Starting phenix.real_space_refine on Wed May 21 04:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj2_63131/05_2025/9lj2_63131.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 12448 2.51 5 N 3821 2.21 5 O 4524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21131 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3002 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3025 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4921 Classifications: {'peptide': 598} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Chain: "N" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4066 Classifications: {'peptide': 495} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 477} Chain breaks: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.17, per 1000 atoms: 0.58 Number of scatterers: 21131 At special positions: 0 Unit cell: (114.745, 117.992, 194.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 298 15.00 Mg 2 11.99 O 4524 8.00 N 3821 7.00 C 12448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.0 seconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 60.6% alpha, 4.1% beta 137 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 8.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.533A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.741A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.249A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.584A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.598A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.548A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.652A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.016A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.780A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.562A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 82 through 90 removed outlier: 4.049A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 129 removed outlier: 3.705A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER K 125 " --> pdb=" O HIS K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 143 removed outlier: 3.654A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 removed outlier: 3.867A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 315 removed outlier: 3.676A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 4.037A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 340 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.935A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.829A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 Processing helix chain 'K' and resid 405 through 409 removed outlier: 4.050A pdb=" N LEU K 409 " --> pdb=" O GLN K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 417 removed outlier: 3.880A pdb=" N VAL K 417 " --> pdb=" O LYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 removed outlier: 3.639A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 497 through 500 removed outlier: 3.578A pdb=" N ASN K 500 " --> pdb=" O LEU K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 497 through 500' Processing helix chain 'K' and resid 501 through 518 Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.693A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 609 removed outlier: 3.777A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 609 through 614 removed outlier: 3.778A pdb=" N HIS K 613 " --> pdb=" O MET K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.795A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.701A pdb=" N LEU K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 730 through 735 Processing helix chain 'N' and resid 102 through 115 removed outlier: 3.648A pdb=" N PHE N 109 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU N 110 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 133 through 139 removed outlier: 3.731A pdb=" N VAL N 139 " --> pdb=" O GLN N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 143 Processing helix chain 'N' and resid 197 through 214 removed outlier: 3.850A pdb=" N ILE N 201 " --> pdb=" O ARG N 197 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN N 202 " --> pdb=" O PRO N 198 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY N 203 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 241 removed outlier: 4.095A pdb=" N PHE N 234 " --> pdb=" O GLN N 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 235 " --> pdb=" O THR N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 256 through 268 removed outlier: 3.650A pdb=" N TRP N 260 " --> pdb=" O THR N 256 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU N 261 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG N 266 " --> pdb=" O ARG N 262 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 290 removed outlier: 3.545A pdb=" N ARG N 283 " --> pdb=" O ASP N 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 284 " --> pdb=" O LYS N 280 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 307 removed outlier: 3.618A pdb=" N ILE N 307 " --> pdb=" O TYR N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.567A pdb=" N LEU N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 329 Processing helix chain 'N' and resid 334 through 341 removed outlier: 3.518A pdb=" N ARG N 341 " --> pdb=" O SER N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 371 removed outlier: 3.769A pdb=" N TRP N 364 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA N 365 " --> pdb=" O HIS N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 391 removed outlier: 3.859A pdb=" N THR N 390 " --> pdb=" O SER N 386 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU N 391 " --> pdb=" O SER N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 405 removed outlier: 3.695A pdb=" N THR N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 446 Processing helix chain 'N' and resid 467 through 478 Processing helix chain 'N' and resid 479 through 483 removed outlier: 3.695A pdb=" N ASP N 483 " --> pdb=" O TYR N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 500 removed outlier: 4.060A pdb=" N VAL N 498 " --> pdb=" O ASP N 494 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN N 500 " --> pdb=" O HIS N 496 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 516 removed outlier: 3.647A pdb=" N LYS N 509 " --> pdb=" O GLN N 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS N 515 " --> pdb=" O LEU N 511 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 541 removed outlier: 3.594A pdb=" N ASP N 532 " --> pdb=" O SER N 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 533 " --> pdb=" O ARG N 529 " (cutoff:3.500A) Processing helix chain 'N' and resid 553 through 565 Processing helix chain 'N' and resid 601 through 613 removed outlier: 3.507A pdb=" N ASP N 605 " --> pdb=" O ASN N 601 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA N 608 " --> pdb=" O ALA N 604 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA N 612 " --> pdb=" O ALA N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 651 removed outlier: 4.199A pdb=" N LYS N 635 " --> pdb=" O SER N 631 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU N 638 " --> pdb=" O GLU N 634 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP N 647 " --> pdb=" O LYS N 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN N 648 " --> pdb=" O LEU N 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.518A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.629A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.861A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 248 through 251 removed outlier: 5.973A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 273 through 275 Processing sheet with id=AB3, first strand: chain 'K' and resid 429 through 431 removed outlier: 6.953A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU K 576 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 523 " --> pdb=" O LEU K 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 320 through 324 removed outlier: 6.030A pdb=" N ILE N 321 " --> pdb=" O LEU N 349 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 351 " --> pdb=" O ILE N 321 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE N 323 " --> pdb=" O ILE N 351 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY N 217 " --> pdb=" O ARG N 348 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU N 350 " --> pdb=" O GLY N 217 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 218 " --> pdb=" O LEU N 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 425 through 426 removed outlier: 6.325A pdb=" N LYS N 425 " --> pdb=" O VAL N 623 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG N 625 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL N 521 " --> pdb=" O PHE N 574 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU N 576 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE N 523 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS N 546 " --> pdb=" O LEU N 575 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N THR N 577 " --> pdb=" O CYS N 546 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 430 through 431 731 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 672 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 9.11 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4790 1.33 - 1.45: 5736 1.45 - 1.57: 10933 1.57 - 1.69: 593 1.69 - 1.81: 64 Bond restraints: 22116 Sorted by residual: bond pdb=" CA ASP N 483 " pdb=" C ASP N 483 " ideal model delta sigma weight residual 1.532 1.498 0.035 9.60e-03 1.09e+04 1.31e+01 bond pdb=" CB PRO N 567 " pdb=" CG PRO N 567 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.24e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" C PHE N 482 " pdb=" N ASP N 483 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.19e-02 7.06e+03 6.07e+00 bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.522 1.494 0.029 1.20e-02 6.94e+03 5.72e+00 ... (remaining 22111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30775 2.61 - 5.22: 319 5.22 - 7.83: 31 7.83 - 10.44: 3 10.44 - 13.05: 1 Bond angle restraints: 31129 Sorted by residual: angle pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" CD PRO N 567 " ideal model delta sigma weight residual 112.00 98.95 13.05 1.40e+00 5.10e-01 8.69e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 114.62 108.50 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.46 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO N 567 " pdb=" CD PRO N 567 " pdb=" CG PRO N 567 " ideal model delta sigma weight residual 103.20 96.53 6.67 1.50e+00 4.44e-01 1.98e+01 angle pdb=" N THR A 80 " pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 108.65 100.87 7.78 1.85e+00 2.92e-01 1.77e+01 ... (remaining 31124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 11134 35.33 - 70.66: 1473 70.66 - 105.99: 23 105.99 - 141.32: 16 141.32 - 176.65: 6 Dihedral angle restraints: 12652 sinusoidal: 7205 harmonic: 5447 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual 300.00 123.35 176.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " pdb=" O2A ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 83.29 -143.29 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C4' ADP K1202 " pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " ideal model delta sinusoidal sigma weight residual -180.00 -71.47 -108.53 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 12649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2461 0.039 - 0.078: 808 0.078 - 0.116: 200 0.116 - 0.155: 34 0.155 - 0.194: 6 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" C PRO N 567 " pdb=" CB PRO N 567 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CG LEU N 576 " pdb=" CB LEU N 576 " pdb=" CD1 LEU N 576 " pdb=" CD2 LEU N 576 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3506 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 566 " 0.089 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO N 567 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO N 567 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 567 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 566 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 567 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 567 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 567 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 72 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO K 73 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO K 73 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 73 " -0.031 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 370 2.62 - 3.19: 18745 3.19 - 3.76: 36812 3.76 - 4.33: 49438 4.33 - 4.90: 73321 Nonbonded interactions: 178686 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 2.044 2.170 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.083 3.120 nonbonded pdb=" O2 DC I 92 " pdb=" N2 DG J 56 " model vdw 2.119 2.496 nonbonded pdb=" OG SER K 434 " pdb=" OE1 GLN K 437 " model vdw 2.120 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3B ADP N1202 " model vdw 2.155 2.170 ... (remaining 178681 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid 1 through 55 or resid 57 through 64 or resid 67 or resid 6 \ 9 through 74 or resid 76 through 77 or resid 79 or resid 83 through 88 or resid \ 90 through 91 or resid 93 through 147)) selection = (chain 'J' and (resid 1 through 55 or resid 57 through 61 or resid 63 through 65 \ or resid 68 or resid 71 through 72 or resid 74 through 79 or resid 81 or resid \ 84 through 91 or resid 93 through 147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 53.560 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.005 0.176 22116 Z= 0.230 Angle : 0.732 13.049 31129 Z= 0.422 Chirality : 0.041 0.194 3509 Planarity : 0.005 0.124 2931 Dihedral : 24.540 176.649 9116 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.18 % Allowed : 0.49 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1825 helix: 0.80 (0.17), residues: 1001 sheet: -2.56 (0.51), residues: 103 loop : -1.96 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 260 HIS 0.005 0.001 HIS B 18 PHE 0.018 0.002 PHE K 574 TYR 0.015 0.002 TYR K 543 ARG 0.015 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.14049 ( 1073) hydrogen bonds : angle 5.30456 ( 2808) covalent geometry : bond 0.00512 (22116) covalent geometry : angle 0.73215 (31129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8126 (mm-30) REVERT: E 106 ASP cc_start: 0.7891 (m-30) cc_final: 0.7425 (m-30) REVERT: E 120 MET cc_start: 0.7563 (mtt) cc_final: 0.7217 (mtt) REVERT: G 104 GLN cc_start: 0.8512 (mm110) cc_final: 0.8281 (mm110) REVERT: H 90 GLU cc_start: 0.8250 (mp0) cc_final: 0.7835 (mp0) REVERT: K 183 PHE cc_start: 0.8833 (m-10) cc_final: 0.8311 (m-10) REVERT: K 722 LEU cc_start: 0.7881 (mm) cc_final: 0.7619 (mm) REVERT: N 645 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8913 (ttp80) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 1.5013 time to fit residues: 404.7943 Evaluate side-chains 162 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 122 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 0.0870 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 44 GLN G 104 GLN K 111 HIS ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS N 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067338 restraints weight = 62263.594| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.70 r_work: 0.3084 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22116 Z= 0.165 Angle : 0.669 8.500 31129 Z= 0.362 Chirality : 0.039 0.190 3509 Planarity : 0.005 0.056 2931 Dihedral : 28.545 171.874 5297 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.66 % Allowed : 10.26 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1825 helix: 1.15 (0.17), residues: 1019 sheet: -2.31 (0.47), residues: 113 loop : -1.78 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 260 HIS 0.013 0.001 HIS K 361 PHE 0.014 0.002 PHE N 234 TYR 0.014 0.001 TYR K 543 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05568 ( 1073) hydrogen bonds : angle 4.13242 ( 2808) covalent geometry : bond 0.00361 (22116) covalent geometry : angle 0.66918 (31129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8618 (t0) cc_final: 0.8309 (t0) REVERT: D 33 SER cc_start: 0.8603 (t) cc_final: 0.8390 (t) REVERT: D 105 LYS cc_start: 0.8734 (mtpm) cc_final: 0.8495 (mttp) REVERT: E 73 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8686 (tm-30) REVERT: E 106 ASP cc_start: 0.8336 (m-30) cc_final: 0.8005 (m-30) REVERT: E 120 MET cc_start: 0.8211 (mtt) cc_final: 0.7893 (mtt) REVERT: F 93 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: G 104 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8742 (mm110) REVERT: H 39 TYR cc_start: 0.8728 (t80) cc_final: 0.8499 (t80) REVERT: H 53 SER cc_start: 0.9373 (t) cc_final: 0.9162 (p) REVERT: H 90 GLU cc_start: 0.8805 (mp0) cc_final: 0.8577 (mp0) REVERT: K 183 PHE cc_start: 0.8751 (m-10) cc_final: 0.8534 (m-10) REVERT: K 525 SER cc_start: 0.9129 (m) cc_final: 0.8519 (t) REVERT: K 722 LEU cc_start: 0.7732 (mm) cc_final: 0.7455 (mm) REVERT: N 279 ASP cc_start: 0.8656 (t0) cc_final: 0.8442 (t70) REVERT: N 606 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8212 (tm) REVERT: N 645 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8733 (ttp80) outliers start: 27 outliers final: 7 residues processed: 218 average time/residue: 1.3959 time to fit residues: 344.0857 Evaluate side-chains 181 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 201 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 85 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN K 361 HIS ** N 288 GLN ** 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 = 0.3783 r_free = 0.3783 target = 0.091600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064043 restraints weight = 61776.750| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.70 r_work: 0.3005 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 22116 Z= 0.286 Angle : 0.701 9.253 31129 Z= 0.380 Chirality : 0.042 0.169 3509 Planarity : 0.005 0.053 2931 Dihedral : 28.650 168.082 5295 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.77 % Allowed : 14.26 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1825 helix: 1.07 (0.16), residues: 1029 sheet: -2.22 (0.47), residues: 112 loop : -1.83 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 267 HIS 0.014 0.001 HIS K 361 PHE 0.025 0.002 PHE N 122 TYR 0.017 0.002 TYR N 499 ARG 0.008 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.06324 ( 1073) hydrogen bonds : angle 4.10875 ( 2808) covalent geometry : bond 0.00653 (22116) covalent geometry : angle 0.70051 (31129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8898 (tm) REVERT: C 90 ASP cc_start: 0.8626 (t0) cc_final: 0.8399 (t0) REVERT: D 105 LYS cc_start: 0.8990 (mtpm) cc_final: 0.8759 (mttp) REVERT: E 73 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8681 (tm-30) REVERT: E 106 ASP cc_start: 0.8429 (m-30) cc_final: 0.8081 (m-30) REVERT: E 120 MET cc_start: 0.8361 (mtt) cc_final: 0.8024 (mtt) REVERT: F 93 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: G 104 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8799 (mm110) REVERT: H 39 TYR cc_start: 0.8795 (t80) cc_final: 0.8541 (t80) REVERT: H 90 GLU cc_start: 0.8873 (mp0) cc_final: 0.8475 (mp0) REVERT: K 183 PHE cc_start: 0.8845 (m-10) cc_final: 0.8639 (m-10) REVERT: K 424 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: K 722 LEU cc_start: 0.7873 (mm) cc_final: 0.7623 (mm) REVERT: N 279 ASP cc_start: 0.8648 (t0) cc_final: 0.8432 (t70) REVERT: N 370 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8321 (mp) REVERT: N 645 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8767 (ttp80) outliers start: 45 outliers final: 18 residues processed: 198 average time/residue: 1.3606 time to fit residues: 306.2753 Evaluate side-chains 181 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 361 HIS Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 198 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.093737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066756 restraints weight = 62400.766| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.73 r_work: 0.3064 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22116 Z= 0.154 Angle : 0.630 10.500 31129 Z= 0.343 Chirality : 0.037 0.169 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.419 166.242 5295 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.34 % Allowed : 16.78 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1825 helix: 1.29 (0.17), residues: 1040 sheet: -1.95 (0.46), residues: 123 loop : -1.71 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 260 HIS 0.016 0.001 HIS K 361 PHE 0.027 0.002 PHE N 122 TYR 0.016 0.001 TYR N 499 ARG 0.004 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 1073) hydrogen bonds : angle 3.79625 ( 2808) covalent geometry : bond 0.00337 (22116) covalent geometry : angle 0.62967 (31129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8808 (tm) REVERT: A 94 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8577 (mm-30) REVERT: C 90 ASP cc_start: 0.8550 (t0) cc_final: 0.8318 (t0) REVERT: D 33 SER cc_start: 0.8507 (t) cc_final: 0.8305 (t) REVERT: D 39 TYR cc_start: 0.8737 (t80) cc_final: 0.8262 (t80) REVERT: D 105 LYS cc_start: 0.8829 (mtpm) cc_final: 0.8612 (mttp) REVERT: E 68 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: E 73 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8684 (tm-30) REVERT: E 106 ASP cc_start: 0.8339 (m-30) cc_final: 0.8010 (m-30) REVERT: E 120 MET cc_start: 0.8162 (mtt) cc_final: 0.7795 (mtt) REVERT: F 93 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: G 104 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8729 (mm110) REVERT: H 53 SER cc_start: 0.9383 (t) cc_final: 0.9169 (p) REVERT: H 90 GLU cc_start: 0.8896 (mp0) cc_final: 0.8483 (mp0) REVERT: K 279 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7527 (p0) REVERT: K 722 LEU cc_start: 0.7806 (mm) cc_final: 0.7564 (mm) REVERT: N 221 ASP cc_start: 0.6608 (m-30) cc_final: 0.6325 (m-30) REVERT: N 469 MET cc_start: 0.8272 (tpp) cc_final: 0.8040 (tpp) REVERT: N 470 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: N 606 LEU cc_start: 0.8663 (mt) cc_final: 0.8403 (tm) REVERT: N 645 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8643 (ttp80) outliers start: 38 outliers final: 9 residues processed: 209 average time/residue: 1.3294 time to fit residues: 314.4320 Evaluate side-chains 176 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 470 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 112 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN N 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.093447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066434 restraints weight = 62603.075| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.68 r_work: 0.3073 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22116 Z= 0.167 Angle : 0.634 12.329 31129 Z= 0.342 Chirality : 0.038 0.163 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.304 165.589 5295 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.77 % Allowed : 17.89 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1825 helix: 1.31 (0.17), residues: 1047 sheet: -1.98 (0.45), residues: 120 loop : -1.68 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 267 HIS 0.009 0.001 HIS K 361 PHE 0.027 0.002 PHE N 122 TYR 0.020 0.001 TYR N 499 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 1073) hydrogen bonds : angle 3.69940 ( 2808) covalent geometry : bond 0.00375 (22116) covalent geometry : angle 0.63377 (31129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8868 (tm) REVERT: A 94 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 90 ASP cc_start: 0.8589 (t0) cc_final: 0.8356 (t0) REVERT: D 33 SER cc_start: 0.8502 (t) cc_final: 0.8301 (t) REVERT: D 105 LYS cc_start: 0.8847 (mtpm) cc_final: 0.8642 (mttp) REVERT: E 68 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: E 73 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8670 (tm-30) REVERT: E 106 ASP cc_start: 0.8332 (m-30) cc_final: 0.8023 (m-30) REVERT: E 120 MET cc_start: 0.8114 (mtt) cc_final: 0.7756 (mtt) REVERT: F 93 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: G 104 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8697 (mm110) REVERT: H 39 TYR cc_start: 0.8685 (t80) cc_final: 0.8483 (t80) REVERT: H 53 SER cc_start: 0.9341 (t) cc_final: 0.9140 (p) REVERT: H 90 GLU cc_start: 0.8892 (mp0) cc_final: 0.8491 (mp0) REVERT: K 426 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7886 (mm-30) REVERT: K 722 LEU cc_start: 0.7905 (mm) cc_final: 0.7666 (mm) REVERT: N 527 MET cc_start: 0.8235 (mtp) cc_final: 0.7625 (ttm) REVERT: N 606 LEU cc_start: 0.8673 (mt) cc_final: 0.8463 (tm) REVERT: N 645 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8732 (ttp80) outliers start: 45 outliers final: 16 residues processed: 203 average time/residue: 1.3508 time to fit residues: 313.2812 Evaluate side-chains 179 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 85 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.091665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064335 restraints weight = 62066.613| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.65 r_work: 0.3026 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 22116 Z= 0.277 Angle : 0.689 13.453 31129 Z= 0.371 Chirality : 0.041 0.180 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.468 166.577 5295 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.64 % Allowed : 19.42 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1825 helix: 1.15 (0.16), residues: 1053 sheet: -2.31 (0.46), residues: 115 loop : -1.65 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 384 HIS 0.011 0.002 HIS K 121 PHE 0.026 0.002 PHE N 122 TYR 0.020 0.002 TYR N 499 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05858 ( 1073) hydrogen bonds : angle 3.85825 ( 2808) covalent geometry : bond 0.00635 (22116) covalent geometry : angle 0.68904 (31129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8897 (tm) REVERT: A 94 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8618 (mm-30) REVERT: C 90 ASP cc_start: 0.8709 (t0) cc_final: 0.8455 (t0) REVERT: D 33 SER cc_start: 0.8653 (t) cc_final: 0.8445 (t) REVERT: D 90 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: D 105 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8787 (mttp) REVERT: E 68 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: E 73 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8669 (tm-30) REVERT: E 106 ASP cc_start: 0.8341 (m-30) cc_final: 0.8051 (m-30) REVERT: E 120 MET cc_start: 0.8257 (mtt) cc_final: 0.7887 (mtt) REVERT: F 93 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: G 36 LYS cc_start: 0.9048 (mmtm) cc_final: 0.8819 (mmpt) REVERT: G 64 GLU cc_start: 0.8798 (tt0) cc_final: 0.8311 (tm-30) REVERT: G 104 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8754 (mm110) REVERT: H 39 TYR cc_start: 0.8759 (t80) cc_final: 0.8536 (t80) REVERT: H 53 SER cc_start: 0.9380 (t) cc_final: 0.9167 (p) REVERT: H 90 GLU cc_start: 0.8946 (mp0) cc_final: 0.8535 (mp0) REVERT: K 279 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7356 (p0) REVERT: K 426 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7515 (pm20) REVERT: K 722 LEU cc_start: 0.8043 (mm) cc_final: 0.7816 (mm) REVERT: N 370 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8312 (mp) REVERT: N 527 MET cc_start: 0.8196 (mtp) cc_final: 0.7622 (ttm) REVERT: N 645 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8737 (ttp80) outliers start: 43 outliers final: 20 residues processed: 193 average time/residue: 1.3812 time to fit residues: 302.4276 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 46 HIS K 437 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** 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 = 0.3827 r_free = 0.3827 target = 0.094017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067014 restraints weight = 62000.182| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.70 r_work: 0.3079 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22116 Z= 0.153 Angle : 0.643 14.130 31129 Z= 0.344 Chirality : 0.038 0.229 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.266 167.119 5295 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.21 % Allowed : 20.16 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1825 helix: 1.34 (0.17), residues: 1059 sheet: -2.14 (0.44), residues: 126 loop : -1.60 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 384 HIS 0.009 0.001 HIS K 361 PHE 0.028 0.002 PHE N 122 TYR 0.017 0.001 TYR N 499 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 1073) hydrogen bonds : angle 3.62810 ( 2808) covalent geometry : bond 0.00341 (22116) covalent geometry : angle 0.64289 (31129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8820 (tm) REVERT: A 94 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8539 (mm-30) REVERT: C 90 ASP cc_start: 0.8496 (t0) cc_final: 0.8241 (t0) REVERT: D 33 SER cc_start: 0.8468 (t) cc_final: 0.8251 (t) REVERT: D 105 LYS cc_start: 0.8831 (mtpm) cc_final: 0.8621 (mttp) REVERT: E 59 GLU cc_start: 0.8721 (pt0) cc_final: 0.8484 (pm20) REVERT: E 68 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 106 ASP cc_start: 0.8346 (m-30) cc_final: 0.8010 (m-30) REVERT: F 93 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: G 36 LYS cc_start: 0.9109 (mmtm) cc_final: 0.8864 (mmpt) REVERT: G 64 GLU cc_start: 0.8764 (tt0) cc_final: 0.8250 (tm-30) REVERT: G 104 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8716 (mm110) REVERT: H 39 TYR cc_start: 0.8687 (t80) cc_final: 0.8442 (t80) REVERT: H 90 GLU cc_start: 0.8948 (mp0) cc_final: 0.8510 (mp0) REVERT: K 722 LEU cc_start: 0.7983 (mm) cc_final: 0.7758 (mm) REVERT: N 370 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (mp) REVERT: N 527 MET cc_start: 0.8210 (mtp) cc_final: 0.7702 (ttm) REVERT: N 606 LEU cc_start: 0.8695 (mt) cc_final: 0.8446 (tm) REVERT: N 645 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8716 (ttp80) outliers start: 36 outliers final: 14 residues processed: 204 average time/residue: 1.3094 time to fit residues: 304.9686 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS K 437 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** 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 = 0.3819 r_free = 0.3819 target = 0.093375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066276 restraints weight = 62581.116| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.69 r_work: 0.3075 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22116 Z= 0.177 Angle : 0.649 14.735 31129 Z= 0.347 Chirality : 0.038 0.294 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.236 166.627 5295 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.15 % Allowed : 21.20 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1825 helix: 1.38 (0.17), residues: 1048 sheet: -2.08 (0.47), residues: 114 loop : -1.55 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP K 384 HIS 0.009 0.001 HIS K 361 PHE 0.021 0.002 PHE N 234 TYR 0.022 0.001 TYR N 199 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 1073) hydrogen bonds : angle 3.63299 ( 2808) covalent geometry : bond 0.00400 (22116) covalent geometry : angle 0.64891 (31129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8848 (tm) REVERT: A 94 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8524 (mm-30) REVERT: C 90 ASP cc_start: 0.8553 (t0) cc_final: 0.8303 (t0) REVERT: D 33 SER cc_start: 0.8467 (t) cc_final: 0.8256 (t) REVERT: E 68 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: E 73 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8611 (tm-30) REVERT: E 106 ASP cc_start: 0.8343 (m-30) cc_final: 0.8032 (m-30) REVERT: E 120 MET cc_start: 0.8169 (mtt) cc_final: 0.7859 (mtt) REVERT: F 93 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: G 36 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8873 (mmpt) REVERT: G 104 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8736 (mm110) REVERT: H 39 TYR cc_start: 0.8705 (t80) cc_final: 0.8459 (t80) REVERT: H 90 GLU cc_start: 0.8963 (mp0) cc_final: 0.8516 (mp0) REVERT: K 210 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8477 (mm) REVERT: K 279 ASP cc_start: 0.8040 (p0) cc_final: 0.7649 (p0) REVERT: K 525 SER cc_start: 0.9065 (m) cc_final: 0.8429 (t) REVERT: K 722 LEU cc_start: 0.8006 (mm) cc_final: 0.7773 (mm) REVERT: N 370 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8329 (mp) REVERT: N 470 MET cc_start: 0.8410 (ttp) cc_final: 0.8121 (ttp) REVERT: N 527 MET cc_start: 0.8219 (mtp) cc_final: 0.7741 (ttm) REVERT: N 645 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8708 (ttp80) outliers start: 35 outliers final: 19 residues processed: 196 average time/residue: 1.3723 time to fit residues: 305.5056 Evaluate side-chains 184 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 133 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066957 restraints weight = 62668.456| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.71 r_work: 0.3089 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22116 Z= 0.160 Angle : 0.647 12.032 31129 Z= 0.346 Chirality : 0.038 0.330 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.165 167.362 5295 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.03 % Allowed : 21.70 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1825 helix: 1.41 (0.17), residues: 1048 sheet: -2.21 (0.46), residues: 119 loop : -1.51 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 384 HIS 0.009 0.001 HIS K 361 PHE 0.028 0.002 PHE N 122 TYR 0.021 0.001 TYR N 499 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 1073) hydrogen bonds : angle 3.59247 ( 2808) covalent geometry : bond 0.00360 (22116) covalent geometry : angle 0.64678 (31129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8866 (tm) REVERT: A 94 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8509 (mm-30) REVERT: C 90 ASP cc_start: 0.8558 (t0) cc_final: 0.8324 (t0) REVERT: E 68 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: E 73 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8610 (tm-30) REVERT: E 106 ASP cc_start: 0.8263 (m-30) cc_final: 0.7972 (m-30) REVERT: E 120 MET cc_start: 0.8135 (mtt) cc_final: 0.7847 (mtt) REVERT: F 93 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: G 36 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8858 (mmpt) REVERT: G 104 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8734 (mm110) REVERT: H 39 TYR cc_start: 0.8707 (t80) cc_final: 0.8481 (t80) REVERT: H 90 GLU cc_start: 0.8937 (mp0) cc_final: 0.8546 (mp0) REVERT: K 108 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8352 (ptp-110) REVERT: K 210 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8459 (mm) REVERT: K 261 LEU cc_start: 0.8897 (tt) cc_final: 0.8683 (tm) REVERT: K 279 ASP cc_start: 0.8002 (p0) cc_final: 0.7545 (p0) REVERT: K 426 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7292 (pm20) REVERT: K 525 SER cc_start: 0.9021 (m) cc_final: 0.8441 (t) REVERT: K 722 LEU cc_start: 0.8008 (mm) cc_final: 0.7773 (mm) REVERT: N 221 ASP cc_start: 0.6244 (m-30) cc_final: 0.5916 (m-30) REVERT: N 370 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8344 (mp) REVERT: N 470 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8162 (ttp) REVERT: N 527 MET cc_start: 0.8312 (mtp) cc_final: 0.7776 (ttm) REVERT: N 645 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8698 (ttp80) outliers start: 33 outliers final: 18 residues processed: 199 average time/residue: 1.3793 time to fit residues: 310.5314 Evaluate side-chains 188 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 470 MET Chi-restraints excluded: chain N residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.093750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066577 restraints weight = 62408.562| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.70 r_work: 0.3077 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22116 Z= 0.176 Angle : 0.652 13.875 31129 Z= 0.349 Chirality : 0.039 0.330 3509 Planarity : 0.004 0.052 2931 Dihedral : 28.164 167.592 5295 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.66 % Allowed : 22.19 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1825 helix: 1.40 (0.17), residues: 1049 sheet: -1.96 (0.48), residues: 114 loop : -1.55 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 384 HIS 0.008 0.001 HIS K 361 PHE 0.022 0.002 PHE N 234 TYR 0.023 0.001 TYR N 499 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 1073) hydrogen bonds : angle 3.61862 ( 2808) covalent geometry : bond 0.00401 (22116) covalent geometry : angle 0.65153 (31129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8942 (pm20) cc_final: 0.8581 (pm20) REVERT: A 65 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8874 (tm) REVERT: A 94 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8514 (mm-30) REVERT: C 90 ASP cc_start: 0.8577 (t0) cc_final: 0.8339 (t0) REVERT: E 68 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: E 73 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8627 (tm-30) REVERT: E 106 ASP cc_start: 0.8324 (m-30) cc_final: 0.8086 (m-30) REVERT: E 120 MET cc_start: 0.8173 (mtt) cc_final: 0.7875 (mtt) REVERT: F 93 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: G 36 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8885 (mmpt) REVERT: G 104 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8744 (mm110) REVERT: H 39 TYR cc_start: 0.8725 (t80) cc_final: 0.8476 (t80) REVERT: H 90 GLU cc_start: 0.8951 (mp0) cc_final: 0.8553 (mp0) REVERT: K 108 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8420 (ptp-110) REVERT: K 210 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8480 (mm) REVERT: K 261 LEU cc_start: 0.8874 (tt) cc_final: 0.8669 (tm) REVERT: K 279 ASP cc_start: 0.7985 (p0) cc_final: 0.7511 (p0) REVERT: K 426 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7365 (pm20) REVERT: K 525 SER cc_start: 0.9030 (m) cc_final: 0.8435 (t) REVERT: K 722 LEU cc_start: 0.8007 (mm) cc_final: 0.7767 (mm) REVERT: N 221 ASP cc_start: 0.6493 (m-30) cc_final: 0.6202 (m-30) REVERT: N 370 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (mp) REVERT: N 433 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7508 (tmm) REVERT: N 470 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8160 (ttp) REVERT: N 527 MET cc_start: 0.8277 (mtp) cc_final: 0.7744 (ttm) REVERT: N 645 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8680 (ttp80) outliers start: 27 outliers final: 18 residues processed: 190 average time/residue: 1.4754 time to fit residues: 314.7985 Evaluate side-chains 189 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Chi-restraints excluded: chain N residue 370 LEU Chi-restraints excluded: chain N residue 433 MET Chi-restraints excluded: chain N residue 470 MET Chi-restraints excluded: chain N residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 117 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 0.0000 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.094913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068084 restraints weight = 62613.775| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.72 r_work: 0.3115 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22116 Z= 0.147 Angle : 0.644 13.600 31129 Z= 0.343 Chirality : 0.038 0.323 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.036 168.275 5295 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.91 % Allowed : 22.19 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1825 helix: 1.48 (0.17), residues: 1052 sheet: -2.05 (0.45), residues: 126 loop : -1.51 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 384 HIS 0.009 0.001 HIS K 361 PHE 0.030 0.002 PHE N 122 TYR 0.027 0.001 TYR N 199 ARG 0.009 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1073) hydrogen bonds : angle 3.53687 ( 2808) covalent geometry : bond 0.00328 (22116) covalent geometry : angle 0.64429 (31129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13118.60 seconds wall clock time: 226 minutes 22.58 seconds (13582.58 seconds total)