Starting phenix.real_space_refine on Thu Sep 18 22:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj2_63131/09_2025/9lj2_63131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj2_63131/09_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_63131/09_2025/9lj2_63131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj2_63131/09_2025/9lj2_63131.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj2_63131/09_2025/9lj2_63131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj2_63131/09_2025/9lj2_63131.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.70, per 1000 atoms: 0.22 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: 2.06 Conformation dependent library (CDL) restraints added in 693.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.03 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: 5.17 Time building geometry restraints manager: 2.68 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: 2.370 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.460 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG C 42 TYR 0.015 0.002 TYR K 543 PHE 0.018 0.002 PHE K 574 TRP 0.020 0.002 TRP N 260 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00512 (22116) covalent geometry : angle 0.73215 (31129) hydrogen bonds : bond 0.14049 ( 1073) hydrogen bonds : angle 5.30456 ( 2808) *********************** 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 : 0.733 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: 0.7767 time to fit residues: 208.4489 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 : 0.691 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS N 121 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.092260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064935 restraints weight = 62166.564| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.71 r_work: 0.3027 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22116 Z= 0.239 Angle : 0.703 8.407 31129 Z= 0.380 Chirality : 0.041 0.186 3509 Planarity : 0.005 0.055 2931 Dihedral : 28.729 173.116 5297 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.97 % Allowed : 10.45 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.20), residues: 1825 helix: 1.00 (0.16), residues: 1016 sheet: -2.40 (0.46), residues: 112 loop : -1.85 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.016 0.002 TYR N 499 PHE 0.016 0.002 PHE N 234 TRP 0.022 0.002 TRP N 260 HIS 0.014 0.001 HIS K 361 Details of bonding type rmsd covalent geometry : bond 0.00545 (22116) covalent geometry : angle 0.70291 (31129) hydrogen bonds : bond 0.06181 ( 1073) hydrogen bonds : angle 4.23913 ( 2808) *********************** 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 211 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9190 (tttp) cc_final: 0.8821 (tttm) REVERT: C 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8301 (t0) REVERT: D 105 LYS cc_start: 0.8977 (mtpm) cc_final: 0.8743 (mttp) REVERT: E 73 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8704 (tm-30) REVERT: E 90 MET cc_start: 0.9079 (mmm) cc_final: 0.8855 (mmp) REVERT: E 106 ASP cc_start: 0.8373 (m-30) cc_final: 0.8068 (m-30) REVERT: E 120 MET cc_start: 0.8360 (mtt) cc_final: 0.8026 (mtt) REVERT: F 93 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: G 104 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8795 (mm110) REVERT: H 39 TYR cc_start: 0.8738 (t80) cc_final: 0.8496 (t80) REVERT: H 90 GLU cc_start: 0.8828 (mp0) cc_final: 0.8361 (mp0) REVERT: K 722 LEU cc_start: 0.7814 (mm) cc_final: 0.7565 (mm) REVERT: N 279 ASP cc_start: 0.8689 (t0) cc_final: 0.8477 (t70) REVERT: N 606 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8314 (tm) outliers start: 32 outliers final: 10 residues processed: 197 average time/residue: 0.6974 time to fit residues: 153.7790 Evaluate side-chains 168 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 50 ILE 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 279 ASP Chi-restraints excluded: chain K residue 361 HIS 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 38 optimal weight: 0.1980 chunk 156 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066907 restraints weight = 62390.536| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.73 r_work: 0.3071 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1497 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= 0.158 Angle : 0.642 9.188 31129 Z= 0.349 Chirality : 0.038 0.167 3509 Planarity : 0.004 0.055 2931 Dihedral : 28.453 167.531 5295 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.21 % Allowed : 14.51 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1825 helix: 1.20 (0.17), residues: 1028 sheet: -2.00 (0.46), residues: 123 loop : -1.77 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.020 0.001 TYR N 499 PHE 0.028 0.002 PHE N 122 TRP 0.033 0.002 TRP N 267 HIS 0.017 0.001 HIS K 361 Details of bonding type rmsd covalent geometry : bond 0.00348 (22116) covalent geometry : angle 0.64212 (31129) hydrogen bonds : bond 0.05195 ( 1073) hydrogen bonds : angle 3.93241 ( 2808) *********************** 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 231 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8613 (mm-30) REVERT: B 59 LYS cc_start: 0.9133 (tttp) cc_final: 0.8751 (tttm) REVERT: D 33 SER cc_start: 0.8552 (t) cc_final: 0.8336 (t) REVERT: D 39 TYR cc_start: 0.8736 (t80) cc_final: 0.8254 (t80) REVERT: D 105 LYS cc_start: 0.8835 (mtpm) cc_final: 0.8599 (mttp) REVERT: E 90 MET cc_start: 0.9009 (mmm) cc_final: 0.8790 (mmp) REVERT: E 106 ASP cc_start: 0.8364 (m-30) cc_final: 0.8019 (m-30) REVERT: E 120 MET cc_start: 0.8182 (mtt) cc_final: 0.7836 (mtt) REVERT: F 93 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: G 104 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8750 (mm110) REVERT: H 39 TYR cc_start: 0.8740 (t80) cc_final: 0.8536 (t80) REVERT: H 53 SER cc_start: 0.9394 (t) cc_final: 0.9186 (p) REVERT: H 90 GLU cc_start: 0.8865 (mp0) cc_final: 0.8476 (mp0) REVERT: K 279 ASP cc_start: 0.7991 (p0) cc_final: 0.7605 (p0) REVERT: K 525 SER cc_start: 0.9069 (m) cc_final: 0.8456 (t) REVERT: K 722 LEU cc_start: 0.7803 (mm) cc_final: 0.7545 (mm) REVERT: N 279 ASP cc_start: 0.8599 (t0) cc_final: 0.8364 (t70) REVERT: N 645 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8684 (ttp80) outliers start: 36 outliers final: 13 residues processed: 218 average time/residue: 0.6617 time to fit residues: 163.1219 Evaluate side-chains 184 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 363 LEU 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 298 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 0.0170 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 E 76 GLN K 111 HIS ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN N 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068516 restraints weight = 62523.278| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.72 r_work: 0.3112 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22116 Z= 0.142 Angle : 0.617 10.474 31129 Z= 0.336 Chirality : 0.037 0.158 3509 Planarity : 0.004 0.055 2931 Dihedral : 28.210 164.782 5295 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.46 % Allowed : 16.84 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1825 helix: 1.35 (0.17), residues: 1036 sheet: -1.85 (0.46), residues: 125 loop : -1.70 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.017 0.001 TYR N 499 PHE 0.028 0.002 PHE N 122 TRP 0.026 0.002 TRP N 267 HIS 0.007 0.001 HIS N 402 Details of bonding type rmsd covalent geometry : bond 0.00308 (22116) covalent geometry : angle 0.61663 (31129) hydrogen bonds : bond 0.04732 ( 1073) hydrogen bonds : angle 3.69741 ( 2808) *********************** 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 236 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8575 (mm-30) REVERT: C 41 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: D 105 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8428 (mttp) REVERT: E 68 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: E 106 ASP cc_start: 0.8343 (m-30) cc_final: 0.7980 (m-30) REVERT: E 120 MET cc_start: 0.8011 (mtt) cc_final: 0.7673 (mtt) REVERT: F 93 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: G 104 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8683 (mm110) REVERT: H 53 SER cc_start: 0.9353 (t) cc_final: 0.9149 (p) REVERT: H 90 GLU cc_start: 0.8893 (mp0) cc_final: 0.8451 (mp0) REVERT: K 324 ASP cc_start: 0.8452 (t0) cc_final: 0.8246 (t70) REVERT: K 525 SER cc_start: 0.8915 (m) cc_final: 0.8381 (t) REVERT: K 722 LEU cc_start: 0.7777 (mm) cc_final: 0.7548 (mm) REVERT: K 733 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8474 (p0) REVERT: N 221 ASP cc_start: 0.6417 (m-30) cc_final: 0.6133 (m-30) REVERT: N 527 MET cc_start: 0.8234 (mtp) cc_final: 0.7586 (ttm) REVERT: N 645 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8689 (ttp80) outliers start: 40 outliers final: 8 residues processed: 227 average time/residue: 0.6299 time to fit residues: 162.3309 Evaluate side-chains 179 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 41 GLU 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 499 TYR Chi-restraints excluded: chain K residue 733 ASP Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 30 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN D 92 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.092905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065491 restraints weight = 62193.036| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.69 r_work: 0.3046 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22116 Z= 0.223 Angle : 0.663 12.211 31129 Z= 0.356 Chirality : 0.039 0.176 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.349 165.428 5295 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.58 % Allowed : 18.99 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.21), residues: 1825 helix: 1.29 (0.17), residues: 1041 sheet: -2.10 (0.44), residues: 131 loop : -1.62 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.018 0.002 TYR N 499 PHE 0.025 0.002 PHE N 122 TRP 0.019 0.002 TRP N 364 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (22116) covalent geometry : angle 0.66326 (31129) hydrogen bonds : bond 0.05472 ( 1073) hydrogen bonds : angle 3.79950 ( 2808) *********************** 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 210 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8906 (tm) REVERT: A 94 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8589 (mm-30) REVERT: D 105 LYS cc_start: 0.8895 (mtpm) cc_final: 0.8693 (mttp) REVERT: E 68 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: E 106 ASP cc_start: 0.8301 (m-30) cc_final: 0.7987 (m-30) REVERT: F 93 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: G 91 GLU cc_start: 0.8233 (pm20) cc_final: 0.7231 (pm20) REVERT: G 104 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8690 (mm110) REVERT: H 39 TYR cc_start: 0.8708 (t80) cc_final: 0.8468 (t80) REVERT: H 90 GLU cc_start: 0.8858 (mp0) cc_final: 0.8474 (mp0) REVERT: K 722 LEU cc_start: 0.7919 (mm) cc_final: 0.7676 (mm) REVERT: N 527 MET cc_start: 0.8240 (mtp) cc_final: 0.7612 (ttm) REVERT: N 645 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8716 (ttp80) outliers start: 42 outliers final: 16 residues processed: 197 average time/residue: 0.6681 time to fit residues: 147.9819 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 433 MET 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 N residue 122 PHE Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 371 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** K 205 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.093544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066479 restraints weight = 62476.637| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.68 r_work: 0.3082 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22116 Z= 0.169 Angle : 0.637 13.515 31129 Z= 0.343 Chirality : 0.038 0.169 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.276 166.512 5295 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.27 % Allowed : 19.91 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1825 helix: 1.34 (0.17), residues: 1046 sheet: -2.15 (0.44), residues: 126 loop : -1.60 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 412 TYR 0.019 0.001 TYR N 499 PHE 0.027 0.002 PHE N 122 TRP 0.044 0.002 TRP K 384 HIS 0.009 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00380 (22116) covalent geometry : angle 0.63676 (31129) hydrogen bonds : bond 0.04970 ( 1073) hydrogen bonds : angle 3.69701 ( 2808) *********************** 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 209 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8882 (tm) REVERT: A 94 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 59 LYS cc_start: 0.9149 (tttp) cc_final: 0.8827 (tttm) REVERT: E 68 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: E 106 ASP cc_start: 0.8274 (m-30) cc_final: 0.7957 (m-30) REVERT: E 120 MET cc_start: 0.8105 (mtt) cc_final: 0.7810 (mtt) REVERT: F 93 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: G 36 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8771 (mmpt) REVERT: G 104 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8718 (mm110) REVERT: H 39 TYR cc_start: 0.8708 (t80) cc_final: 0.8470 (t80) REVERT: H 90 GLU cc_start: 0.8901 (mp0) cc_final: 0.8518 (mp0) REVERT: K 609 MET cc_start: 0.8714 (ptt) cc_final: 0.8510 (ptt) REVERT: K 722 LEU cc_start: 0.7925 (mm) cc_final: 0.7688 (mm) REVERT: N 221 ASP cc_start: 0.6295 (m-30) cc_final: 0.6049 (m-30) REVERT: N 527 MET cc_start: 0.8314 (mtp) cc_final: 0.7672 (ttm) REVERT: N 606 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8367 (tm) REVERT: N 645 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8710 (ttp80) outliers start: 37 outliers final: 15 residues processed: 196 average time/residue: 0.6980 time to fit residues: 153.9109 Evaluate side-chains 181 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 137 LEU 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 546 CYS Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Chi-restraints excluded: chain N residue 606 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 163 optimal weight: 0.1980 chunk 183 optimal weight: 0.0570 chunk 116 optimal weight: 0.6980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067047 restraints weight = 62554.962| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.69 r_work: 0.3091 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22116 Z= 0.158 Angle : 0.634 14.165 31129 Z= 0.340 Chirality : 0.037 0.207 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.172 166.392 5295 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.46 % Allowed : 20.34 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1825 helix: 1.36 (0.17), residues: 1059 sheet: -2.11 (0.44), residues: 126 loop : -1.56 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 197 TYR 0.023 0.001 TYR N 199 PHE 0.027 0.002 PHE N 122 TRP 0.043 0.002 TRP K 384 HIS 0.004 0.001 HIS N 402 Details of bonding type rmsd covalent geometry : bond 0.00355 (22116) covalent geometry : angle 0.63350 (31129) hydrogen bonds : bond 0.04801 ( 1073) hydrogen bonds : angle 3.60478 ( 2808) *********************** 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 217 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8851 (tm) REVERT: A 94 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 59 LYS cc_start: 0.9091 (tttp) cc_final: 0.8752 (tttm) REVERT: D 90 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8433 (pm20) REVERT: E 68 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: E 106 ASP cc_start: 0.8334 (m-30) cc_final: 0.8046 (m-30) REVERT: E 120 MET cc_start: 0.8055 (mtt) cc_final: 0.7750 (mtt) REVERT: F 93 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: G 36 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8843 (mmpt) REVERT: G 104 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8712 (mm110) REVERT: H 39 TYR cc_start: 0.8662 (t80) cc_final: 0.8405 (t80) REVERT: H 90 GLU cc_start: 0.8926 (mp0) cc_final: 0.8525 (mp0) REVERT: K 123 ILE cc_start: 0.7400 (mp) cc_final: 0.7134 (mp) REVERT: K 279 ASP cc_start: 0.8018 (p0) cc_final: 0.7618 (p0) REVERT: K 609 MET cc_start: 0.8703 (ptt) cc_final: 0.8430 (ptt) REVERT: K 722 LEU cc_start: 0.7923 (mm) cc_final: 0.7690 (mm) REVERT: N 527 MET cc_start: 0.8297 (mtp) cc_final: 0.7693 (ttm) REVERT: N 645 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8724 (ttp80) outliers start: 40 outliers final: 20 residues processed: 205 average time/residue: 0.6867 time to fit residues: 158.5758 Evaluate side-chains 187 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 24 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 GLU 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 250 VAL 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 533 ILE Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 20 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 191 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 44 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.093736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066555 restraints weight = 62572.115| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.70 r_work: 0.3080 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22116 Z= 0.178 Angle : 0.644 14.450 31129 Z= 0.345 Chirality : 0.038 0.326 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.175 166.724 5295 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.15 % Allowed : 21.39 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1825 helix: 1.37 (0.17), residues: 1056 sheet: -2.19 (0.44), residues: 129 loop : -1.49 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.023 0.001 TYR N 499 PHE 0.020 0.002 PHE N 234 TRP 0.030 0.002 TRP K 384 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00403 (22116) covalent geometry : angle 0.64400 (31129) hydrogen bonds : bond 0.04904 ( 1073) hydrogen bonds : angle 3.59796 ( 2808) *********************** 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 : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8850 (tm) REVERT: A 94 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8546 (mm-30) REVERT: B 59 LYS cc_start: 0.9092 (tttp) cc_final: 0.8756 (tttm) REVERT: D 90 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: E 68 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: E 106 ASP cc_start: 0.8316 (m-30) cc_final: 0.8024 (m-30) REVERT: E 120 MET cc_start: 0.8102 (mtt) cc_final: 0.7801 (mtt) REVERT: F 93 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: G 36 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8860 (mmpt) REVERT: G 104 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8724 (mm110) REVERT: H 39 TYR cc_start: 0.8683 (t80) cc_final: 0.8430 (t80) REVERT: H 90 GLU cc_start: 0.8940 (mp0) cc_final: 0.8524 (mp0) REVERT: K 279 ASP cc_start: 0.8006 (p0) cc_final: 0.7555 (p0) REVERT: K 609 MET cc_start: 0.8724 (ptt) cc_final: 0.8431 (ptt) REVERT: K 722 LEU cc_start: 0.7985 (mm) cc_final: 0.7760 (mm) REVERT: N 527 MET cc_start: 0.8313 (mtp) cc_final: 0.7733 (ttm) REVERT: N 606 LEU cc_start: 0.8750 (mt) cc_final: 0.8487 (tm) REVERT: N 645 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8677 (ttp80) outliers start: 35 outliers final: 18 residues processed: 193 average time/residue: 0.7038 time to fit residues: 152.2856 Evaluate side-chains 183 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 90 GLU 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 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL 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 K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 44 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.094457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067471 restraints weight = 62161.663| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.71 r_work: 0.3102 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22116 Z= 0.152 Angle : 0.633 11.421 31129 Z= 0.339 Chirality : 0.037 0.334 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.089 167.233 5295 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.72 % Allowed : 22.07 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1825 helix: 1.48 (0.17), residues: 1043 sheet: -1.88 (0.47), residues: 121 loop : -1.47 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 76 TYR 0.023 0.001 TYR N 499 PHE 0.027 0.001 PHE N 122 TRP 0.025 0.002 TRP K 384 HIS 0.004 0.001 HIS K 111 Details of bonding type rmsd covalent geometry : bond 0.00340 (22116) covalent geometry : angle 0.63265 (31129) hydrogen bonds : bond 0.04683 ( 1073) hydrogen bonds : angle 3.52669 ( 2808) *********************** 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 206 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8842 (tm) REVERT: A 94 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 59 LYS cc_start: 0.9096 (tttp) cc_final: 0.8755 (tttm) REVERT: D 44 GLN cc_start: 0.8763 (mt0) cc_final: 0.8496 (mt0) REVERT: D 90 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: E 59 GLU cc_start: 0.8414 (pm20) cc_final: 0.8037 (pm20) REVERT: E 68 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: E 106 ASP cc_start: 0.8306 (m-30) cc_final: 0.8006 (m-30) REVERT: E 120 MET cc_start: 0.8037 (mtt) cc_final: 0.7738 (mtt) REVERT: F 93 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: G 36 LYS cc_start: 0.9103 (mmtm) cc_final: 0.8850 (mmpt) REVERT: G 104 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8716 (mm110) REVERT: H 39 TYR cc_start: 0.8695 (t80) cc_final: 0.8435 (t80) REVERT: H 90 GLU cc_start: 0.8929 (mp0) cc_final: 0.8507 (mp0) REVERT: K 279 ASP cc_start: 0.7976 (p0) cc_final: 0.7765 (p0) REVERT: K 384 TRP cc_start: 0.7762 (t60) cc_final: 0.7487 (t-100) REVERT: K 609 MET cc_start: 0.8727 (ptt) cc_final: 0.8421 (ptt) REVERT: K 722 LEU cc_start: 0.7977 (mm) cc_final: 0.7756 (mm) REVERT: N 221 ASP cc_start: 0.6174 (m-30) cc_final: 0.5832 (m-30) REVERT: N 527 MET cc_start: 0.8291 (mtp) cc_final: 0.7758 (ttm) REVERT: N 606 LEU cc_start: 0.8738 (mt) cc_final: 0.8495 (tm) REVERT: N 645 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8678 (ttp80) outliers start: 28 outliers final: 20 residues processed: 196 average time/residue: 0.7311 time to fit residues: 160.5169 Evaluate side-chains 190 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 D residue 90 GLU 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 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain N residue 363 LEU 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 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3840 r_free = 0.3840 target = 0.094537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067594 restraints weight = 62645.667| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.72 r_work: 0.3104 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22116 Z= 0.156 Angle : 0.647 13.366 31129 Z= 0.345 Chirality : 0.038 0.292 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.050 167.341 5295 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.03 % Allowed : 21.94 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1825 helix: 1.49 (0.17), residues: 1047 sheet: -2.01 (0.46), residues: 126 loop : -1.51 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 262 TYR 0.022 0.001 TYR N 499 PHE 0.020 0.001 PHE N 234 TRP 0.026 0.002 TRP N 267 HIS 0.005 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00353 (22116) covalent geometry : angle 0.64703 (31129) hydrogen bonds : bond 0.04693 ( 1073) hydrogen bonds : angle 3.50780 ( 2808) ********************** 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 204 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8864 (tm) REVERT: A 94 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8490 (mm-30) REVERT: B 59 LYS cc_start: 0.9117 (tttp) cc_final: 0.8770 (tttm) REVERT: D 90 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: E 59 GLU cc_start: 0.8345 (pm20) cc_final: 0.8003 (pm20) REVERT: E 68 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: E 106 ASP cc_start: 0.8293 (m-30) cc_final: 0.8002 (m-30) REVERT: E 120 MET cc_start: 0.8056 (mtt) cc_final: 0.7760 (mtt) REVERT: F 93 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: G 36 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8853 (mmpt) REVERT: G 104 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8735 (mm110) REVERT: H 39 TYR cc_start: 0.8696 (t80) cc_final: 0.8432 (t80) REVERT: H 90 GLU cc_start: 0.8931 (mp0) cc_final: 0.8525 (mp0) REVERT: K 108 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.8443 (ptp-110) REVERT: K 279 ASP cc_start: 0.7924 (p0) cc_final: 0.7616 (p0) REVERT: K 609 MET cc_start: 0.8732 (ptt) cc_final: 0.8416 (ptt) REVERT: K 722 LEU cc_start: 0.7973 (mm) cc_final: 0.7743 (mm) REVERT: N 221 ASP cc_start: 0.6395 (m-30) cc_final: 0.5960 (m-30) REVERT: N 433 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7376 (tmm) REVERT: N 527 MET cc_start: 0.8290 (mtp) cc_final: 0.7776 (ttm) REVERT: N 606 LEU cc_start: 0.8805 (mt) cc_final: 0.8554 (tm) REVERT: N 645 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8666 (ttp80) outliers start: 33 outliers final: 19 residues processed: 194 average time/residue: 0.7124 time to fit residues: 155.7886 Evaluate side-chains 187 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 D residue 90 GLU 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 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 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain N residue 363 LEU Chi-restraints excluded: chain N residue 433 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 185 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 201 optimal weight: 0.0980 chunk 124 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 158 optimal weight: 0.0050 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 44 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN ** 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 = 0.3868 r_free = 0.3868 target = 0.096131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069453 restraints weight = 62671.914| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.73 r_work: 0.3146 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22116 Z= 0.139 Angle : 0.644 13.691 31129 Z= 0.340 Chirality : 0.037 0.287 3509 Planarity : 0.004 0.053 2931 Dihedral : 27.919 167.788 5295 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.41 % Allowed : 22.50 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1825 helix: 1.53 (0.17), residues: 1051 sheet: -1.95 (0.46), residues: 126 loop : -1.47 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 262 TYR 0.026 0.001 TYR N 199 PHE 0.033 0.002 PHE N 122 TRP 0.023 0.002 TRP N 384 HIS 0.006 0.001 HIS N 211 Details of bonding type rmsd covalent geometry : bond 0.00308 (22116) covalent geometry : angle 0.64420 (31129) hydrogen bonds : bond 0.04429 ( 1073) hydrogen bonds : angle 3.43533 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6918.58 seconds wall clock time: 118 minutes 32.17 seconds (7112.17 seconds total)