Starting phenix.real_space_refine on Thu Mar 5 02:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qcs_4511/03_2026/6qcs_4511.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11446 2.51 5 N 3147 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18278 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5740 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 26, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5881 Classifications: {'peptide': 750} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Chain: "C" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5901 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 713} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 139 Unusual residues: {'GTG': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 1, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.14, per 1000 atoms: 0.23 Number of scatterers: 18278 At special positions: 0 Unit cell: (126.327, 127.158, 123.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 36 15.00 Mg 2 11.99 O 3515 8.00 N 3147 7.00 C 11446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 829.8 milliseconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4110 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 25 sheets defined 47.3% alpha, 14.4% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.702A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.526A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.653A pdb=" N HIS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 164 through 184 removed outlier: 3.678A pdb=" N LEU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.520A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.873A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.670A pdb=" N ILE A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 348 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.709A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.755A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.919A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 575 through 596 removed outlier: 4.167A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.729A pdb=" N TYR A 644 " --> pdb=" O CYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.380A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.775A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 3.542A pdb=" N GLU A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 717 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.967A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.672A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.762A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.634A pdb=" N THR B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.668A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.917A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.767A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.588A pdb=" N SER B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.656A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.686A pdb=" N ALA B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.614A pdb=" N LYS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 454 through 472 removed outlier: 3.593A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 Proline residue: B 509 - end of helix removed outlier: 4.105A pdb=" N GLY B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.855A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.857A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.756A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.623A pdb=" N ASN B 602 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 599 through 603' Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.789A pdb=" N MET B 615 " --> pdb=" O TYR B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 670 through 675 removed outlier: 4.253A pdb=" N ILE B 673 " --> pdb=" O ASN B 670 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.697A pdb=" N LEU B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 690 " --> pdb=" O GLN B 686 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 removed outlier: 4.207A pdb=" N SER B 703 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.577A pdb=" N ALA B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 749 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.555A pdb=" N ILE C 70 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.796A pdb=" N THR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 157 through 169 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.612A pdb=" N ALA C 174 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.663A pdb=" N ILE C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 254 through 273 Processing helix chain 'C' and resid 277 through 287 removed outlier: 3.736A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 444 through 450 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.528A pdb=" N ASP C 518 " --> pdb=" O GLY C 515 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 519 " --> pdb=" O ALA C 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 519' Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 567 Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 589 through 607 removed outlier: 3.555A pdb=" N GLN C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 4.061A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 690 through 694 removed outlier: 3.944A pdb=" N VAL C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 7.195A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.823A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.517A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 477 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.517A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.729A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.111A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 187 Processing sheet with id=AB2, first strand: chain 'B' and resid 190 through 191 Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.524A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB5, first strand: chain 'B' and resid 641 through 644 Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.983A pdb=" N MET C 92 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB8, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.121A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AC1, first strand: chain 'C' and resid 294 through 295 removed outlier: 3.569A pdb=" N GLU C 294 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 327 removed outlier: 5.086A pdb=" N ARG C 373 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL C 480 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 386 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR C 482 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 388 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 340 through 347 Processing sheet with id=AC4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC6, first strand: chain 'C' and resid 659 through 662 Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 703 removed outlier: 3.852A pdb=" N GLU C 724 " --> pdb=" O LYS C 740 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4429 1.33 - 1.45: 3707 1.45 - 1.57: 10266 1.57 - 1.69: 69 1.69 - 1.81: 224 Bond restraints: 18695 Sorted by residual: bond pdb=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.424 1.325 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C5A GTG M 1 " pdb=" C6A GTG M 1 " ideal model delta sigma weight residual 1.427 1.338 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C1E GTG M 1 " pdb=" O4E GTG M 1 " ideal model delta sigma weight residual 1.392 1.463 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O3A GTG M 1 " pdb=" PB GTG M 1 " ideal model delta sigma weight residual 1.656 1.590 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1D GTG M 1 " pdb=" O4D GTG M 1 " ideal model delta sigma weight residual 1.383 1.445 -0.062 2.00e-02 2.50e+03 9.53e+00 ... (remaining 18690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 24914 2.40 - 4.79: 389 4.79 - 7.19: 38 7.19 - 9.59: 13 9.59 - 11.98: 4 Bond angle restraints: 25358 Sorted by residual: angle pdb=" C VAL A 720 " pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 121.54 131.95 -10.41 1.91e+00 2.74e-01 2.97e+01 angle pdb=" N ARG B 126 " pdb=" CA ARG B 126 " pdb=" C ARG B 126 " ideal model delta sigma weight residual 111.02 116.81 -5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" C THR B 303 " pdb=" N GLY B 304 " pdb=" CA GLY B 304 " ideal model delta sigma weight residual 122.18 119.24 2.94 6.90e-01 2.10e+00 1.82e+01 angle pdb=" C ILE C 291 " pdb=" N ASP C 292 " pdb=" CA ASP C 292 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C GLN A 620 " pdb=" N GLU A 621 " pdb=" CA GLU A 621 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 ... (remaining 25353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.90: 10552 20.90 - 41.81: 701 41.81 - 62.71: 184 62.71 - 83.62: 45 83.62 - 104.52: 5 Dihedral angle restraints: 11487 sinusoidal: 5108 harmonic: 6379 Sorted by residual: dihedral pdb=" CA GLY B 125 " pdb=" C GLY B 125 " pdb=" N ARG B 126 " pdb=" CA ARG B 126 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA SER B 442 " pdb=" C SER B 442 " pdb=" N SER B 443 " pdb=" CA SER B 443 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual 254.00 179.51 74.49 1 1.70e+01 3.46e-03 2.43e+01 ... (remaining 11484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2135 0.053 - 0.106: 580 0.106 - 0.159: 90 0.159 - 0.211: 9 0.211 - 0.264: 2 Chirality restraints: 2816 Sorted by residual: chirality pdb=" C4D GTG M 1 " pdb=" C3D GTG M 1 " pdb=" C5D GTG M 1 " pdb=" O4D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.79 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1' A M 3 " pdb=" O4' A M 3 " pdb=" C2' A M 3 " pdb=" N9 A M 3 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A 485 " pdb=" CA VAL A 485 " pdb=" CG1 VAL A 485 " pdb=" CG2 VAL A 485 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 2813 not shown) Planarity restraints: 3130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 656 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO C 657 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 657 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 657 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 370 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO B 371 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO A 217 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.031 5.00e-02 4.00e+02 ... (remaining 3127 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 542 2.69 - 3.24: 15969 3.24 - 3.80: 28630 3.80 - 4.35: 39241 4.35 - 4.90: 64813 Nonbonded interactions: 149195 Sorted by model distance: nonbonded pdb=" OE1 GLU A 81 " pdb="MG MG A 801 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.160 2.170 nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 226 " pdb=" O ARG B 350 " model vdw 2.267 3.040 nonbonded pdb=" O LYS A 16 " pdb=" OG1 THR A 20 " model vdw 2.304 3.040 ... (remaining 149190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 18696 Z= 0.276 Angle : 0.779 11.982 25358 Z= 0.423 Chirality : 0.048 0.264 2816 Planarity : 0.006 0.065 3130 Dihedral : 15.396 104.522 7377 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 5.64 % Allowed : 7.99 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.14), residues: 2199 helix: -2.45 (0.12), residues: 938 sheet: -1.68 (0.30), residues: 265 loop : -2.63 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 439 TYR 0.023 0.002 TYR A 644 PHE 0.020 0.002 PHE C 698 TRP 0.027 0.002 TRP B 437 HIS 0.005 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00635 (18695) covalent geometry : angle 0.77921 (25358) hydrogen bonds : bond 0.14310 ( 793) hydrogen bonds : angle 6.34499 ( 2274) Misc. bond : bond 0.03538 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 243 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7711 (mpt-90) REVERT: C 534 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8224 (m) REVERT: C 555 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7978 (tt) REVERT: C 654 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8124 (pttt) REVERT: C 686 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: C 705 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7358 (t0) outliers start: 108 outliers final: 27 residues processed: 337 average time/residue: 0.1611 time to fit residues: 79.7430 Evaluate side-chains 182 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 152 GLN A 222 ASN A 319 GLN A 470 ASN A 610 ASN A 666 GLN A 693 ASN B 47 HIS B 108 GLN B 137 GLN B 247 GLN B 292 ASN B 310 ASN B 670 ASN B 680 ASN B 710 GLN C 11 GLN C 247 HIS C 437 GLN C 552 GLN C 614 GLN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055529 restraints weight = 49616.757| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.43 r_work: 0.2864 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18696 Z= 0.121 Angle : 0.543 9.593 25358 Z= 0.286 Chirality : 0.040 0.222 2816 Planarity : 0.004 0.044 3130 Dihedral : 11.973 82.235 2995 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.98 % Allowed : 11.69 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.16), residues: 2199 helix: -0.34 (0.16), residues: 945 sheet: -1.40 (0.30), residues: 264 loop : -2.05 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.011 0.001 TYR C 246 PHE 0.010 0.001 PHE A 132 TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00270 (18695) covalent geometry : angle 0.54341 (25358) hydrogen bonds : bond 0.03681 ( 793) hydrogen bonds : angle 4.44013 ( 2274) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8717 (tp-100) REVERT: A 51 MET cc_start: 0.8217 (mmm) cc_final: 0.7767 (mmm) REVERT: A 53 PHE cc_start: 0.7164 (m-10) cc_final: 0.6851 (m-10) REVERT: A 114 LYS cc_start: 0.9065 (tptt) cc_final: 0.8863 (tttp) REVERT: A 133 TRP cc_start: 0.8600 (m100) cc_final: 0.8160 (m100) REVERT: A 141 ASN cc_start: 0.8302 (t0) cc_final: 0.8018 (t0) REVERT: B 300 MET cc_start: 0.8895 (mtt) cc_final: 0.8681 (mtm) REVERT: C 218 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7785 (mpt-90) REVERT: C 347 LEU cc_start: 0.8866 (mm) cc_final: 0.8637 (tt) REVERT: C 412 MET cc_start: 0.7503 (tmm) cc_final: 0.7283 (tmm) REVERT: C 555 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (tt) outliers start: 38 outliers final: 22 residues processed: 191 average time/residue: 0.1568 time to fit residues: 44.5121 Evaluate side-chains 160 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 705 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 192 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 176 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055170 restraints weight = 50300.906| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.44 r_work: 0.2856 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18696 Z= 0.123 Angle : 0.506 7.109 25358 Z= 0.264 Chirality : 0.040 0.211 2816 Planarity : 0.004 0.037 3130 Dihedral : 11.355 81.120 2968 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.51 % Allowed : 11.85 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2199 helix: 0.56 (0.17), residues: 958 sheet: -1.27 (0.32), residues: 249 loop : -1.83 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 397 TYR 0.011 0.001 TYR C 246 PHE 0.015 0.001 PHE C 448 TRP 0.020 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00280 (18695) covalent geometry : angle 0.50619 (25358) hydrogen bonds : bond 0.03314 ( 793) hydrogen bonds : angle 4.12020 ( 2274) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8675 (tp-100) REVERT: A 51 MET cc_start: 0.8341 (mmm) cc_final: 0.8049 (mmm) REVERT: A 53 PHE cc_start: 0.7399 (m-10) cc_final: 0.6976 (m-10) REVERT: A 114 LYS cc_start: 0.9093 (tptt) cc_final: 0.8843 (tttp) REVERT: A 133 TRP cc_start: 0.8602 (m100) cc_final: 0.8129 (m100) REVERT: A 141 ASN cc_start: 0.8324 (t0) cc_final: 0.8081 (t0) REVERT: A 143 MET cc_start: 0.8635 (ttt) cc_final: 0.8095 (ttt) REVERT: A 373 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8507 (mm-40) REVERT: B 104 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: B 300 MET cc_start: 0.8903 (mtt) cc_final: 0.8680 (mtm) REVERT: C 218 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6638 (mpt-90) REVERT: C 347 LEU cc_start: 0.8901 (mm) cc_final: 0.8605 (tt) REVERT: C 412 MET cc_start: 0.7607 (tmm) cc_final: 0.7196 (tmm) REVERT: C 449 ASP cc_start: 0.8379 (m-30) cc_final: 0.8082 (m-30) REVERT: C 465 ILE cc_start: 0.3395 (OUTLIER) cc_final: 0.2995 (pp) REVERT: C 534 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8680 (t) REVERT: C 555 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7898 (tt) outliers start: 48 outliers final: 26 residues processed: 185 average time/residue: 0.1459 time to fit residues: 41.0427 Evaluate side-chains 164 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 705 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 314 ASN C 463 HIS C 466 ASN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055481 restraints weight = 50006.231| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.43 r_work: 0.2866 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18696 Z= 0.104 Angle : 0.482 7.667 25358 Z= 0.251 Chirality : 0.039 0.208 2816 Planarity : 0.003 0.034 3130 Dihedral : 11.120 84.535 2962 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.83 % Allowed : 13.05 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2199 helix: 1.03 (0.17), residues: 957 sheet: -0.89 (0.30), residues: 277 loop : -1.59 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 508 TYR 0.011 0.001 TYR B 554 PHE 0.009 0.001 PHE A 629 TRP 0.018 0.001 TRP B 437 HIS 0.002 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00235 (18695) covalent geometry : angle 0.48199 (25358) hydrogen bonds : bond 0.03035 ( 793) hydrogen bonds : angle 3.94635 ( 2274) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8682 (tp-100) REVERT: A 51 MET cc_start: 0.8553 (mmm) cc_final: 0.8078 (mmm) REVERT: A 53 PHE cc_start: 0.7406 (m-10) cc_final: 0.7045 (m-10) REVERT: A 114 LYS cc_start: 0.9100 (tptt) cc_final: 0.8847 (tttp) REVERT: A 133 TRP cc_start: 0.8555 (m100) cc_final: 0.7967 (m100) REVERT: A 141 ASN cc_start: 0.8276 (t0) cc_final: 0.7991 (t0) REVERT: A 143 MET cc_start: 0.8627 (ttt) cc_final: 0.8106 (ttt) REVERT: A 373 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8519 (mm-40) REVERT: A 390 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8483 (mm-30) REVERT: A 571 MET cc_start: 0.8889 (mtp) cc_final: 0.8581 (mtp) REVERT: A 608 ARG cc_start: 0.8914 (mpp80) cc_final: 0.8653 (ttp-110) REVERT: B 104 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: B 300 MET cc_start: 0.8915 (mtt) cc_final: 0.8696 (mtm) REVERT: C 347 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8587 (tt) REVERT: C 412 MET cc_start: 0.7684 (tmm) cc_final: 0.7232 (tmm) REVERT: C 534 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (t) REVERT: C 555 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7884 (tt) outliers start: 35 outliers final: 17 residues processed: 169 average time/residue: 0.1365 time to fit residues: 36.0985 Evaluate side-chains 151 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 78 optimal weight: 0.0970 chunk 141 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056400 restraints weight = 49483.903| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.44 r_work: 0.2889 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18696 Z= 0.083 Angle : 0.463 8.241 25358 Z= 0.241 Chirality : 0.038 0.204 2816 Planarity : 0.003 0.034 3130 Dihedral : 10.942 88.935 2952 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.93 % Allowed : 13.20 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2199 helix: 1.37 (0.17), residues: 957 sheet: -0.87 (0.31), residues: 266 loop : -1.40 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 508 TYR 0.010 0.001 TYR B 554 PHE 0.008 0.001 PHE B 446 TRP 0.016 0.001 TRP B 437 HIS 0.002 0.000 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00183 (18695) covalent geometry : angle 0.46346 (25358) hydrogen bonds : bond 0.02739 ( 793) hydrogen bonds : angle 3.79783 ( 2274) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8674 (tp-100) REVERT: A 50 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8193 (p0) REVERT: A 51 MET cc_start: 0.8566 (mmm) cc_final: 0.8301 (mmm) REVERT: A 53 PHE cc_start: 0.7478 (m-10) cc_final: 0.7140 (m-10) REVERT: A 114 LYS cc_start: 0.9114 (tptt) cc_final: 0.8864 (tttp) REVERT: A 133 TRP cc_start: 0.8595 (m100) cc_final: 0.8008 (m100) REVERT: A 141 ASN cc_start: 0.8302 (t0) cc_final: 0.7758 (t0) REVERT: A 143 MET cc_start: 0.8581 (ttt) cc_final: 0.8024 (ttt) REVERT: A 373 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8675 (tp-100) REVERT: A 390 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8485 (mm-30) REVERT: A 571 MET cc_start: 0.8883 (mtp) cc_final: 0.8525 (mtp) REVERT: A 608 ARG cc_start: 0.8868 (mpp80) cc_final: 0.8658 (ttp-110) REVERT: B 104 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: B 203 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7354 (tpp80) REVERT: B 300 MET cc_start: 0.8894 (mtt) cc_final: 0.8690 (mtm) REVERT: C 218 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6725 (mpt-90) REVERT: C 347 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8595 (tt) REVERT: C 412 MET cc_start: 0.7649 (tmm) cc_final: 0.7230 (tmm) REVERT: C 534 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8591 (t) REVERT: C 555 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7833 (tt) outliers start: 37 outliers final: 20 residues processed: 171 average time/residue: 0.1355 time to fit residues: 36.4601 Evaluate side-chains 157 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 221 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 68 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN C 603 GLN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053980 restraints weight = 49779.782| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.41 r_work: 0.2829 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18696 Z= 0.171 Angle : 0.516 11.962 25358 Z= 0.265 Chirality : 0.041 0.197 2816 Planarity : 0.003 0.034 3130 Dihedral : 10.988 86.256 2952 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.14 % Allowed : 13.67 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2199 helix: 1.40 (0.17), residues: 954 sheet: -0.87 (0.30), residues: 276 loop : -1.33 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 508 TYR 0.014 0.001 TYR C 246 PHE 0.012 0.001 PHE A 132 TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00395 (18695) covalent geometry : angle 0.51605 (25358) hydrogen bonds : bond 0.03343 ( 793) hydrogen bonds : angle 3.97122 ( 2274) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8684 (tp-100) REVERT: A 43 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: A 51 MET cc_start: 0.8642 (mmm) cc_final: 0.8285 (mmm) REVERT: A 53 PHE cc_start: 0.7629 (m-10) cc_final: 0.7330 (m-10) REVERT: A 74 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7974 (ptm-80) REVERT: A 133 TRP cc_start: 0.8619 (m100) cc_final: 0.8027 (m100) REVERT: A 141 ASN cc_start: 0.8311 (t0) cc_final: 0.7729 (t0) REVERT: A 143 MET cc_start: 0.8644 (ttt) cc_final: 0.8123 (ttt) REVERT: A 373 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8500 (mm-40) REVERT: A 571 MET cc_start: 0.8920 (mtp) cc_final: 0.8526 (mtp) REVERT: A 608 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8611 (ttp-110) REVERT: B 104 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: B 203 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7372 (tpp80) REVERT: B 300 MET cc_start: 0.8919 (mtt) cc_final: 0.8708 (mtm) REVERT: B 677 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8684 (t0) REVERT: C 218 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6758 (mpt-90) REVERT: C 292 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8168 (t70) REVERT: C 347 LEU cc_start: 0.8928 (mm) cc_final: 0.8553 (tt) REVERT: C 412 MET cc_start: 0.7747 (tmm) cc_final: 0.7490 (tmm) REVERT: C 529 MET cc_start: 0.9026 (tpp) cc_final: 0.8656 (ttt) REVERT: C 534 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8592 (t) REVERT: C 555 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7957 (tt) outliers start: 41 outliers final: 28 residues processed: 165 average time/residue: 0.1337 time to fit residues: 34.7084 Evaluate side-chains 164 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 174 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 168 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055715 restraints weight = 49752.393| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.42 r_work: 0.2875 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18696 Z= 0.091 Angle : 0.471 10.870 25358 Z= 0.241 Chirality : 0.039 0.197 2816 Planarity : 0.003 0.033 3130 Dihedral : 10.859 85.308 2952 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.98 % Allowed : 13.73 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2199 helix: 1.66 (0.17), residues: 952 sheet: -0.78 (0.30), residues: 275 loop : -1.19 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 508 TYR 0.011 0.001 TYR B 554 PHE 0.008 0.001 PHE A 629 TRP 0.016 0.001 TRP B 437 HIS 0.002 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00206 (18695) covalent geometry : angle 0.47104 (25358) hydrogen bonds : bond 0.02775 ( 793) hydrogen bonds : angle 3.78683 ( 2274) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8669 (tp-100) REVERT: A 51 MET cc_start: 0.8609 (mmm) cc_final: 0.8214 (mmm) REVERT: A 53 PHE cc_start: 0.7744 (m-10) cc_final: 0.7434 (m-10) REVERT: A 74 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7950 (ptm-80) REVERT: A 133 TRP cc_start: 0.8617 (m100) cc_final: 0.7976 (m100) REVERT: A 141 ASN cc_start: 0.8271 (t0) cc_final: 0.7695 (t0) REVERT: A 143 MET cc_start: 0.8615 (ttt) cc_final: 0.8064 (ttt) REVERT: A 233 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9179 (tp) REVERT: A 373 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8693 (tp-100) REVERT: A 390 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8488 (mm-30) REVERT: A 571 MET cc_start: 0.8894 (mtp) cc_final: 0.8485 (mtp) REVERT: A 608 ARG cc_start: 0.8778 (mpp80) cc_final: 0.8555 (ttp-110) REVERT: B 104 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: B 203 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7455 (tpp80) REVERT: B 204 ILE cc_start: 0.9046 (tp) cc_final: 0.8840 (tt) REVERT: B 300 MET cc_start: 0.8883 (mtt) cc_final: 0.8664 (mtm) REVERT: B 677 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8688 (t0) REVERT: C 218 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.6734 (mpt-90) REVERT: C 276 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7957 (p) REVERT: C 347 LEU cc_start: 0.8922 (mm) cc_final: 0.8571 (tt) REVERT: C 412 MET cc_start: 0.7642 (tmm) cc_final: 0.7302 (tmm) REVERT: C 529 MET cc_start: 0.9009 (tpp) cc_final: 0.8628 (ttt) REVERT: C 534 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8576 (t) REVERT: C 555 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7813 (tt) outliers start: 38 outliers final: 25 residues processed: 164 average time/residue: 0.1336 time to fit residues: 34.6511 Evaluate side-chains 160 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 80 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 195 optimal weight: 0.0000 chunk 18 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053043 restraints weight = 50173.594| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.40 r_work: 0.2806 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18696 Z= 0.195 Angle : 0.546 10.516 25358 Z= 0.278 Chirality : 0.042 0.187 2816 Planarity : 0.003 0.035 3130 Dihedral : 11.014 82.630 2952 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.40 % Allowed : 13.62 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2199 helix: 1.51 (0.17), residues: 951 sheet: -0.84 (0.30), residues: 284 loop : -1.22 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 508 TYR 0.015 0.001 TYR C 246 PHE 0.013 0.001 PHE A 132 TRP 0.022 0.001 TRP B 437 HIS 0.003 0.001 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00450 (18695) covalent geometry : angle 0.54604 (25358) hydrogen bonds : bond 0.03591 ( 793) hydrogen bonds : angle 4.06145 ( 2274) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8732 (tp-100) REVERT: A 51 MET cc_start: 0.8670 (mmm) cc_final: 0.8352 (mmm) REVERT: A 53 PHE cc_start: 0.7793 (m-10) cc_final: 0.7540 (m-10) REVERT: A 74 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7082 (ptm160) REVERT: A 133 TRP cc_start: 0.8636 (m100) cc_final: 0.8233 (m100) REVERT: A 141 ASN cc_start: 0.8370 (t0) cc_final: 0.7763 (t0) REVERT: A 143 MET cc_start: 0.8660 (ttt) cc_final: 0.8133 (ttt) REVERT: A 233 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9230 (tp) REVERT: A 373 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8540 (mm-40) REVERT: A 390 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: B 104 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: B 203 ARG cc_start: 0.7722 (mtm180) cc_final: 0.7440 (tpp80) REVERT: B 300 MET cc_start: 0.8931 (mtt) cc_final: 0.8717 (mtm) REVERT: B 677 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8664 (t0) REVERT: C 218 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6741 (mpt-90) REVERT: C 276 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8098 (p) REVERT: C 347 LEU cc_start: 0.8957 (mm) cc_final: 0.8530 (tt) REVERT: C 404 MET cc_start: 0.8467 (mmm) cc_final: 0.8105 (mmt) REVERT: C 412 MET cc_start: 0.7689 (tmm) cc_final: 0.7444 (tmm) REVERT: C 529 MET cc_start: 0.9057 (tpp) cc_final: 0.8729 (ttt) REVERT: C 534 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8646 (t) REVERT: C 555 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7941 (tt) outliers start: 46 outliers final: 32 residues processed: 173 average time/residue: 0.1237 time to fit residues: 34.0011 Evaluate side-chains 168 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 150 optimal weight: 0.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055379 restraints weight = 49647.992| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.42 r_work: 0.2868 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18696 Z= 0.089 Angle : 0.493 11.523 25358 Z= 0.250 Chirality : 0.039 0.188 2816 Planarity : 0.003 0.044 3130 Dihedral : 10.855 84.545 2952 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.98 % Allowed : 14.25 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2199 helix: 1.75 (0.17), residues: 953 sheet: -0.74 (0.31), residues: 263 loop : -1.09 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 508 TYR 0.013 0.001 TYR B 56 PHE 0.010 0.001 PHE A 223 TRP 0.015 0.001 TRP B 437 HIS 0.002 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00197 (18695) covalent geometry : angle 0.49266 (25358) hydrogen bonds : bond 0.02795 ( 793) hydrogen bonds : angle 3.78907 ( 2274) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8695 (tp-100) REVERT: A 51 MET cc_start: 0.8678 (mmm) cc_final: 0.8389 (mmm) REVERT: A 53 PHE cc_start: 0.7770 (m-10) cc_final: 0.7526 (m-10) REVERT: A 74 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7929 (ptm-80) REVERT: A 133 TRP cc_start: 0.8629 (m100) cc_final: 0.7997 (m100) REVERT: A 141 ASN cc_start: 0.8289 (t0) cc_final: 0.7725 (t0) REVERT: A 233 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9188 (tp) REVERT: A 390 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8498 (mm-30) REVERT: A 571 MET cc_start: 0.8779 (mtp) cc_final: 0.8558 (mtp) REVERT: B 104 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: B 203 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7474 (tpp80) REVERT: B 206 MET cc_start: 0.8598 (mmt) cc_final: 0.8252 (mmt) REVERT: B 300 MET cc_start: 0.8887 (mtt) cc_final: 0.8660 (mtm) REVERT: B 677 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (t0) REVERT: C 218 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6787 (mpt-90) REVERT: C 347 LEU cc_start: 0.8959 (mm) cc_final: 0.8570 (tt) REVERT: C 404 MET cc_start: 0.8432 (mmm) cc_final: 0.8143 (mmt) REVERT: C 412 MET cc_start: 0.7561 (tmm) cc_final: 0.7335 (tmm) REVERT: C 529 MET cc_start: 0.9005 (tpp) cc_final: 0.8659 (ttt) REVERT: C 534 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (t) REVERT: C 555 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7788 (tt) outliers start: 38 outliers final: 27 residues processed: 166 average time/residue: 0.1309 time to fit residues: 34.3631 Evaluate side-chains 162 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 211 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 chunk 129 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054409 restraints weight = 49712.854| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.40 r_work: 0.2841 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18696 Z= 0.135 Angle : 0.526 12.354 25358 Z= 0.264 Chirality : 0.040 0.186 2816 Planarity : 0.003 0.049 3130 Dihedral : 10.873 83.587 2952 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.09 % Allowed : 14.25 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2199 helix: 1.75 (0.17), residues: 952 sheet: -0.73 (0.31), residues: 263 loop : -1.06 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 508 TYR 0.011 0.001 TYR B 56 PHE 0.009 0.001 PHE A 132 TRP 0.019 0.001 TRP B 437 HIS 0.002 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00313 (18695) covalent geometry : angle 0.52570 (25358) hydrogen bonds : bond 0.03067 ( 793) hydrogen bonds : angle 3.83571 ( 2274) Misc. bond : bond 0.00048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8714 (tp-100) REVERT: A 51 MET cc_start: 0.8729 (mmm) cc_final: 0.8458 (mmm) REVERT: A 53 PHE cc_start: 0.7822 (m-10) cc_final: 0.7582 (m-10) REVERT: A 74 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6989 (ptm160) REVERT: A 133 TRP cc_start: 0.8642 (m100) cc_final: 0.7953 (m100) REVERT: A 141 ASN cc_start: 0.8292 (t0) cc_final: 0.7710 (t0) REVERT: A 143 MET cc_start: 0.8658 (ttt) cc_final: 0.8425 (ttt) REVERT: A 233 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9197 (tp) REVERT: A 390 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: A 550 GLU cc_start: 0.9107 (pm20) cc_final: 0.8702 (pp20) REVERT: A 571 MET cc_start: 0.8817 (mtp) cc_final: 0.8595 (mtp) REVERT: B 104 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: B 203 ARG cc_start: 0.7744 (mtm180) cc_final: 0.7462 (tpp80) REVERT: B 206 MET cc_start: 0.8671 (mmt) cc_final: 0.8365 (mmt) REVERT: B 300 MET cc_start: 0.8922 (mtt) cc_final: 0.8680 (mtm) REVERT: B 677 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8633 (t0) REVERT: C 218 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.6736 (mpt-90) REVERT: C 276 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 347 LEU cc_start: 0.8960 (mm) cc_final: 0.8541 (tt) REVERT: C 404 MET cc_start: 0.8486 (mmm) cc_final: 0.8184 (mmt) REVERT: C 412 MET cc_start: 0.7581 (tmm) cc_final: 0.7346 (tmm) REVERT: C 529 MET cc_start: 0.9027 (tpp) cc_final: 0.8699 (ttt) REVERT: C 534 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8605 (t) REVERT: C 555 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7933 (tt) outliers start: 40 outliers final: 30 residues processed: 162 average time/residue: 0.1366 time to fit residues: 34.7749 Evaluate side-chains 166 residues out of total 1928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 604 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 217 optimal weight: 8.9990 chunk 220 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055671 restraints weight = 49728.409| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.42 r_work: 0.2872 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18696 Z= 0.092 Angle : 0.501 12.453 25358 Z= 0.251 Chirality : 0.039 0.184 2816 Planarity : 0.003 0.051 3130 Dihedral : 10.773 82.896 2951 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.14 % Allowed : 14.41 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2199 helix: 1.91 (0.17), residues: 953 sheet: -0.66 (0.32), residues: 261 loop : -0.92 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 508 TYR 0.016 0.001 TYR B 56 PHE 0.008 0.001 PHE B 449 TRP 0.014 0.001 TRP B 437 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00208 (18695) covalent geometry : angle 0.50080 (25358) hydrogen bonds : bond 0.02725 ( 793) hydrogen bonds : angle 3.71738 ( 2274) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4516.25 seconds wall clock time: 78 minutes 17.42 seconds (4697.42 seconds total)