Starting phenix.real_space_refine on Thu Jun 19 14:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9v_40250/06_2025/8s9v_40250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9v_40250/06_2025/8s9v_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_40250/06_2025/8s9v_40250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9v_40250/06_2025/8s9v_40250.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9v_40250/06_2025/8s9v_40250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9v_40250/06_2025/8s9v_40250.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.17, per 1000 atoms: 0.67 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: 6.54 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 8.70 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: 12.08 Time building geometry restraints manager: 7.69 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=" CB ARG A 192 " pdb=" CG ARG A 192 " ideal model delta sigma weight residual 1.520 1.406 0.114 3.00e-02 1.11e+03 1.44e+01 bond pdb=" CG1 ILE D 110 " pdb=" CD1 ILE D 110 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.81e+00 bond pdb=" CB ARG B 145 " pdb=" CG ARG B 145 " ideal model delta sigma weight residual 1.520 1.436 0.084 3.00e-02 1.11e+03 7.77e+00 bond pdb=" CG1 ILE A 387 " pdb=" CD1 ILE A 387 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.62e+00 bond pdb=" CB ILE D 324 " pdb=" CG2 ILE D 324 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.53e+00 ... (remaining 23248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 31371 3.73 - 7.46: 397 7.46 - 11.19: 18 11.19 - 14.93: 2 14.93 - 18.66: 1 Bond angle restraints: 31789 Sorted by residual: angle pdb=" N GLY A 17 " pdb=" CA GLY A 17 " pdb=" C GLY A 17 " ideal model delta sigma weight residual 115.08 123.69 -8.61 1.19e+00 7.06e-01 5.23e+01 angle pdb=" C GLY A 17 " pdb=" N THR A 18 " pdb=" CA THR A 18 " ideal model delta sigma weight residual 122.73 112.03 10.70 1.62e+00 3.81e-01 4.36e+01 angle pdb=" N LEU C 410 " pdb=" CA LEU C 410 " pdb=" C LEU C 410 " ideal model delta sigma weight residual 111.07 117.07 -6.00 1.07e+00 8.73e-01 3.14e+01 angle pdb=" N ARG C 436 " pdb=" CA ARG C 436 " pdb=" C ARG C 436 " ideal model delta sigma weight residual 109.81 121.95 -12.14 2.21e+00 2.05e-01 3.02e+01 angle pdb=" CA LEU C 231 " pdb=" CB LEU C 231 " pdb=" CG LEU C 231 " ideal model delta sigma weight residual 116.30 134.96 -18.66 3.50e+00 8.16e-02 2.84e+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: 2616 0.078 - 0.156: 832 0.156 - 0.234: 85 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: 7.490 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: 0.610 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 66.740 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.100 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:14.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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= 0.640 Angle : 1.122 18.658 31770 Z= 0.626 Chirality : 0.071 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.041 0.005 TRP A 14 HIS 0.012 0.003 HIS C 487 PHE 0.037 0.004 PHE C 400 TYR 0.038 0.006 TYR E 458 ARG 0.057 0.006 ARG E 604 Details of bonding type rmsd hydrogen bonds : bond 0.20384 ( 935) hydrogen bonds : angle 8.41351 ( 2569) covalent geometry : bond 0.01517 (23215) covalent geometry : angle 1.12210 (31770) *********************** 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 : 2.451 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: 1.8599 time to fit residues: 917.8801 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 : 4.499 ------------------------------------------------------------------------------- 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 228 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 246 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 246 GLN 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 447 ASN E 746 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100865 restraints weight = 31538.580| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.55 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23215 Z= 0.122 Angle : 0.532 7.024 31770 Z= 0.293 Chirality : 0.041 0.258 3548 Planarity : 0.004 0.037 3898 Dihedral : 15.297 173.029 4015 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.36 % Favored : 97.48 % Rotamer: Outliers : 2.87 % Allowed : 11.68 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2664 helix: 0.89 (0.18), residues: 815 sheet: 0.30 (0.23), residues: 466 loop : 0.02 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 68 HIS 0.006 0.001 HIS E 294 PHE 0.010 0.001 PHE E 790 TYR 0.011 0.001 TYR C 32 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 935) hydrogen bonds : angle 5.35153 ( 2569) covalent geometry : bond 0.00256 (23215) covalent geometry : angle 0.53199 (31770) *********************** 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 330 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 3.836 Fit side-chains REVERT: A 112 GLN cc_start: 0.9005 (tt0) cc_final: 0.8732 (tt0) REVERT: A 198 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8336 (ttm170) REVERT: A 209 GLN cc_start: 0.8190 (tp40) cc_final: 0.7890 (tm-30) REVERT: A 474 THR cc_start: 0.8834 (p) cc_final: 0.8583 (t) REVERT: A 678 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8048 (ttm170) REVERT: A 694 THR cc_start: 0.8367 (m) cc_final: 0.8118 (p) REVERT: B 23 SER cc_start: 0.9018 (t) cc_final: 0.8809 (t) REVERT: C 210 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6318 (tp) REVERT: D 189 ASP cc_start: 0.8394 (t0) cc_final: 0.8071 (t0) REVERT: D 313 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7553 (tppp) REVERT: E 277 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7724 (mtm-85) REVERT: E 296 ARG cc_start: 0.8342 (ptp-110) cc_final: 0.8053 (ptp-110) REVERT: E 369 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: E 409 ASN cc_start: 0.6798 (t0) cc_final: 0.6583 (t0) REVERT: E 453 ILE cc_start: 0.8547 (mm) cc_final: 0.8216 (mm) outliers start: 65 outliers final: 22 residues processed: 308 average time/residue: 1.6476 time to fit residues: 579.3778 Evaluate side-chains 209 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 198 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 678 ARG Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain B residue 41 SER 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 275 ASP Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 252 SER 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 E residue 121 VAL Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 406 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 215 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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 19 ASN C 112 GLN C 116 ASN C 246 GLN D 98 ASN D 213 ASN E 244 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 702 GLN E 746 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094298 restraints weight = 31798.604| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.67 r_work: 0.2955 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23215 Z= 0.247 Angle : 0.592 11.832 31770 Z= 0.314 Chirality : 0.044 0.304 3548 Planarity : 0.004 0.049 3898 Dihedral : 14.950 178.598 3994 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.53 % Favored : 96.32 % Rotamer: Outliers : 4.11 % Allowed : 13.49 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2664 helix: 1.26 (0.19), residues: 795 sheet: 0.19 (0.23), residues: 480 loop : 0.00 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 68 HIS 0.005 0.001 HIS A 733 PHE 0.017 0.002 PHE E 347 TYR 0.022 0.002 TYR E 458 ARG 0.006 0.001 ARG E 239 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 935) hydrogen bonds : angle 5.18377 ( 2569) covalent geometry : bond 0.00571 (23215) covalent geometry : angle 0.59157 (31770) *********************** 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 279 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 186 time to evaluate : 2.604 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8018 (tp40) cc_final: 0.7708 (tm-30) REVERT: A 474 THR cc_start: 0.8865 (p) cc_final: 0.8562 (t) REVERT: A 694 THR cc_start: 0.8453 (m) cc_final: 0.8104 (p) REVERT: B 23 SER cc_start: 0.8960 (t) cc_final: 0.8724 (t) REVERT: B 121 GLN cc_start: 0.8057 (mt0) cc_final: 0.7775 (mt0) REVERT: C 210 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6326 (tp) REVERT: D 189 ASP cc_start: 0.8486 (t0) cc_final: 0.8012 (t0) REVERT: D 201 GLN cc_start: 0.6806 (tm130) cc_final: 0.6288 (tm-30) REVERT: E 288 MET cc_start: 0.6674 (tpt) cc_final: 0.6360 (tpp) REVERT: E 317 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6842 (mpp80) REVERT: E 318 HIS cc_start: 0.6577 (t-90) cc_final: 0.6314 (t-170) REVERT: E 320 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: E 369 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: E 377 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6183 (tpp-160) REVERT: E 529 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 548 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8217 (mm) outliers start: 93 outliers final: 47 residues processed: 251 average time/residue: 1.2702 time to fit residues: 369.0557 Evaluate side-chains 222 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain A residue 164 ASP 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 576 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 210 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 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 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 173 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 317 ARG 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 548 ILE Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 680 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 241 optimal weight: 0.0050 chunk 266 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 140 optimal weight: 0.7980 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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 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 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS E 748 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098760 restraints weight = 31990.576| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.68 r_work: 0.3010 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23215 Z= 0.096 Angle : 0.450 5.981 31770 Z= 0.245 Chirality : 0.039 0.263 3548 Planarity : 0.003 0.034 3898 Dihedral : 14.733 175.043 3992 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.15 % Rotamer: Outliers : 2.52 % Allowed : 15.57 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2664 helix: 1.77 (0.19), residues: 810 sheet: 0.20 (0.24), residues: 466 loop : 0.13 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 PHE 0.012 0.001 PHE E 347 TYR 0.010 0.001 TYR E 118 ARG 0.005 0.000 ARG E 239 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 935) hydrogen bonds : angle 4.65708 ( 2569) covalent geometry : bond 0.00203 (23215) covalent geometry : angle 0.45031 (31770) *********************** 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 259 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 2.581 Fit side-chains REVERT: A 209 GLN cc_start: 0.7954 (tp40) cc_final: 0.7654 (tm-30) REVERT: A 229 GLN cc_start: 0.6624 (mt0) cc_final: 0.6345 (mt0) REVERT: C 210 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6262 (tp) REVERT: D 81 LYS cc_start: 0.8658 (mttt) cc_final: 0.8283 (mmtm) REVERT: D 164 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8646 (mtt180) REVERT: D 189 ASP cc_start: 0.8416 (t0) cc_final: 0.8012 (t0) REVERT: D 201 GLN cc_start: 0.6637 (tm130) cc_final: 0.6084 (tm-30) REVERT: D 496 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: E 241 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: E 288 MET cc_start: 0.6663 (tpt) cc_final: 0.6439 (tpp) REVERT: E 296 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8111 (ptp-110) REVERT: E 317 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7138 (mpp80) REVERT: E 318 HIS cc_start: 0.6810 (t-90) cc_final: 0.6465 (t-90) REVERT: E 377 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6040 (tpp-160) REVERT: E 444 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7002 (ptpt) REVERT: E 548 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8108 (mm) REVERT: E 561 SER cc_start: 0.8887 (t) cc_final: 0.8675 (p) REVERT: E 681 LYS cc_start: 0.8207 (tptp) cc_final: 0.7901 (ttmt) outliers start: 57 outliers final: 21 residues processed: 244 average time/residue: 1.2456 time to fit residues: 352.6547 Evaluate side-chains 210 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 2.621 ------------------------------------------------------------------------------- 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 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain D residue 164 ARG 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 496 GLU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 680 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 44 optimal weight: 0.0050 chunk 155 optimal weight: 0.5980 chunk 236 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 43 GLN B 121 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 246 GLN D 412 GLN E 145 HIS ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095759 restraints weight = 31710.950| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.69 r_work: 0.2953 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23215 Z= 0.177 Angle : 0.497 5.834 31770 Z= 0.267 Chirality : 0.041 0.285 3548 Planarity : 0.004 0.040 3898 Dihedral : 14.632 177.591 3992 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Rotamer: Outliers : 3.58 % Allowed : 15.66 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2664 helix: 1.80 (0.19), residues: 803 sheet: 0.07 (0.23), residues: 484 loop : 0.09 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 68 HIS 0.005 0.001 HIS E 394 PHE 0.015 0.001 PHE E 633 TYR 0.018 0.001 TYR D 221 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 935) hydrogen bonds : angle 4.70625 ( 2569) covalent geometry : bond 0.00404 (23215) covalent geometry : angle 0.49735 (31770) *********************** 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 260 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 2.415 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8010 (tp40) cc_final: 0.7693 (tm-30) REVERT: A 229 GLN cc_start: 0.6802 (mt0) cc_final: 0.6464 (mt0) REVERT: A 456 GLU cc_start: 0.8469 (tt0) cc_final: 0.8198 (tp30) REVERT: D 81 LYS cc_start: 0.8745 (mttt) cc_final: 0.8352 (mmtm) REVERT: D 189 ASP cc_start: 0.8451 (t0) cc_final: 0.8126 (t0) REVERT: D 201 GLN cc_start: 0.6727 (tm130) cc_final: 0.6162 (tm-30) REVERT: E 241 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: E 288 MET cc_start: 0.6824 (tpt) cc_final: 0.6559 (tpp) REVERT: E 296 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8145 (ptp-110) REVERT: E 317 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7118 (mpp80) REVERT: E 318 HIS cc_start: 0.6815 (t-90) cc_final: 0.6420 (t-90) REVERT: E 377 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6150 (tpp-160) REVERT: E 444 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6978 (ptpt) REVERT: E 548 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8166 (mm) REVERT: E 681 LYS cc_start: 0.8230 (tptp) cc_final: 0.7916 (ttmt) outliers start: 81 outliers final: 48 residues processed: 236 average time/residue: 1.2955 time to fit residues: 354.0047 Evaluate side-chains 225 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 164 ASP 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 576 ASP Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 694 THR 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 172 SER 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 387 GLN 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 307 SER Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 365 ILE 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 519 ASN Chi-restraints excluded: chain E residue 548 ILE 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 243 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 259 optimal weight: 0.0670 chunk 163 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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 246 GLN D 213 ASN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** 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 = 0.3451 r_free = 0.3451 target = 0.119635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096467 restraints weight = 31620.925| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.69 r_work: 0.2966 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23215 Z= 0.146 Angle : 0.468 5.812 31770 Z= 0.252 Chirality : 0.040 0.276 3548 Planarity : 0.003 0.038 3898 Dihedral : 14.555 177.104 3992 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 16.41 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2664 helix: 1.89 (0.19), residues: 809 sheet: 0.00 (0.23), residues: 483 loop : 0.12 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 PHE 0.012 0.001 PHE E 633 TYR 0.011 0.001 TYR C 511 ARG 0.006 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 935) hydrogen bonds : angle 4.60330 ( 2569) covalent geometry : bond 0.00331 (23215) covalent geometry : angle 0.46816 (31770) *********************** 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 254 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.7980 (tp40) cc_final: 0.7666 (tm-30) REVERT: A 229 GLN cc_start: 0.6789 (mt0) cc_final: 0.6548 (mt0) REVERT: A 268 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8803 (t) REVERT: A 456 GLU cc_start: 0.8489 (tt0) cc_final: 0.8183 (tp30) REVERT: C 490 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7793 (ttm-80) REVERT: D 81 LYS cc_start: 0.8740 (mttt) cc_final: 0.8355 (mmtm) REVERT: D 189 ASP cc_start: 0.8413 (t0) cc_final: 0.8066 (t0) REVERT: D 201 GLN cc_start: 0.6690 (tm130) cc_final: 0.6141 (tm-30) REVERT: E 241 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: E 288 MET cc_start: 0.6827 (tpt) cc_final: 0.6554 (tpp) REVERT: E 296 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8152 (ptp-110) REVERT: E 317 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7083 (mpp80) REVERT: E 318 HIS cc_start: 0.6737 (t-90) cc_final: 0.6451 (t-90) REVERT: E 377 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6163 (tpp-160) REVERT: E 548 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8161 (mm) REVERT: E 561 SER cc_start: 0.8963 (t) cc_final: 0.8710 (p) REVERT: E 681 LYS cc_start: 0.8154 (tptp) cc_final: 0.7914 (ttmt) outliers start: 71 outliers final: 49 residues processed: 235 average time/residue: 1.2614 time to fit residues: 346.2321 Evaluate side-chains 234 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 268 VAL 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 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 694 THR 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 70 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 61 LEU 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 311 THR Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 490 ARG 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 307 SER Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 296 ARG 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 365 ILE Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 406 SER Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 548 ILE 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 157 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 264 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 191 optimal weight: 0.0020 chunk 138 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS 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 ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092181 restraints weight = 32464.382| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.69 r_work: 0.2910 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 23215 Z= 0.321 Angle : 0.617 6.704 31770 Z= 0.325 Chirality : 0.046 0.304 3548 Planarity : 0.005 0.051 3898 Dihedral : 14.688 177.524 3992 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 4.42 % Allowed : 15.88 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2664 helix: 1.43 (0.19), residues: 796 sheet: -0.20 (0.23), residues: 481 loop : -0.16 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 624 HIS 0.007 0.001 HIS C 487 PHE 0.017 0.002 PHE E 790 TYR 0.019 0.002 TYR E 458 ARG 0.005 0.001 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 935) hydrogen bonds : angle 5.03294 ( 2569) covalent geometry : bond 0.00750 (23215) covalent geometry : angle 0.61714 (31770) *********************** 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 280 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 180 time to evaluate : 2.423 Fit side-chains REVERT: A 209 GLN cc_start: 0.8038 (tp40) cc_final: 0.7705 (tm-30) REVERT: A 229 GLN cc_start: 0.6863 (mt0) cc_final: 0.6559 (mt0) REVERT: A 450 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8409 (p0) REVERT: A 456 GLU cc_start: 0.8459 (tt0) cc_final: 0.8168 (tp30) REVERT: A 754 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 765 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: C 134 LYS cc_start: 0.7615 (pttt) cc_final: 0.7344 (tppp) REVERT: C 490 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7802 (ttm-80) REVERT: D 81 LYS cc_start: 0.8813 (mttt) cc_final: 0.8427 (mmtm) REVERT: D 189 ASP cc_start: 0.8465 (t0) cc_final: 0.8038 (t0) REVERT: D 201 GLN cc_start: 0.6904 (tm130) cc_final: 0.6397 (tm-30) REVERT: D 254 VAL cc_start: 0.8106 (t) cc_final: 0.7870 (p) REVERT: D 496 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: E 241 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: E 288 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6505 (tpp) REVERT: E 296 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8089 (ptp-110) REVERT: E 317 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6451 (mpp80) REVERT: E 318 HIS cc_start: 0.6794 (t-90) cc_final: 0.6446 (t-90) REVERT: E 320 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.6299 (mp10) REVERT: E 377 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6342 (tpp-160) REVERT: E 548 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8286 (mm) REVERT: E 681 LYS cc_start: 0.8279 (tptp) cc_final: 0.8041 (ttmt) outliers start: 100 outliers final: 59 residues processed: 254 average time/residue: 1.1977 time to fit residues: 354.2418 Evaluate side-chains 239 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 164 ASP Chi-restraints excluded: chain A residue 273 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 450 ASP Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 679 SER 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 754 GLU Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 CYS 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 172 SER Chi-restraints excluded: chain C residue 223 GLN 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 387 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR 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 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 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 240 ILE Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 320 GLN 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 406 SER Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 548 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 214 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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 246 GLN D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** 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 = 0.3457 r_free = 0.3457 target = 0.120274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097570 restraints weight = 31768.937| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.61 r_work: 0.2995 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 23215 Z= 0.107 Angle : 0.446 5.689 31770 Z= 0.242 Chirality : 0.039 0.262 3548 Planarity : 0.003 0.038 3898 Dihedral : 14.539 177.561 3992 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 2.61 % Allowed : 17.74 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2664 helix: 1.92 (0.19), residues: 801 sheet: -0.07 (0.24), residues: 455 loop : -0.02 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 PHE 0.009 0.001 PHE E 633 TYR 0.010 0.001 TYR C 32 ARG 0.004 0.000 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 935) hydrogen bonds : angle 4.57696 ( 2569) covalent geometry : bond 0.00234 (23215) covalent geometry : angle 0.44637 (31770) *********************** 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 252 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 2.636 Fit side-chains REVERT: A 229 GLN cc_start: 0.6919 (mt0) cc_final: 0.6631 (mt0) REVERT: A 456 GLU cc_start: 0.8448 (tt0) cc_final: 0.8166 (tp30) REVERT: A 638 GLU cc_start: 0.8017 (pp20) cc_final: 0.7616 (pt0) REVERT: A 765 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: C 134 LYS cc_start: 0.7519 (pttt) cc_final: 0.7297 (mptm) REVERT: C 490 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7762 (ttm-80) REVERT: D 81 LYS cc_start: 0.8746 (mttt) cc_final: 0.8343 (mmtm) REVERT: D 189 ASP cc_start: 0.8382 (t0) cc_final: 0.8002 (t0) REVERT: D 201 GLN cc_start: 0.6700 (tm130) cc_final: 0.6223 (tm-30) REVERT: D 496 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: E 173 ILE cc_start: 0.8577 (mt) cc_final: 0.8370 (tp) REVERT: E 227 MET cc_start: 0.9014 (mmt) cc_final: 0.8711 (mtm) REVERT: E 241 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: E 288 MET cc_start: 0.6744 (tpt) cc_final: 0.6438 (tpp) REVERT: E 296 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7950 (ptp-110) REVERT: E 317 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6291 (mpp80) REVERT: E 318 HIS cc_start: 0.6801 (t-90) cc_final: 0.6068 (t-170) REVERT: E 320 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.6082 (mp10) REVERT: E 345 GLU cc_start: 0.6839 (pt0) cc_final: 0.6414 (tt0) REVERT: E 377 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6175 (tpp-160) REVERT: E 561 SER cc_start: 0.8920 (t) cc_final: 0.8674 (p) REVERT: E 681 LYS cc_start: 0.8189 (tptp) cc_final: 0.7951 (ttmt) outliers start: 59 outliers final: 36 residues processed: 234 average time/residue: 1.3381 time to fit residues: 360.9619 Evaluate side-chains 227 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 164 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 469 THR 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 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 694 THR 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 88 SER Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 490 ARG 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 313 LYS Chi-restraints excluded: chain D residue 320 ASP Chi-restraints excluded: chain D residue 452 VAL 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 240 ILE Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 320 GLN 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 406 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 171 optimal weight: 0.0010 chunk 110 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** 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 = 0.3413 r_free = 0.3413 target = 0.116924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093607 restraints weight = 31934.113| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.69 r_work: 0.2941 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23215 Z= 0.222 Angle : 0.522 6.313 31770 Z= 0.277 Chirality : 0.042 0.297 3548 Planarity : 0.004 0.045 3898 Dihedral : 14.570 179.753 3992 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.98 % Favored : 95.87 % Rotamer: Outliers : 3.23 % Allowed : 17.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2664 helix: 1.79 (0.19), residues: 795 sheet: -0.27 (0.23), residues: 486 loop : -0.08 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.005 0.001 HIS C 487 PHE 0.016 0.002 PHE E 633 TYR 0.023 0.002 TYR A 502 ARG 0.005 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 935) hydrogen bonds : angle 4.75163 ( 2569) covalent geometry : bond 0.00514 (23215) covalent geometry : angle 0.52241 (31770) *********************** 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 248 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 2.446 Fit side-chains REVERT: A 229 GLN cc_start: 0.6925 (mt0) cc_final: 0.6610 (mt0) REVERT: A 450 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8209 (p0) REVERT: A 456 GLU cc_start: 0.8476 (tt0) cc_final: 0.8212 (tp30) REVERT: A 638 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: A 765 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: C 134 LYS cc_start: 0.7574 (pttt) cc_final: 0.7360 (mptm) REVERT: C 490 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7786 (ttm-80) REVERT: D 81 LYS cc_start: 0.8791 (mttt) cc_final: 0.8426 (mmtm) REVERT: D 189 ASP cc_start: 0.8397 (t0) cc_final: 0.7995 (t0) REVERT: D 201 GLN cc_start: 0.6844 (tm130) cc_final: 0.6355 (tm-30) REVERT: E 241 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6690 (mm-30) REVERT: E 278 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7495 (mp) REVERT: E 288 MET cc_start: 0.6829 (tpt) cc_final: 0.6498 (tpp) REVERT: E 296 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (ptp-110) REVERT: E 317 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6384 (mpp80) REVERT: E 318 HIS cc_start: 0.6790 (t-90) cc_final: 0.6572 (t-90) REVERT: E 320 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6125 (mp10) REVERT: E 377 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6173 (tpp-160) REVERT: E 395 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8097 (ttmm) REVERT: E 681 LYS cc_start: 0.8287 (tptp) cc_final: 0.8040 (ttmt) outliers start: 73 outliers final: 45 residues processed: 226 average time/residue: 1.2877 time to fit residues: 340.8146 Evaluate side-chains 229 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 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 450 ASP Chi-restraints excluded: chain A residue 469 THR 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 585 ILE 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 694 THR 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 70 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER 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 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 252 SER 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 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 406 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 84 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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** D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093854 restraints weight = 31970.910| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.67 r_work: 0.2953 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23215 Z= 0.194 Angle : 0.507 6.312 31770 Z= 0.270 Chirality : 0.042 0.289 3548 Planarity : 0.004 0.045 3898 Dihedral : 14.573 179.565 3992 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.90 % Favored : 95.95 % Rotamer: Outliers : 2.92 % Allowed : 17.96 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2664 helix: 1.79 (0.19), residues: 795 sheet: -0.27 (0.23), residues: 474 loop : -0.11 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 68 HIS 0.004 0.001 HIS E 394 PHE 0.017 0.001 PHE E 347 TYR 0.015 0.001 TYR C 32 ARG 0.005 0.000 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 935) hydrogen bonds : angle 4.74651 ( 2569) covalent geometry : bond 0.00447 (23215) covalent geometry : angle 0.50737 (31770) ********************** 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 239 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 2.695 Fit side-chains REVERT: A 229 GLN cc_start: 0.6900 (mt0) cc_final: 0.6618 (mt0) REVERT: A 450 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8187 (p0) REVERT: A 456 GLU cc_start: 0.8476 (tt0) cc_final: 0.8227 (tp30) REVERT: A 638 GLU cc_start: 0.8056 (pp20) cc_final: 0.7668 (pt0) REVERT: A 765 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: C 490 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7792 (ttm-80) REVERT: D 81 LYS cc_start: 0.8794 (mttt) cc_final: 0.8422 (mmtm) REVERT: D 189 ASP cc_start: 0.8391 (t0) cc_final: 0.7987 (t0) REVERT: D 201 GLN cc_start: 0.6844 (tm130) cc_final: 0.6359 (tm-30) REVERT: E 241 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: E 278 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7484 (mp) REVERT: E 288 MET cc_start: 0.6828 (tpt) cc_final: 0.6493 (tpp) REVERT: E 296 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8125 (ptp-110) REVERT: E 317 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6403 (mpp80) REVERT: E 320 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: E 377 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6180 (tpp-160) REVERT: E 395 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8096 (ttmm) REVERT: E 561 SER cc_start: 0.8975 (t) cc_final: 0.8721 (p) REVERT: E 681 LYS cc_start: 0.8276 (tptp) cc_final: 0.8024 (ttmt) outliers start: 66 outliers final: 49 residues processed: 218 average time/residue: 1.2532 time to fit residues: 317.8677 Evaluate side-chains 232 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 2.526 ------------------------------------------------------------------------------- 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 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 450 ASP Chi-restraints excluded: chain A residue 469 THR 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 585 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 THR 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 70 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 88 SER 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 387 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 45 TYR 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 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 D residue 462 THR 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 241 GLU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 317 ARG Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 395 LYS Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 406 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 263 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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** D 213 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN E 746 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093374 restraints weight = 32200.959| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.71 r_work: 0.2938 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23215 Z= 0.222 Angle : 0.528 6.487 31770 Z= 0.281 Chirality : 0.043 0.292 3548 Planarity : 0.004 0.047 3898 Dihedral : 14.590 179.415 3992 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 3.10 % Allowed : 17.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2664 helix: 1.70 (0.19), residues: 795 sheet: -0.30 (0.23), residues: 474 loop : -0.21 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.004 0.001 HIS C 487 PHE 0.015 0.002 PHE E 633 TYR 0.015 0.002 TYR C 511 ARG 0.005 0.000 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 935) hydrogen bonds : angle 4.81858 ( 2569) covalent geometry : bond 0.00513 (23215) covalent geometry : angle 0.52829 (31770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15313.05 seconds wall clock time: 266 minutes 31.03 seconds (15991.03 seconds total)