Starting phenix.real_space_refine on Fri Aug 7 15:42:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9v_40250/08_2026/8s9v_40250.cif" } resolution = 3.0 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= 0.075 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: 7 Type Number sf(0) Gaussians P 70 5.49 5 Mg 5 5.21 5 S 50 5.16 5 C 14003 2.51 5 N 3982 2.21 5 O 4525 1.98 5 H 38 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22673 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5982 Classifications: {'peptide': 767} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 732} Chain breaks: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4272 Classifications: {'peptide': 543} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 526} Chain breaks: 2 Chain: "D" Number of atoms: 3967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3967 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 25, 'TRANS': 492} Chain: "E" Number of atoms: 5455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5455 Classifications: {'peptide': 678} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 634} Chain breaks: 1 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 18} Chain: "G" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 18} Link IDs: {'rna2p': 8, 'rna3p': 25} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 30 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 4.21, per 1000 atoms: 0.19 Number of scatterers: 22673 At special positions: 0 Unit cell: (107.483, 120.814, 188.303, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 50 16.00 P 70 15.00 Mg 5 11.99 O 4525 8.00 N 3982 7.00 C 14003 6.00 H 38 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 867.4 milliseconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 38 sheets defined 36.6% alpha, 21.2% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.679A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.501A pdb=" N ILE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.578A pdb=" N ILE A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 396 through 399 Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.608A pdb=" N LYS A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.511A pdb=" N LYS A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 508 Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 589 through 594 removed outlier: 3.587A pdb=" N SER A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 649 removed outlier: 3.566A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 670 through 682 removed outlier: 3.512A pdb=" N VAL A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 689 through 702 removed outlier: 3.692A pdb=" N VAL A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 715 through 726 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.679A pdb=" N THR A 742 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 780 removed outlier: 5.413A pdb=" N ALA A 757 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'C' and resid 10 through 17 removed outlier: 3.658A pdb=" N SER C 17 " --> pdb=" O HIS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 35 removed outlier: 4.164A pdb=" N THR C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.032A pdb=" N PHE C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 135 through 154 removed outlier: 3.882A pdb=" N GLU C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 204 through 214 removed outlier: 4.352A pdb=" N LYS C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 318 through 337 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.724A pdb=" N VAL C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.589A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.576A pdb=" N LEU C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.800A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.665A pdb=" N ALA C 488 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR C 494 " --> pdb=" O ARG C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.887A pdb=" N PHE C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 75 removed outlier: 4.017A pdb=" N ILE D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 206 through 212 removed outlier: 3.674A pdb=" N LEU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 284 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.643A pdb=" N VAL D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.618A pdb=" N ALA D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 416 through 424 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 430 through 447 removed outlier: 4.260A pdb=" N ALA D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 483 Processing helix chain 'D' and resid 495 through 511 Processing helix chain 'E' and resid 130 through 134 removed outlier: 4.201A pdb=" N LEU E 133 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 210 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 260 through 264 removed outlier: 4.061A pdb=" N ASN E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 394 removed outlier: 3.797A pdb=" N HIS E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.591A pdb=" N ILE E 418 " --> pdb=" O SER E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.529A pdb=" N LEU E 466 " --> pdb=" O VAL E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 4.147A pdb=" N LEU E 479 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 590 through 594 removed outlier: 4.234A pdb=" N GLN E 593 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 599 Processing helix chain 'E' and resid 641 through 653 Processing helix chain 'E' and resid 665 through 669 Processing helix chain 'E' and resid 679 through 682 Processing helix chain 'E' and resid 687 through 694 removed outlier: 3.642A pdb=" N ASP E 692 " --> pdb=" O ALA E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 707 Processing helix chain 'E' and resid 708 through 724 Processing helix chain 'E' and resid 732 through 744 Processing helix chain 'E' and resid 766 through 776 removed outlier: 4.036A pdb=" N PHE E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 5.236A pdb=" N GLU A 157 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 101 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR A 155 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 103 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS A 153 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 130 removed outlier: 5.919A pdb=" N PHE A 141 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 305 removed outlier: 6.802A pdb=" N THR A 412 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 309 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 265 removed outlier: 3.751A pdb=" N ARG A 263 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS A 271 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 407 " --> pdb=" O CYS A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.723A pdb=" N TYR A 360 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.714A pdb=" N ARG A 393 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.630A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.630A pdb=" N LYS A 510 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.679A pdb=" N LEU A 538 " --> pdb=" O GLN A 533 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 661 through 663 Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49 removed outlier: 3.552A pdb=" N GLU B 72 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY B 92 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 123 removed outlier: 6.690A pdb=" N ARG B 162 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU B 191 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 164 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS B 189 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR B 166 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU B 187 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU B 168 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU B 185 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR B 170 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'C' and resid 82 through 88 removed outlier: 6.641A pdb=" N ILE C 93 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 87 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 121 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 7.635A pdb=" N ILE C 300 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG C 315 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 313 " --> pdb=" O PRO C 302 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C 354 " --> pdb=" O ASN C 242 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 404 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC3, first strand: chain 'D' and resid 87 through 89 removed outlier: 3.664A pdb=" N GLY D 13 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 8 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER D 185 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS D 10 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 183 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 12 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU D 181 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU D 183 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'D' and resid 103 through 110 removed outlier: 10.719A pdb=" N GLU D 103 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N SER D 124 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N ARG D 105 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N LYS D 122 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N GLY D 107 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLY D 120 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLY D 109 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.040A pdb=" N ASN D 229 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL D 465 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 251 through 254 removed outlier: 3.758A pdb=" N ASP D 257 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 311 through 312 Processing sheet with id=AC9, first strand: chain 'D' and resid 378 through 383 Processing sheet with id=AD1, first strand: chain 'E' and resid 750 through 751 removed outlier: 4.076A pdb=" N SER E 750 " --> pdb=" O ASN E 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AD3, first strand: chain 'E' and resid 501 through 508 removed outlier: 4.183A pdb=" N VAL E 506 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR E 632 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS E 508 " --> pdb=" O GLU E 630 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU E 630 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 501 through 508 removed outlier: 4.183A pdb=" N VAL E 506 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR E 632 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS E 508 " --> pdb=" O GLU E 630 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU E 630 " --> pdb=" O CYS E 508 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TYR E 149 " --> pdb=" O ASN E 639 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 172 through 174 Processing sheet with id=AD6, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AD7, first strand: chain 'E' and resid 371 through 374 removed outlier: 6.729A pdb=" N TYR E 433 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU E 448 " --> pdb=" O TYR E 433 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS E 435 " --> pdb=" O LEU E 446 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 269 through 272 removed outlier: 7.104A pdb=" N TRP E 270 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLN E 314 " --> pdb=" O TRP E 270 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 316 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP E 298 " --> pdb=" O ARG E 313 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE E 315 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG E 296 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ARG E 317 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N HIS E 294 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 362 " --> pdb=" O TYR E 349 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 487 through 489 Processing sheet with id=AE1, first strand: chain 'E' and resid 514 through 516 removed outlier: 3.596A pdb=" N TRP E 624 " --> pdb=" O ASP E 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 548 through 549 removed outlier: 6.472A pdb=" N ILE E 548 " --> pdb=" O ASP E 543 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 38 1.03 - 1.23: 827 1.23 - 1.42: 9166 1.42 - 1.62: 13150 1.62 - 1.81: 72 Bond restraints: 23253 Sorted by residual: bond pdb=" N1 C F 24 " pdb=" C6 C F 24 " ideal model delta sigma weight residual 1.367 1.333 0.034 6.00e-03 2.78e+04 3.28e+01 bond pdb=" C5 G G 33 " pdb=" C4 G G 33 " ideal model delta sigma weight residual 1.379 1.343 0.036 7.00e-03 2.04e+04 2.70e+01 bond pdb=" C5 A F 12 " pdb=" C4 A F 12 " ideal model delta sigma weight residual 1.383 1.348 0.035 7.00e-03 2.04e+04 2.45e+01 bond pdb=" C5 A F 18 " pdb=" C4 A F 18 " ideal model delta sigma weight residual 1.383 1.349 0.034 7.00e-03 2.04e+04 2.38e+01 bond pdb=" N9 A F 12 " pdb=" C8 A F 12 " ideal model delta sigma weight residual 1.373 1.334 0.039 8.00e-03 1.56e+04 2.33e+01 ... (remaining 23248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 31357 3.73 - 7.46: 410 7.46 - 11.19: 19 11.19 - 14.93: 2 14.93 - 18.66: 1 Bond angle restraints: 31789 Sorted by residual: angle pdb=" O5' U F 32 " pdb=" C5' U F 32 " pdb=" C4' U F 32 " ideal model delta sigma weight residual 109.40 117.56 -8.16 8.00e-01 1.56e+00 1.04e+02 angle pdb=" O5' C F 30 " pdb=" C5' C F 30 " pdb=" C4' C F 30 " ideal model delta sigma weight residual 109.40 116.84 -7.44 8.00e-01 1.56e+00 8.66e+01 angle pdb=" O4' G F 27 " pdb=" C1' G F 27 " pdb=" N9 G F 27 " ideal model delta sigma weight residual 108.20 115.24 -7.04 8.00e-01 1.56e+00 7.74e+01 angle pdb=" O5' C F 2 " pdb=" C5' C F 2 " pdb=" C4' C F 2 " ideal model delta sigma weight residual 109.40 116.06 -6.66 8.00e-01 1.56e+00 6.94e+01 angle pdb=" O5' A G 25 " pdb=" C5' A G 25 " pdb=" C4' A G 25 " ideal model delta sigma weight residual 109.40 115.64 -6.24 8.00e-01 1.56e+00 6.09e+01 ... (remaining 31784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 13648 35.85 - 71.70: 361 71.70 - 107.54: 44 107.54 - 143.39: 6 143.39 - 179.24: 3 Dihedral angle restraints: 14062 sinusoidal: 6367 harmonic: 7695 Sorted by residual: dihedral pdb=" O4' C F 2 " pdb=" C1' C F 2 " pdb=" N1 C F 2 " pdb=" C2 C F 2 " ideal model delta sinusoidal sigma weight residual 232.00 52.76 179.24 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual 232.00 61.72 170.28 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C5' G G 24 " pdb=" C4' G G 24 " pdb=" C3' G G 24 " pdb=" O3' G G 24 " ideal model delta sinusoidal sigma weight residual 147.00 98.82 48.18 1 8.00e+00 1.56e-02 5.00e+01 ... (remaining 14059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2556 0.078 - 0.156: 884 0.156 - 0.234: 93 0.234 - 0.311: 12 0.311 - 0.389: 3 Chirality restraints: 3548 Sorted by residual: chirality pdb=" C3' U G 50 " pdb=" C4' U G 50 " pdb=" O3' U G 50 " pdb=" C2' U G 50 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C4' G G 24 " pdb=" C5' G G 24 " pdb=" O4' G G 24 " pdb=" C3' G G 24 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA ARG C 436 " pdb=" N ARG C 436 " pdb=" C ARG C 436 " pdb=" CB ARG C 436 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 3545 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 19 " 0.055 2.00e-02 2.50e+03 2.98e-02 2.00e+01 pdb=" N1 C F 19 " -0.068 2.00e-02 2.50e+03 pdb=" C2 C F 19 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C F 19 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C F 19 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C F 19 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C F 19 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C F 19 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C F 19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 419 " 0.317 9.50e-02 1.11e+02 1.44e-01 1.82e+01 pdb=" NE ARG D 419 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG D 419 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG D 419 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 419 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 27 " -0.051 2.00e-02 2.50e+03 2.45e-02 1.79e+01 pdb=" N9 G F 27 " 0.066 2.00e-02 2.50e+03 pdb=" C8 G F 27 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G F 27 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G F 27 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G F 27 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G F 27 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G F 27 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G F 27 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G F 27 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G F 27 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G F 27 " 0.000 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 112 2.16 - 2.77: 4660 2.77 - 3.38: 25643 3.38 - 3.99: 46023 3.99 - 4.60: 70712 Nonbonded interactions: 147150 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" H2 HOH D 702 " model vdw 1.551 1.700 nonbonded pdb="MG MG A 802 " pdb=" H2 HOH A 902 " model vdw 1.551 1.700 nonbonded pdb="MG MG D 601 " pdb=" H2 HOH A 906 " model vdw 1.574 1.700 nonbonded pdb="MG MG D 602 " pdb=" H2 HOH D 703 " model vdw 1.583 1.700 nonbonded pdb="MG MG A 801 " pdb=" O HOH A 904 " model vdw 1.605 2.050 ... (remaining 147145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.800 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: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 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 : 0.015 0.114 23215 Z= 0.773 Angle : 1.138 18.658 31770 Z= 0.692 Chirality : 0.073 0.389 3548 Planarity : 0.010 0.144 3898 Dihedral : 16.147 179.238 9130 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.57 % Favored : 96.13 % Rotamer: Outliers : 2.08 % Allowed : 3.94 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 2664 helix: -1.18 (0.15), residues: 797 sheet: 0.17 (0.23), residues: 484 loop : -0.27 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.006 ARG E 604 TYR 0.038 0.006 TYR E 458 PHE 0.037 0.004 PHE C 400 TRP 0.041 0.005 TRP A 14 HIS 0.012 0.003 HIS C 487 Details of bonding type rmsd/Z covalent geometry : bond 0.01518 / 0.77 (23215) covalent geometry : angle 1.13809 / 0.69 (31770) hydrogen bonds : bond 0.20384 / 13.46 ( 935) hydrogen bonds : angle 8.41351 / 5.95 ( 2569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 638 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: D 16 ILE cc_start: 0.8624 (mp) cc_final: 0.8390 (pt) REVERT: D 209 GLN cc_start: 0.7580 (tt0) cc_final: 0.7280 (mt0) REVERT: D 282 ILE cc_start: 0.8382 (mt) cc_final: 0.8086 (mt) REVERT: E 604 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7167 (ttp80) outliers start: 47 outliers final: 12 residues processed: 432 average time/residue: 0.6840 time to fit residues: 334.9490 Evaluate side-chains 189 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 604 ARG Chi-restraints excluded: chain E residue 771 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN A 779 GLN B 16 GLN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 223 GLN C 246 GLN C 408 HIS D 98 ASN D 213 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN E 425 ASN E 746 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096807 restraints weight = 31589.848| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.66 r_work: 0.3002 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23215 Z= 0.145 Angle : 0.599 7.230 31770 Z= 0.330 Chirality : 0.043 0.314 3548 Planarity : 0.004 0.052 3898 Dihedral : 15.393 170.326 4015 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.44 % Favored : 97.41 % Rotamer: Outliers : 3.27 % Allowed : 11.76 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2664 helix: 0.54 (0.18), residues: 805 sheet: 0.11 (0.23), residues: 465 loop : -0.07 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 514 TYR 0.019 0.002 TYR E 458 PHE 0.015 0.001 PHE E 633 TRP 0.018 0.002 TRP A 68 HIS 0.013 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (23215) covalent geometry : angle 0.59922 / 0.33 (31770) hydrogen bonds : bond 0.05235 / 3.46 ( 935) hydrogen bonds : angle 5.78414 / 4.09 ( 2569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 243 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8968 (tt0) cc_final: 0.8745 (tt0) REVERT: A 198 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8305 (ttp-170) REVERT: A 335 LYS cc_start: 0.7668 (mptt) cc_final: 0.7371 (mppt) REVERT: A 512 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8113 (pptt) REVERT: A 638 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: A 678 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7974 (ttm170) REVERT: A 694 THR cc_start: 0.8486 (m) cc_final: 0.8211 (p) REVERT: A 765 ASP cc_start: 0.8248 (t70) cc_final: 0.7903 (t70) REVERT: B 23 SER cc_start: 0.8955 (t) cc_final: 0.8700 (t) REVERT: D 189 ASP cc_start: 0.8477 (t0) cc_final: 0.8007 (t0) REVERT: D 209 GLN cc_start: 0.7843 (tt0) cc_final: 0.7492 (tt0) REVERT: E 227 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7493 (mpt) REVERT: E 296 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.8163 (ptp-110) REVERT: E 318 HIS cc_start: 0.6201 (t-90) cc_final: 0.5347 (t-90) REVERT: E 409 ASN cc_start: 0.6807 (t0) cc_final: 0.6602 (t0) REVERT: E 477 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8381 (mmmt) REVERT: E 529 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8213 (mt) outliers start: 74 outliers final: 29 residues processed: 294 average time/residue: 0.5942 time to fit residues: 200.3724 Evaluate side-chains 221 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 678 ARG Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 680 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 90 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 209 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 116 ASN C 246 GLN C 408 HIS D 98 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN E 244 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 425 ASN E 447 ASN E 746 HIS E 748 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092174 restraints weight = 32126.752| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.65 r_work: 0.2929 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 23215 Z= 0.322 Angle : 0.678 7.383 31770 Z= 0.360 Chirality : 0.049 0.267 3548 Planarity : 0.005 0.054 3898 Dihedral : 15.170 178.024 4006 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.79 % Favored : 96.06 % Rotamer: Outliers : 4.47 % Allowed : 13.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2664 helix: 0.71 (0.18), residues: 801 sheet: -0.07 (0.23), residues: 469 loop : -0.28 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 419 TYR 0.024 0.002 TYR E 458 PHE 0.020 0.002 PHE E 790 TRP 0.019 0.002 TRP A 68 HIS 0.014 0.002 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.32 (23215) covalent geometry : angle 0.67795 / 0.36 (31770) hydrogen bonds : bond 0.05167 / 3.37 ( 935) hydrogen bonds : angle 5.54935 / 3.93 ( 2569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 185 time to evaluate : 0.781 Fit side-chains REVERT: A 112 GLN cc_start: 0.9041 (tt0) cc_final: 0.8810 (tt0) REVERT: A 198 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8289 (ttp-170) REVERT: A 209 GLN cc_start: 0.8111 (tp40) cc_final: 0.7779 (tm-30) REVERT: A 335 LYS cc_start: 0.7885 (mptt) cc_final: 0.7581 (mppt) REVERT: A 630 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 678 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8138 (ttm170) REVERT: A 694 THR cc_start: 0.8584 (m) cc_final: 0.8285 (p) REVERT: A 754 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: A 765 ASP cc_start: 0.8380 (t70) cc_final: 0.7951 (t70) REVERT: B 23 SER cc_start: 0.8976 (t) cc_final: 0.8763 (t) REVERT: D 3 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7139 (ttt180) REVERT: D 189 ASP cc_start: 0.8544 (t0) cc_final: 0.8118 (t0) REVERT: D 254 VAL cc_start: 0.8222 (t) cc_final: 0.8014 (p) REVERT: E 288 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6404 (tpp) REVERT: E 296 ARG cc_start: 0.8484 (ptp-110) cc_final: 0.8134 (mtp-110) REVERT: E 318 HIS cc_start: 0.6617 (t-90) cc_final: 0.5685 (t-170) REVERT: E 320 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6495 (mp10) REVERT: E 369 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: E 377 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6338 (tpp-160) REVERT: E 529 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8508 (mm) outliers start: 101 outliers final: 52 residues processed: 258 average time/residue: 0.5451 time to fit residues: 162.4465 Evaluate side-chains 224 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 678 ARG Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 408 HIS D 98 ASN D 201 GLN D 412 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS ** E 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096461 restraints weight = 31947.288| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.72 r_work: 0.2985 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23215 Z= 0.114 Angle : 0.500 19.779 31770 Z= 0.270 Chirality : 0.040 0.222 3548 Planarity : 0.003 0.042 3898 Dihedral : 14.894 175.316 4003 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.00 % Favored : 96.85 % Rotamer: Outliers : 3.01 % Allowed : 15.66 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2664 helix: 1.38 (0.19), residues: 803 sheet: -0.05 (0.23), residues: 472 loop : -0.13 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.012 0.001 TYR E 302 PHE 0.010 0.001 PHE E 633 TRP 0.015 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23215) covalent geometry : angle 0.50019 / 0.27 (31770) hydrogen bonds : bond 0.03982 / 2.62 ( 935) hydrogen bonds : angle 5.02358 / 3.57 ( 2569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.6624 (mt0) cc_final: 0.6375 (mt0) REVERT: A 335 LYS cc_start: 0.7844 (mptt) cc_final: 0.7611 (mppt) REVERT: A 474 THR cc_start: 0.8842 (p) cc_final: 0.8556 (t) REVERT: A 625 GLN cc_start: 0.8656 (tt0) cc_final: 0.8411 (tt0) REVERT: A 678 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8025 (ttm170) REVERT: A 694 THR cc_start: 0.8409 (m) cc_final: 0.8062 (p) REVERT: A 765 ASP cc_start: 0.8321 (t70) cc_final: 0.8066 (m-30) REVERT: C 210 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6299 (tp) REVERT: C 231 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7399 (mp) REVERT: D 70 ILE cc_start: 0.9059 (mm) cc_final: 0.8827 (mt) REVERT: D 189 ASP cc_start: 0.8469 (t0) cc_final: 0.8093 (t0) REVERT: D 201 GLN cc_start: 0.6814 (tm130) cc_final: 0.6241 (tm-30) REVERT: E 296 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8182 (mtp-110) REVERT: E 318 HIS cc_start: 0.6884 (t-90) cc_final: 0.6681 (t-170) REVERT: E 377 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6128 (tpp-160) REVERT: E 548 ILE cc_start: 0.8489 (mt) cc_final: 0.8231 (tp) outliers start: 68 outliers final: 29 residues processed: 241 average time/residue: 0.6053 time to fit residues: 168.2756 Evaluate side-chains 201 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 678 ARG Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 269 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 493 ASN A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 213 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS ** E 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092857 restraints weight = 31675.516| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.66 r_work: 0.2935 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 23215 Z= 0.245 Angle : 0.582 8.294 31770 Z= 0.309 Chirality : 0.045 0.236 3548 Planarity : 0.004 0.049 3898 Dihedral : 14.797 178.196 4000 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.68 % Rotamer: Outliers : 3.89 % Allowed : 15.75 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2664 helix: 1.33 (0.19), residues: 796 sheet: -0.21 (0.23), residues: 478 loop : -0.23 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.018 0.002 TYR E 458 PHE 0.016 0.002 PHE E 633 TRP 0.016 0.002 TRP A 68 HIS 0.005 0.001 HIS C 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.25 (23215) covalent geometry : angle 0.58194 / 0.31 (31770) hydrogen bonds : bond 0.04385 / 2.86 ( 935) hydrogen bonds : angle 5.08890 / 3.62 ( 2569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 169 time to evaluate : 0.872 Fit side-chains REVERT: A 229 GLN cc_start: 0.6807 (mt0) cc_final: 0.6541 (mt0) REVERT: A 335 LYS cc_start: 0.7931 (mptt) cc_final: 0.7717 (mppt) REVERT: A 474 THR cc_start: 0.8874 (p) cc_final: 0.8581 (t) REVERT: A 568 GLU cc_start: 0.7820 (tp30) cc_final: 0.7563 (tp30) REVERT: A 625 GLN cc_start: 0.8768 (tt0) cc_final: 0.8532 (tt0) REVERT: A 638 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: A 765 ASP cc_start: 0.8452 (t70) cc_final: 0.8109 (OUTLIER) REVERT: D 81 LYS cc_start: 0.8818 (mttt) cc_final: 0.8450 (mmtm) REVERT: D 189 ASP cc_start: 0.8494 (t0) cc_final: 0.8071 (t0) REVERT: D 201 GLN cc_start: 0.6943 (tm130) cc_final: 0.6370 (tm-30) REVERT: D 496 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: E 288 MET cc_start: 0.6705 (tpt) cc_final: 0.6405 (tpp) REVERT: E 296 ARG cc_start: 0.8527 (ptp-110) cc_final: 0.8155 (mtp-110) REVERT: E 317 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7187 (mpp80) REVERT: E 377 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6196 (tpp-160) REVERT: E 548 ILE cc_start: 0.8524 (mt) cc_final: 0.8239 (tp) outliers start: 88 outliers final: 60 residues processed: 235 average time/residue: 0.5822 time to fit residues: 159.2421 Evaluate side-chains 230 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 73 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS ** E 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095469 restraints weight = 31737.119| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.71 r_work: 0.2972 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23215 Z= 0.123 Angle : 0.473 5.999 31770 Z= 0.259 Chirality : 0.040 0.222 3548 Planarity : 0.003 0.042 3898 Dihedral : 14.684 175.844 4000 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Rotamer: Outliers : 2.92 % Allowed : 16.85 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2664 helix: 1.63 (0.19), residues: 797 sheet: -0.21 (0.24), residues: 463 loop : -0.16 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.020 0.001 TYR D 221 PHE 0.012 0.001 PHE D 134 TRP 0.015 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23215) covalent geometry : angle 0.47299 / 0.26 (31770) hydrogen bonds : bond 0.03781 / 2.48 ( 935) hydrogen bonds : angle 4.83442 / 3.45 ( 2569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.6819 (mt0) cc_final: 0.6566 (mt0) REVERT: A 335 LYS cc_start: 0.7928 (mptt) cc_final: 0.7704 (mppt) REVERT: A 474 THR cc_start: 0.8852 (p) cc_final: 0.8588 (t) REVERT: A 568 GLU cc_start: 0.7853 (tp30) cc_final: 0.7554 (tp30) REVERT: A 625 GLN cc_start: 0.8686 (tt0) cc_final: 0.8475 (tt0) REVERT: A 638 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: A 765 ASP cc_start: 0.8383 (t70) cc_final: 0.8067 (m-30) REVERT: C 210 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6352 (tp) REVERT: C 230 GLU cc_start: 0.7763 (pp20) cc_final: 0.7349 (pp20) REVERT: C 231 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7576 (mp) REVERT: C 490 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7835 (ttm-80) REVERT: D 81 LYS cc_start: 0.8796 (mttt) cc_final: 0.8381 (mmtm) REVERT: D 189 ASP cc_start: 0.8483 (t0) cc_final: 0.8065 (t0) REVERT: D 201 GLN cc_start: 0.6852 (tm130) cc_final: 0.6271 (tm-30) REVERT: E 288 MET cc_start: 0.6748 (tpt) cc_final: 0.6535 (tpp) REVERT: E 296 ARG cc_start: 0.8585 (ptp-110) cc_final: 0.8060 (ptp-110) REVERT: E 317 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6544 (mtp85) REVERT: E 320 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: E 377 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6129 (tpp-160) REVERT: E 548 ILE cc_start: 0.8483 (mt) cc_final: 0.8246 (tp) REVERT: E 681 LYS cc_start: 0.8225 (tptp) cc_final: 0.7856 (mtmt) outliers start: 66 outliers final: 34 residues processed: 234 average time/residue: 0.6488 time to fit residues: 174.7729 Evaluate side-chains 211 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 318 HIS Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 709 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 132 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 167 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 151 optimal weight: 0.0170 overall best weight: 0.4828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098620 restraints weight = 31669.435| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.67 r_work: 0.3043 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23215 Z= 0.091 Angle : 0.427 6.179 31770 Z= 0.233 Chirality : 0.038 0.225 3548 Planarity : 0.003 0.034 3898 Dihedral : 14.573 170.922 3995 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 2.17 % Allowed : 17.87 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2664 helix: 2.01 (0.19), residues: 810 sheet: -0.14 (0.23), residues: 480 loop : 0.05 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 239 TYR 0.011 0.001 TYR D 366 PHE 0.008 0.001 PHE C 366 TRP 0.014 0.001 TRP A 532 HIS 0.007 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (23215) covalent geometry : angle 0.42664 / 0.23 (31770) hydrogen bonds : bond 0.03265 / 2.16 ( 935) hydrogen bonds : angle 4.51008 / 3.22 ( 2569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7194 (mmt-90) cc_final: 0.6619 (mmp-170) REVERT: A 229 GLN cc_start: 0.6795 (mt0) cc_final: 0.6569 (mt0) REVERT: A 335 LYS cc_start: 0.7938 (mptt) cc_final: 0.7618 (mppt) REVERT: A 456 GLU cc_start: 0.8379 (tt0) cc_final: 0.8120 (tp30) REVERT: A 474 THR cc_start: 0.8816 (p) cc_final: 0.8594 (t) REVERT: A 568 GLU cc_start: 0.7818 (tp30) cc_final: 0.7431 (tp30) REVERT: A 625 GLN cc_start: 0.8531 (tt0) cc_final: 0.8309 (tt0) REVERT: A 638 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: C 142 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7721 (ttmt) REVERT: C 210 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6241 (tp) REVERT: C 230 GLU cc_start: 0.7762 (pp20) cc_final: 0.7468 (pp20) REVERT: C 231 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7432 (mp) REVERT: C 490 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7758 (ttm-80) REVERT: D 70 ILE cc_start: 0.9029 (mm) cc_final: 0.8650 (mt) REVERT: D 81 LYS cc_start: 0.8719 (mttt) cc_final: 0.8289 (mmtm) REVERT: D 189 ASP cc_start: 0.8432 (t0) cc_final: 0.8007 (t0) REVERT: D 201 GLN cc_start: 0.6666 (tm130) cc_final: 0.6067 (tm-30) REVERT: D 496 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: E 288 MET cc_start: 0.6718 (tpt) cc_final: 0.6454 (tpp) REVERT: E 317 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6972 (mpp80) REVERT: E 377 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6146 (tpp-160) REVERT: E 444 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6845 (ptpt) REVERT: E 548 ILE cc_start: 0.8417 (mt) cc_final: 0.8210 (tp) REVERT: E 561 SER cc_start: 0.8861 (t) cc_final: 0.8621 (p) REVERT: E 681 LYS cc_start: 0.8184 (tptp) cc_final: 0.7900 (ttmt) REVERT: E 714 ASN cc_start: 0.7868 (m-40) cc_final: 0.7658 (m-40) outliers start: 49 outliers final: 24 residues processed: 233 average time/residue: 0.6545 time to fit residues: 176.1788 Evaluate side-chains 214 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 172 optimal weight: 0.2980 chunk 250 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 246 GLN D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS ** E 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093606 restraints weight = 31902.187| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.75 r_work: 0.2934 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23215 Z= 0.256 Angle : 0.561 5.795 31770 Z= 0.296 Chirality : 0.044 0.231 3548 Planarity : 0.004 0.044 3898 Dihedral : 14.623 175.559 3995 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 3.05 % Allowed : 17.65 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2664 helix: 1.75 (0.19), residues: 798 sheet: -0.21 (0.23), residues: 481 loop : -0.11 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 263 TYR 0.017 0.002 TYR C 511 PHE 0.016 0.002 PHE D 134 TRP 0.014 0.002 TRP A 68 HIS 0.005 0.001 HIS C 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (23215) covalent geometry : angle 0.56083 / 0.30 (31770) hydrogen bonds : bond 0.04081 / 2.65 ( 935) hydrogen bonds : angle 4.81980 / 3.44 ( 2569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 180 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.6871 (mt0) cc_final: 0.6647 (mt0) REVERT: A 335 LYS cc_start: 0.8007 (mptt) cc_final: 0.7673 (mppt) REVERT: A 456 GLU cc_start: 0.8428 (tt0) cc_final: 0.8150 (tp30) REVERT: A 474 THR cc_start: 0.8871 (p) cc_final: 0.8593 (t) REVERT: A 625 GLN cc_start: 0.8714 (tt0) cc_final: 0.8493 (tt0) REVERT: A 638 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: C 490 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7804 (ttm-80) REVERT: D 81 LYS cc_start: 0.8822 (mttt) cc_final: 0.8399 (mmtm) REVERT: D 189 ASP cc_start: 0.8481 (t0) cc_final: 0.8038 (t0) REVERT: D 201 GLN cc_start: 0.6838 (tm130) cc_final: 0.6266 (tm-30) REVERT: D 496 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: E 288 MET cc_start: 0.6800 (tpt) cc_final: 0.6562 (tpp) REVERT: E 377 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6249 (tpp-160) REVERT: E 548 ILE cc_start: 0.8498 (mt) cc_final: 0.8249 (tp) REVERT: E 561 SER cc_start: 0.8925 (t) cc_final: 0.8686 (p) REVERT: E 681 LYS cc_start: 0.8281 (tptp) cc_final: 0.7970 (ttmt) outliers start: 69 outliers final: 44 residues processed: 226 average time/residue: 0.5370 time to fit residues: 140.9595 Evaluate side-chains 222 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095967 restraints weight = 31788.312| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.74 r_work: 0.2965 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23215 Z= 0.119 Angle : 0.469 5.991 31770 Z= 0.254 Chirality : 0.040 0.220 3548 Planarity : 0.003 0.040 3898 Dihedral : 14.592 173.953 3995 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 18.89 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2664 helix: 1.88 (0.19), residues: 803 sheet: -0.20 (0.23), residues: 476 loop : -0.05 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 263 TYR 0.010 0.001 TYR A 554 PHE 0.010 0.001 PHE E 633 TRP 0.016 0.001 TRP A 68 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (23215) covalent geometry : angle 0.46944 / 0.25 (31770) hydrogen bonds : bond 0.03641 / 2.37 ( 935) hydrogen bonds : angle 4.68362 / 3.34 ( 2569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.6922 (mt0) cc_final: 0.6693 (mt0) REVERT: A 335 LYS cc_start: 0.8009 (mptt) cc_final: 0.7698 (mppt) REVERT: A 456 GLU cc_start: 0.8423 (tt0) cc_final: 0.8172 (tp30) REVERT: A 474 THR cc_start: 0.8851 (p) cc_final: 0.8613 (t) REVERT: A 638 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: C 210 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6364 (tp) REVERT: C 490 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: D 81 LYS cc_start: 0.8784 (mttt) cc_final: 0.8371 (mmtm) REVERT: D 189 ASP cc_start: 0.8450 (t0) cc_final: 0.8025 (t0) REVERT: D 201 GLN cc_start: 0.6773 (tm130) cc_final: 0.6202 (tm-30) REVERT: E 288 MET cc_start: 0.6825 (tpt) cc_final: 0.6555 (tpp) REVERT: E 317 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6608 (mpp80) REVERT: E 377 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6165 (tpp-160) REVERT: E 548 ILE cc_start: 0.8478 (mt) cc_final: 0.8243 (tp) REVERT: E 561 SER cc_start: 0.8939 (t) cc_final: 0.8685 (p) REVERT: E 681 LYS cc_start: 0.8245 (tptp) cc_final: 0.7952 (ttmt) outliers start: 46 outliers final: 33 residues processed: 210 average time/residue: 0.5139 time to fit residues: 125.5971 Evaluate side-chains 212 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 85 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 162 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 225 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 213 ASN D 253 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS ** E 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098113 restraints weight = 31781.379| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.59 r_work: 0.2992 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23215 Z= 0.092 Angle : 0.441 6.215 31770 Z= 0.241 Chirality : 0.039 0.222 3548 Planarity : 0.003 0.037 3898 Dihedral : 14.561 172.020 3995 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 1.99 % Allowed : 19.06 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2664 helix: 2.02 (0.19), residues: 810 sheet: -0.18 (0.24), residues: 467 loop : -0.01 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.034 0.001 TYR A 502 PHE 0.009 0.001 PHE E 633 TRP 0.015 0.001 TRP A 68 HIS 0.006 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (23215) covalent geometry : angle 0.44113 / 0.24 (31770) hydrogen bonds : bond 0.03431 / 2.26 ( 935) hydrogen bonds : angle 4.55979 / 3.25 ( 2569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.6916 (mt0) cc_final: 0.6613 (mt0) REVERT: A 335 LYS cc_start: 0.7988 (mptt) cc_final: 0.7681 (mppt) REVERT: A 456 GLU cc_start: 0.8458 (tt0) cc_final: 0.8204 (tp30) REVERT: A 474 THR cc_start: 0.8828 (p) cc_final: 0.8604 (t) REVERT: A 638 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: C 210 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6305 (tp) REVERT: C 490 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: D 81 LYS cc_start: 0.8761 (mttt) cc_final: 0.8364 (mmtm) REVERT: D 189 ASP cc_start: 0.8443 (t0) cc_final: 0.8035 (t0) REVERT: D 201 GLN cc_start: 0.6725 (tm130) cc_final: 0.6123 (tm-30) REVERT: E 277 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7654 (ptm160) REVERT: E 296 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8106 (ptp-110) REVERT: E 377 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6166 (tpp-160) REVERT: E 548 ILE cc_start: 0.8454 (mt) cc_final: 0.8237 (tp) REVERT: E 561 SER cc_start: 0.8895 (t) cc_final: 0.8673 (p) REVERT: E 681 LYS cc_start: 0.8207 (tptp) cc_final: 0.7933 (ttmt) outliers start: 45 outliers final: 33 residues processed: 207 average time/residue: 0.5640 time to fit residues: 135.0253 Evaluate side-chains 211 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 676 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 96 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095542 restraints weight = 31770.004| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.72 r_work: 0.2974 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23215 Z= 0.151 Angle : 0.467 6.108 31770 Z= 0.252 Chirality : 0.040 0.220 3548 Planarity : 0.003 0.038 3898 Dihedral : 14.563 172.503 3995 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.64 % Favored : 96.21 % Rotamer: Outliers : 2.26 % Allowed : 18.66 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2664 helix: 1.94 (0.19), residues: 814 sheet: -0.21 (0.23), residues: 484 loop : 0.00 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.019 0.001 TYR D 221 PHE 0.012 0.001 PHE E 633 TRP 0.013 0.001 TRP A 68 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (23215) covalent geometry : angle 0.46697 / 0.25 (31770) hydrogen bonds : bond 0.03568 / 2.34 ( 935) hydrogen bonds : angle 4.58220 / 3.27 ( 2569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6389.29 seconds wall clock time: 110 minutes 3.26 seconds (6603.26 seconds total)