Starting phenix.real_space_refine on Mon Aug 25 12:11:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ilz_60677/08_2025/9ilz_60677.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 Zn 1 6.06 5 P 18 5.49 5 S 133 5.16 5 C 17685 2.51 5 N 4676 2.21 5 O 5263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27776 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 6218 Classifications: {'peptide': 768} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 732} Chain breaks: 2 Chain: "B" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3764 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain: "C" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3756 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 442} Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3764 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain: "E" Number of atoms: 5599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5599 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 661} Chain breaks: 1 Chain: "F" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4414 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 519} Chain: "X" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23451 SG CYS F 282 75.604 70.562 20.569 1.00214.96 S ATOM 23470 SG CYS F 285 74.478 67.044 19.401 1.00212.46 S ATOM 23704 SG CYS F 314 72.225 70.068 18.723 1.00205.19 S Time building chain proxies: 6.15, per 1000 atoms: 0.22 Number of scatterers: 27776 At special positions: 0 Unit cell: (135.52, 136.4, 168.08, 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) Zn 1 29.99 S 133 16.00 P 18 15.00 O 5263 8.00 N 4676 7.00 C 17685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" NE2 HIS F 290 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 314 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 282 " Number of angles added : 3 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6520 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 43 sheets defined 43.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.780A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.737A pdb=" N PHE A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.714A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 148' Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.614A pdb=" N ARG A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.642A pdb=" N LEU A 208 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.782A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.227A pdb=" N ASN A 262 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.535A pdb=" N ASN A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.467A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.661A pdb=" N GLU A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.616A pdb=" N GLU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 486 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.601A pdb=" N THR A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.537A pdb=" N THR A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 4.127A pdb=" N ALA A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.620A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 removed outlier: 3.531A pdb=" N ARG A 619 " --> pdb=" O ALA A 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 619' Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 654 through 661 removed outlier: 3.551A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 693 through 706 removed outlier: 4.553A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 700 " --> pdb=" O PHE A 696 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Proline residue: A 715 - end of helix Processing helix chain 'A' and resid 716 through 723 removed outlier: 4.133A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 747 removed outlier: 3.864A pdb=" N TYR A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.597A pdb=" N ILE A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.803A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.978A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.571A pdb=" N ASP B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.820A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.616A pdb=" N GLU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.854A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 578 removed outlier: 4.065A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.760A pdb=" N MET B 618 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 619 " --> pdb=" O ALA B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.673A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.530A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 704 removed outlier: 4.487A pdb=" N PHE B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.772A pdb=" N PHE B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 779 through 783 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.721A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 removed outlier: 4.147A pdb=" N LYS C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 375 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.837A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.853A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.705A pdb=" N LEU C 486 " --> pdb=" O TYR C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.725A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.739A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 4.272A pdb=" N ILE C 621 " --> pdb=" O MET C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 removed outlier: 3.629A pdb=" N GLU C 640 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.558A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 removed outlier: 3.655A pdb=" N LYS C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 703 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR C 704 " --> pdb=" O LEU C 700 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 706 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 722 removed outlier: 3.662A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.773A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 5.384A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.505A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.920A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.550A pdb=" N ASP D 432 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.620A pdb=" N ILE D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 547 removed outlier: 3.501A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.787A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 619 removed outlier: 3.631A pdb=" N ARG D 619 " --> pdb=" O ALA D 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 635 through 639 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.084A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.984A pdb=" N LEU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 671 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 704 removed outlier: 4.155A pdb=" N PHE D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 700 " --> pdb=" O PHE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 735 through 743 removed outlier: 3.822A pdb=" N LYS D 742 " --> pdb=" O THR D 738 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 743 " --> pdb=" O PHE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 removed outlier: 3.666A pdb=" N SER D 758 " --> pdb=" O HIS D 754 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 759 " --> pdb=" O ASP D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 removed outlier: 3.765A pdb=" N SER D 783 " --> pdb=" O ILE D 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 27 removed outlier: 3.684A pdb=" N ARG E 24 " --> pdb=" O PRO E 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 3.629A pdb=" N ASN E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 104 Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.017A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.529A pdb=" N ARG E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 removed outlier: 3.560A pdb=" N SER E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 removed outlier: 6.474A pdb=" N ALA E 172 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL E 173 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.984A pdb=" N LEU E 208 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.600A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 371 removed outlier: 3.531A pdb=" N LYS E 366 " --> pdb=" O PRO E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.765A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 431 through 434 Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 469 removed outlier: 4.120A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 541 through 547 removed outlier: 3.939A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'E' and resid 614 through 620 removed outlier: 4.375A pdb=" N ARG E 620 " --> pdb=" O ALA E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 641 Processing helix chain 'E' and resid 653 through 662 Processing helix chain 'E' and resid 664 through 678 removed outlier: 3.621A pdb=" N LEU E 671 " --> pdb=" O ALA E 667 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 706 removed outlier: 3.567A pdb=" N ALA E 697 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU E 700 " --> pdb=" O PHE E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 712 No H-bonds generated for 'chain 'E' and resid 710 through 712' Processing helix chain 'E' and resid 713 through 722 removed outlier: 3.938A pdb=" N THR E 718 " --> pdb=" O ILE E 714 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 745 Processing helix chain 'E' and resid 752 through 762 removed outlier: 3.766A pdb=" N ILE E 756 " --> pdb=" O PHE E 752 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 778 through 783 removed outlier: 3.736A pdb=" N ILE E 782 " --> pdb=" O PHE E 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 Processing helix chain 'F' and resid 260 through 264 removed outlier: 3.537A pdb=" N LEU F 264 " --> pdb=" O PHE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 Processing helix chain 'F' and resid 362 through 371 removed outlier: 4.087A pdb=" N LYS F 366 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.698A pdb=" N LEU F 375 " --> pdb=" O ARG F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.798A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.866A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.524A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 455 through 460' Processing helix chain 'F' and resid 460 through 469 removed outlier: 3.817A pdb=" N ILE F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 removed outlier: 3.876A pdb=" N LYS F 484 " --> pdb=" O GLU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 removed outlier: 3.993A pdb=" N THR F 512 " --> pdb=" O GLY F 508 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.763A pdb=" N THR F 533 " --> pdb=" O GLN F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 547 removed outlier: 3.904A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 578 removed outlier: 4.314A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 619 removed outlier: 3.598A pdb=" N MET F 618 " --> pdb=" O ASN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 641 removed outlier: 3.806A pdb=" N GLU F 640 " --> pdb=" O ARG F 636 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 641' Processing helix chain 'F' and resid 654 through 661 Processing helix chain 'F' and resid 664 through 680 removed outlier: 3.559A pdb=" N PHE F 668 " --> pdb=" O TYR F 664 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU F 669 " --> pdb=" O ARG F 665 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR F 670 " --> pdb=" O PHE F 666 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 671 " --> pdb=" O ALA F 667 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS F 674 " --> pdb=" O TYR F 670 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR F 679 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 705 removed outlier: 3.753A pdb=" N GLY F 703 " --> pdb=" O TYR F 699 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR F 704 " --> pdb=" O LEU F 700 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 705 " --> pdb=" O LYS F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 715 removed outlier: 3.600A pdb=" N HIS F 713 " --> pdb=" O SER F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 736 through 743 removed outlier: 4.190A pdb=" N GLN F 740 " --> pdb=" O LEU F 736 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN F 741 " --> pdb=" O THR F 737 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 742 " --> pdb=" O THR F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 761 removed outlier: 4.768A pdb=" N PHE F 759 " --> pdb=" O ASP F 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.874A pdb=" N PHE A 12 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 180 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 71 removed outlier: 3.849A pdb=" N ILE A 67 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR A 140 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 12.105A pdb=" N MET A 69 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N LEU A 138 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 12.194A pdb=" N VAL A 71 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N ILE A 136 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 219 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 141 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 221 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 143 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 299 Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 526 removed outlier: 7.174A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA8, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.236A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB2, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.784A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR B 604 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE B 501 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 581 through 583 removed outlier: 3.574A pdb=" N ASN B 594 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.690A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 706 through 707 removed outlier: 3.831A pdb=" N VAL B 707 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB8, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.690A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 503 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC1, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AC2, first strand: chain 'C' and resid 727 through 728 removed outlier: 3.561A pdb=" N TYR C 728 " --> pdb=" O VAL C 731 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.583A pdb=" N LYS C 765 " --> pdb=" O TYR C 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC5, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AC6, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.701A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 628 through 631 removed outlier: 3.745A pdb=" N HIS D 629 " --> pdb=" O LYS D 647 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 649 " --> pdb=" O HIS D 629 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 707 through 708 Processing sheet with id=AC9, first strand: chain 'D' and resid 727 through 728 Processing sheet with id=AD1, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.584A pdb=" N PHE E 12 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER E 55 " --> pdb=" O PHE E 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.763A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.763A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR E 219 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP E 139 " --> pdb=" O TYR E 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.906A pdb=" N LYS E 124 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD6, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD7, first strand: chain 'E' and resid 524 through 526 removed outlier: 6.365A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 628 through 631 removed outlier: 3.577A pdb=" N LYS E 649 " --> pdb=" O HIS E 629 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 631 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.602A pdb=" N LYS F 317 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AE2, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AE3, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.328A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AE5, first strand: chain 'F' and resid 628 through 631 removed outlier: 3.939A pdb=" N LYS F 649 " --> pdb=" O HIS F 629 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 706 through 707 Processing sheet with id=AE7, first strand: chain 'F' and resid 734 through 735 removed outlier: 3.623A pdb=" N LEU F 734 " --> pdb=" O LEU F 774 " (cutoff:3.500A) 873 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8898 1.34 - 1.46: 6133 1.46 - 1.58: 13128 1.58 - 1.70: 29 1.70 - 1.82: 193 Bond restraints: 28381 Sorted by residual: bond pdb=" CB PRO A 199 " pdb=" CG PRO A 199 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.82e+00 bond pdb=" CB TRP A 236 " pdb=" CG TRP A 236 " ideal model delta sigma weight residual 1.498 1.569 -0.071 3.10e-02 1.04e+03 5.25e+00 bond pdb=" CA TRP A 236 " pdb=" CB TRP A 236 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.15e-02 7.56e+03 3.78e+00 bond pdb=" CA LYS A 286 " pdb=" CB LYS A 286 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.30e-02 5.92e+03 2.64e+00 bond pdb=" N MET A 116 " pdb=" CA MET A 116 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.10e-02 8.26e+03 1.63e+00 ... (remaining 28376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 38074 2.66 - 5.31: 281 5.31 - 7.97: 38 7.97 - 10.63: 18 10.63 - 13.28: 9 Bond angle restraints: 38420 Sorted by residual: angle pdb=" CA PRO A 199 " pdb=" N PRO A 199 " pdb=" CD PRO A 199 " ideal model delta sigma weight residual 112.00 103.86 8.14 1.40e+00 5.10e-01 3.38e+01 angle pdb=" C SER A 115 " pdb=" N MET A 116 " pdb=" CA MET A 116 " ideal model delta sigma weight residual 122.83 115.07 7.76 1.54e+00 4.22e-01 2.54e+01 angle pdb=" CB MET F 547 " pdb=" CG MET F 547 " pdb=" SD MET F 547 " ideal model delta sigma weight residual 112.70 125.98 -13.28 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CB MET A 547 " pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 112.70 125.90 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" CB MET E 547 " pdb=" CG MET E 547 " pdb=" SD MET E 547 " ideal model delta sigma weight residual 112.70 125.86 -13.16 3.00e+00 1.11e-01 1.92e+01 ... (remaining 38415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.29: 16667 30.29 - 60.59: 623 60.59 - 90.88: 33 90.88 - 121.18: 0 121.18 - 151.47: 1 Dihedral angle restraints: 17324 sinusoidal: 7285 harmonic: 10039 Sorted by residual: dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -59.93 151.47 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" CA TYR A 679 " pdb=" C TYR A 679 " pdb=" N HIS A 680 " pdb=" CA HIS A 680 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU A 237 " pdb=" C GLU A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 17321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2725 0.032 - 0.064: 1091 0.064 - 0.096: 320 0.096 - 0.128: 160 0.128 - 0.160: 14 Chirality restraints: 4310 Sorted by residual: chirality pdb=" CA MET A 116 " pdb=" N MET A 116 " pdb=" C MET A 116 " pdb=" CB MET A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE F 683 " pdb=" N ILE F 683 " pdb=" C ILE F 683 " pdb=" CB ILE F 683 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE B 683 " pdb=" N ILE B 683 " pdb=" C ILE B 683 " pdb=" CB ILE B 683 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 4307 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 198 " -0.080 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 199 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 236 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C TRP A 236 " 0.060 2.00e-02 2.50e+03 pdb=" O TRP A 236 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU A 237 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 236 " -0.014 2.00e-02 2.50e+03 1.88e-02 8.79e+00 pdb=" CG TRP A 236 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 236 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 236 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 236 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 236 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 236 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 236 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 236 " 0.001 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1253 2.73 - 3.27: 28393 3.27 - 3.81: 43572 3.81 - 4.36: 52039 4.36 - 4.90: 87340 Nonbonded interactions: 212597 Sorted by model distance: nonbonded pdb=" N GLU A 361 " pdb=" OE1 GLU A 361 " model vdw 2.183 3.120 nonbonded pdb=" O ASN E 546 " pdb=" NZ LYS E 550 " model vdw 2.190 3.120 nonbonded pdb=" N GLU F 405 " pdb=" OE1 GLU F 405 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR D 342 " pdb=" OD1 ASP D 346 " model vdw 2.203 3.040 nonbonded pdb=" N ASN F 260 " pdb=" OD1 ASN F 260 " model vdw 2.206 3.120 ... (remaining 212592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 226 or resid 320 through 785)) selection = (chain 'E' and (resid 2 through 73 or resid 84 through 125 or resid 132 through \ 785)) } ncs_group { reference = (chain 'B' and resid 322 through 785) selection = (chain 'C' and resid 322 through 785) selection = (chain 'D' and resid 322 through 785) selection = (chain 'F' and resid 322 through 785) } 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: 10.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 27.520 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.003 0.121 28385 Z= 0.116 Angle : 0.633 13.284 38423 Z= 0.323 Chirality : 0.041 0.160 4310 Planarity : 0.004 0.116 4878 Dihedral : 14.475 151.472 10804 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer: Outliers : 0.70 % Allowed : 14.73 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3381 helix: 0.66 (0.16), residues: 1076 sheet: -0.07 (0.27), residues: 430 loop : 0.16 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 99 TYR 0.016 0.001 TYR E 687 PHE 0.013 0.001 PHE F 752 TRP 0.050 0.001 TRP A 236 HIS 0.003 0.000 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00256 (28381) covalent geometry : angle 0.63271 (38420) hydrogen bonds : bond 0.19087 ( 866) hydrogen bonds : angle 6.22548 ( 2445) metal coordination : bond 0.00221 ( 4) metal coordination : angle 1.10500 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9626 (mp) cc_final: 0.9357 (tm) REVERT: D 766 PHE cc_start: 0.7770 (p90) cc_final: 0.7300 (p90) REVERT: F 245 ASP cc_start: 0.9038 (t70) cc_final: 0.8816 (t70) REVERT: F 462 MET cc_start: 0.8044 (mmp) cc_final: 0.7671 (mpp) REVERT: F 684 MET cc_start: 0.7085 (tpp) cc_final: 0.6850 (ttm) outliers start: 22 outliers final: 18 residues processed: 141 average time/residue: 0.6548 time to fit residues: 108.4361 Evaluate side-chains 129 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 563 CYS Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 593 ASN B 328 ASN B 660 GLN ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 ASN F 775 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.105334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066850 restraints weight = 104460.055| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.56 r_work: 0.3018 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28385 Z= 0.166 Angle : 0.564 8.334 38423 Z= 0.290 Chirality : 0.042 0.192 4310 Planarity : 0.004 0.074 4878 Dihedral : 8.850 150.801 3911 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.48 % Rotamer: Outliers : 2.05 % Allowed : 13.71 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3381 helix: 0.76 (0.16), residues: 1158 sheet: -0.26 (0.26), residues: 436 loop : 0.14 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 514 TYR 0.019 0.001 TYR F 699 PHE 0.019 0.001 PHE A 269 TRP 0.031 0.001 TRP A 236 HIS 0.005 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00390 (28381) covalent geometry : angle 0.56424 (38420) hydrogen bonds : bond 0.04345 ( 866) hydrogen bonds : angle 4.72998 ( 2445) metal coordination : bond 0.00326 ( 4) metal coordination : angle 1.19699 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9655 (mp) cc_final: 0.9380 (tm) REVERT: A 197 MET cc_start: 0.8220 (tpp) cc_final: 0.7968 (tpp) REVERT: A 264 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 469 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 554 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: C 706 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8308 (tm) REVERT: D 448 ASP cc_start: 0.8902 (t0) cc_final: 0.8637 (t0) REVERT: D 766 PHE cc_start: 0.7881 (p90) cc_final: 0.7463 (p90) REVERT: E 197 MET cc_start: 0.8911 (tpp) cc_final: 0.8695 (tpp) REVERT: E 462 MET cc_start: 0.9370 (mmp) cc_final: 0.9148 (mmp) REVERT: F 458 MET cc_start: 0.8853 (tmt) cc_final: 0.8652 (tmm) REVERT: F 462 MET cc_start: 0.8524 (mmp) cc_final: 0.8205 (mpm) outliers start: 64 outliers final: 19 residues processed: 173 average time/residue: 0.5594 time to fit residues: 115.6101 Evaluate side-chains 127 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 320 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.103983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065445 restraints weight = 105306.909| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.54 r_work: 0.2994 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28385 Z= 0.191 Angle : 0.573 8.253 38423 Z= 0.292 Chirality : 0.042 0.175 4310 Planarity : 0.004 0.066 4878 Dihedral : 8.700 148.240 3889 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 15.15 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3381 helix: 0.79 (0.16), residues: 1157 sheet: -0.21 (0.26), residues: 439 loop : 0.11 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 514 TYR 0.018 0.001 TYR B 482 PHE 0.016 0.001 PHE D 588 TRP 0.012 0.001 TRP A 236 HIS 0.008 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00447 (28381) covalent geometry : angle 0.57276 (38420) hydrogen bonds : bond 0.04381 ( 866) hydrogen bonds : angle 4.62115 ( 2445) metal coordination : bond 0.00779 ( 4) metal coordination : angle 1.65322 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 115 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9654 (mp) cc_final: 0.9376 (tm) REVERT: A 197 MET cc_start: 0.8454 (tpp) cc_final: 0.8110 (tpp) REVERT: A 264 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7572 (mm) REVERT: A 469 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: B 554 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: C 706 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8480 (tm) REVERT: D 448 ASP cc_start: 0.8856 (t0) cc_final: 0.8589 (t0) REVERT: D 766 PHE cc_start: 0.7868 (p90) cc_final: 0.7468 (p90) REVERT: E 462 MET cc_start: 0.9395 (mmp) cc_final: 0.9176 (mmp) REVERT: F 420 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9320 (tt) REVERT: F 498 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8519 (tm) outliers start: 65 outliers final: 21 residues processed: 170 average time/residue: 0.6088 time to fit residues: 123.6256 Evaluate side-chains 131 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 173 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 243 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 HIS B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.104649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066346 restraints weight = 103532.324| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.46 r_work: 0.3003 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28385 Z= 0.125 Angle : 0.543 9.536 38423 Z= 0.274 Chirality : 0.041 0.196 4310 Planarity : 0.004 0.065 4878 Dihedral : 8.344 146.426 3884 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.19 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 15.08 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.15), residues: 3381 helix: 0.97 (0.16), residues: 1147 sheet: -0.24 (0.26), residues: 450 loop : 0.12 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 176 TYR 0.015 0.001 TYR B 482 PHE 0.023 0.001 PHE A 269 TRP 0.007 0.001 TRP A 236 HIS 0.006 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00294 (28381) covalent geometry : angle 0.54325 (38420) hydrogen bonds : bond 0.03496 ( 866) hydrogen bonds : angle 4.32602 ( 2445) metal coordination : bond 0.00547 ( 4) metal coordination : angle 0.98046 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 115 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9634 (mp) cc_final: 0.9348 (tm) REVERT: A 197 MET cc_start: 0.8436 (tpp) cc_final: 0.8213 (tpp) REVERT: A 264 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7266 (mm) REVERT: A 469 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: B 554 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: B 717 MET cc_start: -0.0872 (OUTLIER) cc_final: -0.1306 (tmt) REVERT: C 451 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: C 706 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8461 (tm) REVERT: D 766 PHE cc_start: 0.7834 (p90) cc_final: 0.7433 (p90) REVERT: E 462 MET cc_start: 0.9380 (mmp) cc_final: 0.9162 (mmp) REVERT: E 548 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8033 (m-70) REVERT: F 377 LYS cc_start: 0.8917 (tptp) cc_final: 0.8650 (tptp) REVERT: F 498 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8605 (tm) outliers start: 74 outliers final: 29 residues processed: 179 average time/residue: 0.5791 time to fit residues: 123.3630 Evaluate side-chains 142 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 305 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 241 optimal weight: 0.5980 chunk 162 optimal weight: 0.1980 chunk 183 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 596 ASN B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.104526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.066091 restraints weight = 103553.547| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.50 r_work: 0.2997 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28385 Z= 0.123 Angle : 0.544 9.232 38423 Z= 0.273 Chirality : 0.041 0.200 4310 Planarity : 0.004 0.064 4878 Dihedral : 8.162 144.714 3884 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.22 % Favored : 96.63 % Rotamer: Outliers : 2.11 % Allowed : 16.08 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3381 helix: 1.01 (0.16), residues: 1149 sheet: -0.22 (0.26), residues: 450 loop : 0.12 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 176 TYR 0.016 0.001 TYR B 482 PHE 0.014 0.001 PHE D 588 TRP 0.035 0.001 TRP A 236 HIS 0.006 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00290 (28381) covalent geometry : angle 0.54423 (38420) hydrogen bonds : bond 0.03451 ( 866) hydrogen bonds : angle 4.27814 ( 2445) metal coordination : bond 0.00500 ( 4) metal coordination : angle 0.94674 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 111 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9612 (mp) cc_final: 0.9318 (tm) REVERT: A 197 MET cc_start: 0.8455 (tpp) cc_final: 0.8165 (tpp) REVERT: A 244 GLU cc_start: 0.9161 (tp30) cc_final: 0.8907 (tp30) REVERT: A 264 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 469 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: B 554 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: C 451 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: C 534 ASP cc_start: 0.8643 (t0) cc_final: 0.8431 (t0) REVERT: C 706 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8449 (tm) REVERT: D 451 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: D 547 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8871 (ppp) REVERT: D 762 ARG cc_start: 0.8785 (tpt170) cc_final: 0.7914 (mmm160) REVERT: D 766 PHE cc_start: 0.7851 (p90) cc_final: 0.7451 (p90) REVERT: E 458 MET cc_start: 0.9148 (pmm) cc_final: 0.8803 (pmm) REVERT: E 462 MET cc_start: 0.9384 (mmp) cc_final: 0.9047 (mmm) REVERT: F 317 LYS cc_start: 0.9358 (tppp) cc_final: 0.9081 (tppp) REVERT: F 377 LYS cc_start: 0.8907 (tptp) cc_final: 0.8624 (tptp) REVERT: F 420 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9328 (tt) REVERT: F 498 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8640 (tm) outliers start: 66 outliers final: 28 residues processed: 167 average time/residue: 0.5377 time to fit residues: 106.4429 Evaluate side-chains 143 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 451 PHE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 256 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN D 347 HIS ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN E 478 ASN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.109438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070019 restraints weight = 99951.201| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.69 r_work: 0.2905 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 28385 Z= 0.295 Angle : 0.684 10.219 38423 Z= 0.347 Chirality : 0.045 0.195 4310 Planarity : 0.005 0.064 4878 Dihedral : 8.497 141.541 3884 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 2.75 % Allowed : 16.01 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3381 helix: 0.50 (0.15), residues: 1163 sheet: -0.39 (0.25), residues: 494 loop : -0.08 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 551 TYR 0.023 0.002 TYR B 482 PHE 0.017 0.002 PHE F 668 TRP 0.012 0.002 TRP D 675 HIS 0.014 0.002 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00683 (28381) covalent geometry : angle 0.68335 (38420) hydrogen bonds : bond 0.05356 ( 866) hydrogen bonds : angle 4.84407 ( 2445) metal coordination : bond 0.01619 ( 4) metal coordination : angle 3.11662 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 115 time to evaluate : 0.921 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 154 LEU cc_start: 0.9635 (mp) cc_final: 0.9305 (pp) REVERT: A 244 GLU cc_start: 0.9269 (tp30) cc_final: 0.9057 (tp30) REVERT: A 264 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 469 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: B 554 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: B 752 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.5040 (m-80) REVERT: C 534 ASP cc_start: 0.8904 (t0) cc_final: 0.8625 (t0) REVERT: C 567 LYS cc_start: 0.8952 (mttm) cc_final: 0.8541 (mppt) REVERT: C 706 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8613 (tm) REVERT: D 762 ARG cc_start: 0.8891 (tpt170) cc_final: 0.8032 (mmm160) REVERT: D 766 PHE cc_start: 0.7966 (p90) cc_final: 0.7553 (p90) REVERT: E 426 MET cc_start: 0.8834 (tpp) cc_final: 0.8535 (tpp) REVERT: E 458 MET cc_start: 0.9214 (pmm) cc_final: 0.8961 (pmm) REVERT: E 462 MET cc_start: 0.9355 (mmp) cc_final: 0.9094 (mmm) REVERT: E 548 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8046 (m-70) outliers start: 86 outliers final: 37 residues processed: 189 average time/residue: 0.4953 time to fit residues: 112.9076 Evaluate side-chains 146 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 593 ASN Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 529 GLN Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 205 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 141 optimal weight: 0.0270 chunk 261 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 265 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.109869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070339 restraints weight = 94130.925| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.00 r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28385 Z= 0.125 Angle : 0.583 10.611 38423 Z= 0.290 Chirality : 0.042 0.223 4310 Planarity : 0.004 0.060 4878 Dihedral : 8.176 140.339 3884 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 17.03 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3381 helix: 0.84 (0.16), residues: 1147 sheet: -0.37 (0.25), residues: 475 loop : -0.02 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 176 TYR 0.015 0.001 TYR B 482 PHE 0.023 0.001 PHE A 269 TRP 0.010 0.001 TRP A 236 HIS 0.006 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00296 (28381) covalent geometry : angle 0.58283 (38420) hydrogen bonds : bond 0.03549 ( 866) hydrogen bonds : angle 4.35385 ( 2445) metal coordination : bond 0.00755 ( 4) metal coordination : angle 1.12138 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 112 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9623 (mp) cc_final: 0.9276 (pp) REVERT: A 260 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8723 (t0) REVERT: A 264 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7433 (mm) REVERT: B 360 GLU cc_start: 0.9017 (mp0) cc_final: 0.8770 (pm20) REVERT: B 554 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 752 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.5451 (m-80) REVERT: C 534 ASP cc_start: 0.8911 (t0) cc_final: 0.8599 (t0) REVERT: C 567 LYS cc_start: 0.8846 (mttm) cc_final: 0.8469 (mppt) REVERT: C 706 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (tm) REVERT: D 762 ARG cc_start: 0.8786 (tpt170) cc_final: 0.7881 (mmm160) REVERT: E 197 MET cc_start: 0.8891 (tpp) cc_final: 0.8639 (tpp) REVERT: E 458 MET cc_start: 0.9252 (pmm) cc_final: 0.9045 (pmm) REVERT: F 377 LYS cc_start: 0.8897 (tptp) cc_final: 0.8592 (tptp) REVERT: F 420 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9341 (tt) REVERT: F 462 MET cc_start: 0.8280 (mmm) cc_final: 0.7875 (mpp) REVERT: F 498 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8745 (tm) REVERT: F 554 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8486 (t80) outliers start: 67 outliers final: 35 residues processed: 172 average time/residue: 0.5637 time to fit residues: 115.2308 Evaluate side-chains 148 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 253 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.108117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068907 restraints weight = 96377.767| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.78 r_work: 0.2947 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28385 Z= 0.161 Angle : 0.608 11.390 38423 Z= 0.300 Chirality : 0.042 0.229 4310 Planarity : 0.004 0.060 4878 Dihedral : 8.077 139.312 3884 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.82 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 17.29 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3381 helix: 0.82 (0.16), residues: 1153 sheet: -0.38 (0.25), residues: 477 loop : -0.04 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 514 TYR 0.022 0.001 TYR E 482 PHE 0.011 0.001 PHE E 89 TRP 0.055 0.002 TRP A 236 HIS 0.007 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00382 (28381) covalent geometry : angle 0.60767 (38420) hydrogen bonds : bond 0.03855 ( 866) hydrogen bonds : angle 4.37089 ( 2445) metal coordination : bond 0.00607 ( 4) metal coordination : angle 1.48312 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9610 (mp) cc_final: 0.9328 (tm) REVERT: A 260 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8727 (t0) REVERT: A 264 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 360 GLU cc_start: 0.9002 (mp0) cc_final: 0.8785 (pm20) REVERT: B 554 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: B 747 PHE cc_start: 0.5769 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: B 752 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: C 534 ASP cc_start: 0.8934 (t0) cc_final: 0.8595 (t0) REVERT: C 567 LYS cc_start: 0.8871 (mttm) cc_final: 0.8487 (mppt) REVERT: D 762 ARG cc_start: 0.8754 (tpt170) cc_final: 0.7860 (mmm160) REVERT: D 766 PHE cc_start: 0.8014 (p90) cc_final: 0.7579 (p90) REVERT: E 426 MET cc_start: 0.8693 (tpp) cc_final: 0.8445 (tpp) REVERT: E 548 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (m-70) REVERT: F 377 LYS cc_start: 0.8938 (tptp) cc_final: 0.8633 (tptp) REVERT: F 420 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9349 (tt) REVERT: F 498 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8732 (tm) outliers start: 62 outliers final: 36 residues processed: 157 average time/residue: 0.5572 time to fit residues: 104.2551 Evaluate side-chains 148 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 149 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.113711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074135 restraints weight = 98900.792| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.85 r_work: 0.2893 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 28385 Z= 0.300 Angle : 0.713 12.199 38423 Z= 0.358 Chirality : 0.045 0.364 4310 Planarity : 0.004 0.061 4878 Dihedral : 8.420 139.352 3883 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 2.01 % Allowed : 17.67 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3381 helix: 0.37 (0.15), residues: 1175 sheet: -0.54 (0.25), residues: 485 loop : -0.20 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 249 TYR 0.025 0.002 TYR D 428 PHE 0.027 0.002 PHE A 269 TRP 0.027 0.002 TRP A 236 HIS 0.012 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00698 (28381) covalent geometry : angle 0.71303 (38420) hydrogen bonds : bond 0.05239 ( 866) hydrogen bonds : angle 4.83981 ( 2445) metal coordination : bond 0.01599 ( 4) metal coordination : angle 2.92656 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 112 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9633 (mp) cc_final: 0.9360 (tm) REVERT: A 260 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8801 (t0) REVERT: A 686 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7366 (tt) REVERT: B 554 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8685 (m-80) REVERT: B 618 MET cc_start: 0.8387 (ppp) cc_final: 0.7795 (mmt) REVERT: B 747 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5472 (m-80) REVERT: B 752 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: C 534 ASP cc_start: 0.9013 (t0) cc_final: 0.8681 (t0) REVERT: C 567 LYS cc_start: 0.9004 (mttm) cc_final: 0.8624 (mppt) REVERT: D 618 MET cc_start: 0.9396 (mtm) cc_final: 0.9181 (mtp) REVERT: D 762 ARG cc_start: 0.8878 (tpt170) cc_final: 0.7943 (mmm160) REVERT: E 197 MET cc_start: 0.8922 (tpp) cc_final: 0.8704 (tpp) REVERT: F 377 LYS cc_start: 0.8953 (tptp) cc_final: 0.8635 (tptp) REVERT: F 462 MET cc_start: 0.8346 (mmm) cc_final: 0.8015 (mpp) REVERT: F 554 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (t80) outliers start: 63 outliers final: 38 residues processed: 168 average time/residue: 0.5238 time to fit residues: 105.3312 Evaluate side-chains 152 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain C residue 754 HIS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 593 ASN Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 597 HIS Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 266 optimal weight: 0.9980 chunk 287 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 713 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.113507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074767 restraints weight = 99227.869| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.85 r_work: 0.2974 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28385 Z= 0.110 Angle : 0.641 13.323 38423 Z= 0.313 Chirality : 0.043 0.314 4310 Planarity : 0.004 0.058 4878 Dihedral : 8.028 137.739 3883 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.25 % Favored : 96.54 % Rotamer: Outliers : 1.28 % Allowed : 18.54 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3381 helix: 0.72 (0.16), residues: 1162 sheet: -0.46 (0.25), residues: 482 loop : -0.11 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 152 TYR 0.014 0.001 TYR E 679 PHE 0.032 0.001 PHE E 698 TRP 0.038 0.001 TRP A 236 HIS 0.004 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00255 (28381) covalent geometry : angle 0.64109 (38420) hydrogen bonds : bond 0.03194 ( 866) hydrogen bonds : angle 4.27280 ( 2445) metal coordination : bond 0.00323 ( 4) metal coordination : angle 1.44324 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9607 (mp) cc_final: 0.9376 (tm) REVERT: A 260 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8674 (t0) REVERT: A 264 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 686 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7423 (tt) REVERT: B 554 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 618 MET cc_start: 0.8410 (ppp) cc_final: 0.7570 (mmt) REVERT: B 752 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: C 458 MET cc_start: 0.7682 (tpp) cc_final: 0.7205 (tpp) REVERT: C 534 ASP cc_start: 0.9008 (t0) cc_final: 0.8665 (t0) REVERT: C 567 LYS cc_start: 0.8895 (mttm) cc_final: 0.8567 (mppt) REVERT: D 618 MET cc_start: 0.9319 (mtm) cc_final: 0.9115 (mtp) REVERT: D 762 ARG cc_start: 0.8702 (tpt170) cc_final: 0.7728 (mmm160) REVERT: E 197 MET cc_start: 0.8968 (tpp) cc_final: 0.8722 (tpp) REVERT: E 641 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8847 (p0) REVERT: E 650 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8721 (tm) REVERT: F 351 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8922 (tt) REVERT: F 377 LYS cc_start: 0.8881 (tptp) cc_final: 0.8569 (tptp) REVERT: F 462 MET cc_start: 0.8268 (mmm) cc_final: 0.7909 (mpp) REVERT: F 498 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8824 (tm) REVERT: F 615 ASN cc_start: 0.9053 (p0) cc_final: 0.8656 (t0) outliers start: 40 outliers final: 23 residues processed: 154 average time/residue: 0.5949 time to fit residues: 108.7133 Evaluate side-chains 137 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 747 PHE Chi-restraints excluded: chain B residue 752 PHE Chi-restraints excluded: chain C residue 737 THR Chi-restraints excluded: chain C residue 739 PHE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 543 PHE Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 660 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 290 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 269 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 301 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN B 680 HIS ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074230 restraints weight = 83690.137| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.09 r_work: 0.2957 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 28385 Z= 0.145 Angle : 0.742 59.199 38423 Z= 0.393 Chirality : 0.050 1.728 4310 Planarity : 0.004 0.118 4878 Dihedral : 8.026 137.743 3883 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.19 % Favored : 96.60 % Rotamer: Outliers : 1.44 % Allowed : 18.47 % Favored : 80.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 3381 helix: 0.71 (0.16), residues: 1162 sheet: -0.45 (0.25), residues: 482 loop : -0.11 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 152 TYR 0.013 0.001 TYR E 482 PHE 0.114 0.001 PHE A 243 TRP 0.036 0.001 TRP A 236 HIS 0.004 0.001 HIS D 548 Details of bonding type rmsd covalent geometry : bond 0.00313 (28381) covalent geometry : angle 0.74206 (38420) hydrogen bonds : bond 0.03214 ( 866) hydrogen bonds : angle 4.27945 ( 2445) metal coordination : bond 0.00325 ( 4) metal coordination : angle 1.45420 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11029.77 seconds wall clock time: 188 minutes 21.66 seconds (11301.66 seconds total)