: 0.4076 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28730 Z= 0.251 Angle : 0.727 13.203 39255 Z= 0.375 Chirality : 0.044 0.298 4495 Planarity : 0.005 0.071 4524 Dihedral : 18.729 179.081 4710 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 3.36 % Allowed : 17.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.43 (0.15), residues: 3096 helix: 1.93 (0.11), residues: 1985 sheet: -0.21 (0.29), residues: 280 loop : -1.06 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 101 TYR 0.040 0.003 TYR L 207 PHE 0.020 0.002 PHE O 287 TRP 0.018 0.002 TRP L 265 HIS 0.010 0.002 HIS N 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (28729) covalent geometry : angle 0.72542 / 0.37 (39253) SS BOND : bond 0.02130 / 1.12 ( 1) SS BOND : angle 6.53083 / 3.70 ( 2) hydrogen bonds : bond 0.05937 / 3.96 ( 1806) hydrogen bonds : angle 4.09610 / 3.01 ( 5226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 263 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 92 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7880 (OUTLIER) REVERT: M 132 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: S 74 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7302 (mtm-85) REVERT: U 329 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6849 (mmp-170) REVERT: W 83 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8334 (mp) REVERT: I 168 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8310 (tt) REVERT: I 394 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: K 257 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: L 107 LEU cc_start: 0.8257 (mt) cc_final: 0.8001 (mt) REVERT: L 177 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7854 (p0) REVERT: L 238 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: N 82 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8528 (t) REVERT: N 97 ASP cc_start: 0.7163 (t0) cc_final: 0.6959 (t0) REVERT: N 114 ARG cc_start: 0.7864 (tmm160) cc_final: 0.7454 (tmm160) REVERT: N 157 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8312 (mt0) outliers start: 96 outliers final: 60 residues processed: 338 average time/residue: 0.7741 time to fit residues: 300.7739 Evaluate side-chains 318 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 514 ASP Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 496 SER Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 650 CYS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 157 GLN Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain C residue 304 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 294 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 290 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 47 HIS ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 269 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.248264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215352 restraints weight = 31720.149| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.47 r_work: 0.4140 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28730 Z= 0.159 Angle : 0.665 13.253 39255 Z= 0.344 Chirality : 0.040 0.293 4495 Planarity : 0.005 0.071 4524 Dihedral : 18.661 179.326 4710 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 17.90 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.72 (0.15), residues: 3096 helix: 2.15 (0.11), residues: 1984 sheet: -0.13 (0.29), residues: 279 loop : -0.92 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 70 TYR 0.030 0.002 TYR L 207 PHE 0.021 0.001 PHE O 287 TRP 0.014 0.001 TRP L 265 HIS 0.013 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (28729) covalent geometry : angle 0.66385 / 0.34 (39253) SS BOND : bond 0.01962 / 1.03 ( 1) SS BOND : angle 5.06304 / 2.88 ( 2) hydrogen bonds : bond 0.05230 / 3.49 ( 1806) hydrogen bonds : angle 3.95725 / 2.91 ( 5226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 132 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: S 74 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: U 329 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6785 (mmp-170) REVERT: K 257 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: L 107 LEU cc_start: 0.8206 (mt) cc_final: 0.7983 (mt) REVERT: L 177 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7764 (p0) REVERT: L 238 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: N 82 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8576 (t) REVERT: N 114 ARG cc_start: 0.7814 (tmm160) cc_final: 0.7423 (tmm160) outliers start: 82 outliers final: 48 residues processed: 330 average time/residue: 0.7666 time to fit residues: 291.3470 Evaluate side-chains 311 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 553 SER Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 496 SER Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 637 TYR Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 141 ASP Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain P residue 248 GLU Chi-restraints excluded: chain Q residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 31 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN I 495 GLN K 102 GLN L 325 HIS ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.245257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.206323 restraints weight = 31290.903| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.11 r_work: 0.4002 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 28730 Z= 0.410 Angle : 0.876 13.710 39255 Z= 0.450 Chirality : 0.054 0.348 4495 Planarity : 0.006 0.080 4524 Dihedral : 18.806 179.396 4707 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 2.35 % Allowed : 18.92 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.93 (0.15), residues: 3096 helix: 1.52 (0.11), residues: 1986 sheet: -0.20 (0.29), residues: 280 loop : -1.25 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 306 TYR 0.059 0.004 TYR L 207 PHE 0.031 0.004 PHE L 162 TRP 0.025 0.004 TRP L 265 HIS 0.015 0.002 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00994 / 0.41 (28729) covalent geometry : angle 0.87370 / 0.45 (39253) SS BOND : bond 0.02445 / 1.29 ( 1) SS BOND : angle 9.28839 / 5.24 ( 2) hydrogen bonds : bond 0.06922 / 4.63 ( 1806) hydrogen bonds : angle 4.37280 / 3.21 ( 5226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 132 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: U 329 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7084 (mmt180) REVERT: K 257 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: L 107 LEU cc_start: 0.8288 (mt) cc_final: 0.8064 (mt) REVERT: L 238 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: N 114 ARG cc_start: 0.7903 (tmm160) cc_final: 0.7613 (tmm160) REVERT: Q 175 ASN cc_start: 0.7544 (t160) cc_final: 0.7228 (t0) outliers start: 67 outliers final: 50 residues processed: 311 average time/residue: 0.7622 time to fit residues: 272.3627 Evaluate side-chains 301 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain U residue 412 GLU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain I residue 637 TYR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 238 GLU Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 311 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 253 GLN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 276 CYS Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain C residue 304 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 114 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 315 optimal weight: 50.0000 chunk 221 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 320 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 283 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 GLN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.247743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211867 restraints weight = 31503.319| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.81 r_work: 0.4081 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28730 Z= 0.167 Angle : 0.700 13.163 39255 Z= 0.361 Chirality : 0.041 0.284 4495 Planarity : 0.005 0.090 4524 Dihedral : 18.683 179.885 4705 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 2.10 % Allowed : 19.38 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.44 (0.15), residues: 3096 helix: 1.95 (0.11), residues: 1981 sheet: -0.12 (0.29), residues: 279 loop : -1.08 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 101 TYR 0.034 0.002 TYR L 207 PHE 0.020 0.002 PHE O 287 TRP 0.015 0.002 TRP L 265 HIS 0.012 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (28729) covalent geometry : angle 0.69822 / 0.36 (39253) SS BOND : bond 0.01959 / 1.03 ( 1) SS BOND : angle 6.01915 / 3.40 ( 2) hydrogen bonds : bond 0.05371 / 3.59 ( 1806) hydrogen bonds : angle 4.06907 / 2.99 ( 5226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10786.13 seconds wall clock time: 184 minutes 36.91 seconds (11076.91 seconds total)