Starting phenix.real_space_refine on Tue Aug 26 08:59:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.map" model { file = "/net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k59_22678/08_2025/7k59_22678.cif" } resolution = 4.2 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= 0.004 sd= 0.091 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: 4 Type Number sf(0) Gaussians S 186 5.16 5 C 22044 2.51 5 N 6180 2.21 5 O 6642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 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: 35052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "B" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "C" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "D" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "E" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Chain: "F" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Time building chain proxies: 6.74, per 1000 atoms: 0.19 Number of scatterers: 35052 At special positions: 0 Unit cell: (181.643, 172.328, 119.543, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 186 16.00 O 6642 8.00 N 6180 7.00 C 22044 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: 2.74 Conformation dependent library (CDL) restraints added in 996.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 30 sheets defined 42.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.619A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.535A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.720A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.090A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.683A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 751 through 762 removed outlier: 3.612A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.409A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.617A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.672A pdb=" N LEU B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.681A pdb=" N THR B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.138A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 751 through 762 removed outlier: 3.612A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.532A pdb=" N ILE C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.670A pdb=" N LEU C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.509A pdb=" N ILE C 479 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 501 through 506 removed outlier: 4.088A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.138A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.118A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.179A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.531A pdb=" N ILE E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.618A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.535A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.522A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.509A pdb=" N ILE E 479 " --> pdb=" O TRP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.720A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.681A pdb=" N THR E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.710A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.621A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 660 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 686 through 711 removed outlier: 3.692A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 751 through 762 removed outlier: 3.611A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 4.119A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.410A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.180A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.532A pdb=" N ILE F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.619A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.671A pdb=" N LEU F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.534A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.521A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.510A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.721A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 removed outlier: 4.089A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.226A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.682A pdb=" N THR F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.711A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.620A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 660 Processing helix chain 'F' and resid 672 through 677 Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.693A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.137A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 751 through 762 removed outlier: 3.610A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA A 67 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP A 304 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 301 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 344 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.504A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP B 304 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 301 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 344 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 514 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP C 304 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 301 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET C 344 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 514 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA D 67 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AC1, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP D 304 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 342 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 301 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 344 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 514 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.505A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'E' and resid 266 through 269 removed outlier: 3.670A pdb=" N ASP E 304 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 342 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 301 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E 344 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 573 through 575 removed outlier: 6.487A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 514 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.504A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD1, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AD2, first strand: chain 'F' and resid 266 through 269 removed outlier: 3.671A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 342 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 301 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 344 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 573 through 575 removed outlier: 6.486A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 514 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3096 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: 6.23 Time building geometry restraints manager: 3.65 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: 11924 1.34 - 1.46: 6187 1.46 - 1.58: 17227 1.58 - 1.70: 2 1.70 - 1.82: 300 Bond restraints: 35640 Sorted by residual: bond pdb=" CB VAL A 514 " pdb=" CG1 VAL A 514 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.39e+00 bond pdb=" CB VAL D 514 " pdb=" CG1 VAL D 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.37e+00 bond pdb=" CB VAL C 514 " pdb=" CG1 VAL C 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" CB VAL F 514 " pdb=" CG1 VAL F 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.35e+00 bond pdb=" CB VAL E 514 " pdb=" CG1 VAL E 514 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.31e+00 ... (remaining 35635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 46563 2.57 - 5.15: 1277 5.15 - 7.72: 203 7.72 - 10.30: 53 10.30 - 12.87: 30 Bond angle restraints: 48126 Sorted by residual: angle pdb=" CB GLU B 546 " pdb=" CG GLU B 546 " pdb=" CD GLU B 546 " ideal model delta sigma weight residual 112.60 122.00 -9.40 1.70e+00 3.46e-01 3.06e+01 angle pdb=" CB GLU C 546 " pdb=" CG GLU C 546 " pdb=" CD GLU C 546 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" CB GLU A 546 " pdb=" CG GLU A 546 " pdb=" CD GLU A 546 " ideal model delta sigma weight residual 112.60 121.98 -9.38 1.70e+00 3.46e-01 3.04e+01 angle pdb=" CB GLU D 546 " pdb=" CG GLU D 546 " pdb=" CD GLU D 546 " ideal model delta sigma weight residual 112.60 121.98 -9.38 1.70e+00 3.46e-01 3.04e+01 angle pdb=" CB GLU E 546 " pdb=" CG GLU E 546 " pdb=" CD GLU E 546 " ideal model delta sigma weight residual 112.60 121.97 -9.37 1.70e+00 3.46e-01 3.04e+01 ... (remaining 48121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 19347 17.22 - 34.44: 2268 34.44 - 51.66: 423 51.66 - 68.87: 138 68.87 - 86.09: 48 Dihedral angle restraints: 22224 sinusoidal: 9360 harmonic: 12864 Sorted by residual: dihedral pdb=" CA PHE F 506 " pdb=" C PHE F 506 " pdb=" N GLY F 507 " pdb=" CA GLY F 507 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE A 506 " pdb=" C PHE A 506 " pdb=" N GLY A 507 " pdb=" CA GLY A 507 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE C 506 " pdb=" C PHE C 506 " pdb=" N GLY C 507 " pdb=" CA GLY C 507 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 22221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4114 0.066 - 0.132: 1032 0.132 - 0.198: 224 0.198 - 0.264: 30 0.264 - 0.330: 6 Chirality restraints: 5406 Sorted by residual: chirality pdb=" CB ILE C 114 " pdb=" CA ILE C 114 " pdb=" CG1 ILE C 114 " pdb=" CG2 ILE C 114 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE F 114 " pdb=" CA ILE F 114 " pdb=" CG1 ILE F 114 " pdb=" CG2 ILE F 114 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB ILE D 114 " pdb=" CA ILE D 114 " pdb=" CG1 ILE D 114 " pdb=" CG2 ILE D 114 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5403 not shown) Planarity restraints: 6390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 122 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C THR E 122 " 0.051 2.00e-02 2.50e+03 pdb=" O THR E 122 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL E 123 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 122 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.44e+00 pdb=" C THR F 122 " 0.050 2.00e-02 2.50e+03 pdb=" O THR F 122 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL F 123 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 122 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C THR B 122 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 122 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 123 " 0.017 2.00e-02 2.50e+03 ... (remaining 6387 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3649 2.74 - 3.28: 33927 3.28 - 3.82: 56495 3.82 - 4.36: 63706 4.36 - 4.90: 105050 Nonbonded interactions: 262827 Sorted by model distance: nonbonded pdb=" OG SER D 276 " pdb=" OG SER E 326 " model vdw 2.198 3.040 nonbonded pdb=" O THR A 122 " pdb=" OG1 THR A 122 " model vdw 2.210 3.040 nonbonded pdb=" O THR F 122 " pdb=" OG1 THR F 122 " model vdw 2.211 3.040 nonbonded pdb=" O THR E 122 " pdb=" OG1 THR E 122 " model vdw 2.211 3.040 nonbonded pdb=" O THR D 122 " pdb=" OG1 THR D 122 " model vdw 2.211 3.040 ... (remaining 262822 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.180 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35640 Z= 0.293 Angle : 1.078 12.875 48126 Z= 0.569 Chirality : 0.061 0.330 5406 Planarity : 0.008 0.066 6390 Dihedral : 15.769 86.094 13860 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.19 % Allowed : 6.79 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -4.45 (0.10), residues: 4422 helix: -3.19 (0.09), residues: 1602 sheet: -2.97 (0.19), residues: 558 loop : -2.74 (0.11), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 465 TYR 0.018 0.002 TYR F 173 PHE 0.035 0.003 PHE F 552 TRP 0.010 0.002 TRP E 476 HIS 0.009 0.002 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00630 (35640) covalent geometry : angle 1.07816 (48126) hydrogen bonds : bond 0.18545 ( 1098) hydrogen bonds : angle 7.25820 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 477 time to evaluate : 1.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1151 (mmp) cc_final: 0.0276 (tpt) REVERT: A 47 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6925 (p0) REVERT: A 80 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.3960 (tp30) REVERT: A 114 ILE cc_start: 0.5048 (OUTLIER) cc_final: 0.4733 (mt) REVERT: A 639 LEU cc_start: 0.9362 (mt) cc_final: 0.9025 (mp) REVERT: A 640 ASP cc_start: 0.8444 (p0) cc_final: 0.7872 (p0) REVERT: A 687 LEU cc_start: 0.9338 (pt) cc_final: 0.9051 (mp) REVERT: B 32 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5581 (mp) REVERT: B 46 MET cc_start: 0.1256 (mmp) cc_final: 0.0308 (tpt) REVERT: B 47 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7214 (p0) REVERT: B 114 ILE cc_start: 0.4839 (OUTLIER) cc_final: 0.4602 (mt) REVERT: B 242 LEU cc_start: 0.9410 (mt) cc_final: 0.8429 (tt) REVERT: B 604 ILE cc_start: 0.9674 (mt) cc_final: 0.9446 (mm) REVERT: B 620 ILE cc_start: 0.9467 (pt) cc_final: 0.9235 (tp) REVERT: B 639 LEU cc_start: 0.9101 (mt) cc_final: 0.8661 (mp) REVERT: B 640 ASP cc_start: 0.8336 (p0) cc_final: 0.7864 (p0) REVERT: B 687 LEU cc_start: 0.9007 (pt) cc_final: 0.8789 (mp) REVERT: B 764 GLN cc_start: 0.7319 (tt0) cc_final: 0.6452 (tp40) REVERT: C 32 ILE cc_start: 0.4499 (OUTLIER) cc_final: 0.4083 (mp) REVERT: C 46 MET cc_start: -0.0833 (mmp) cc_final: -0.1369 (tpt) REVERT: C 47 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6509 (p0) REVERT: C 114 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.5230 (mt) REVERT: C 242 LEU cc_start: 0.9651 (mt) cc_final: 0.9106 (tt) REVERT: C 332 MET cc_start: 0.8975 (tpp) cc_final: 0.8640 (tpp) REVERT: C 639 LEU cc_start: 0.9162 (mt) cc_final: 0.8829 (mp) REVERT: C 640 ASP cc_start: 0.8151 (p0) cc_final: 0.7590 (p0) REVERT: C 661 LEU cc_start: 0.9186 (mt) cc_final: 0.8961 (pp) REVERT: C 687 LEU cc_start: 0.9133 (pt) cc_final: 0.8901 (mp) REVERT: C 764 GLN cc_start: 0.7233 (tt0) cc_final: 0.7016 (tt0) REVERT: D 46 MET cc_start: 0.1152 (mmp) cc_final: 0.0138 (tpt) REVERT: D 47 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6891 (p0) REVERT: D 307 ASP cc_start: 0.9269 (p0) cc_final: 0.8735 (m-30) REVERT: D 353 ILE cc_start: 0.9334 (mt) cc_final: 0.8939 (mp) REVERT: D 464 LEU cc_start: 0.7986 (tt) cc_final: 0.7722 (tp) REVERT: D 639 LEU cc_start: 0.9372 (mt) cc_final: 0.9000 (mp) REVERT: D 640 ASP cc_start: 0.8441 (p0) cc_final: 0.7922 (p0) REVERT: D 687 LEU cc_start: 0.9280 (pt) cc_final: 0.9037 (mp) REVERT: E 32 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5327 (mp) REVERT: E 46 MET cc_start: 0.0572 (mmp) cc_final: -0.0384 (tpt) REVERT: E 47 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7382 (p0) REVERT: E 604 ILE cc_start: 0.9635 (mt) cc_final: 0.9426 (mm) REVERT: E 620 ILE cc_start: 0.9483 (pt) cc_final: 0.9248 (tp) REVERT: E 639 LEU cc_start: 0.9132 (mt) cc_final: 0.8685 (mp) REVERT: E 640 ASP cc_start: 0.8314 (p0) cc_final: 0.7925 (p0) REVERT: F 46 MET cc_start: -0.0479 (mmp) cc_final: -0.0832 (tpt) REVERT: F 47 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6704 (p0) REVERT: F 219 MET cc_start: 0.8553 (mtt) cc_final: 0.8319 (mmm) REVERT: F 332 MET cc_start: 0.8914 (tpp) cc_final: 0.8637 (tpp) REVERT: F 640 ASP cc_start: 0.8167 (p0) cc_final: 0.7720 (p0) REVERT: F 651 LYS cc_start: 0.9520 (mttt) cc_final: 0.9319 (ptmm) REVERT: F 661 LEU cc_start: 0.9210 (mt) cc_final: 0.9002 (pp) REVERT: F 687 LEU cc_start: 0.9133 (pt) cc_final: 0.8913 (mp) outliers start: 84 outliers final: 16 residues processed: 555 average time/residue: 0.2290 time to fit residues: 197.7026 Evaluate side-chains 280 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 91 ASN A 199 ASN A 260 ASN A 285 ASN A 384 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 660 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 199 ASN B 215 GLN B 260 ASN B 285 ASN B 384 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 660 ASN C 90 ASN C 91 ASN C 260 ASN C 285 ASN C 384 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN C 660 ASN D 90 ASN D 91 ASN D 199 ASN D 260 ASN D 285 ASN D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN D 660 ASN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 91 ASN E 260 ASN E 285 ASN E 337 GLN E 384 HIS ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 660 ASN E 750 ASN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 91 ASN F 215 GLN F 260 ASN F 285 ASN F 337 GLN F 384 HIS ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN F 660 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.092201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059858 restraints weight = 159084.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061441 restraints weight = 96904.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.062459 restraints weight = 70492.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063086 restraints weight = 57428.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063495 restraints weight = 50709.702| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35640 Z= 0.131 Angle : 0.667 10.496 48126 Z= 0.331 Chirality : 0.045 0.176 5406 Planarity : 0.005 0.049 6390 Dihedral : 5.198 20.222 4842 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.31 % Allowed : 4.86 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.93 (0.11), residues: 4422 helix: -1.50 (0.12), residues: 1632 sheet: -2.50 (0.19), residues: 552 loop : -2.10 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 89 TYR 0.020 0.001 TYR D 244 PHE 0.023 0.001 PHE E 363 TRP 0.004 0.001 TRP D 454 HIS 0.001 0.000 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00294 (35640) covalent geometry : angle 0.66653 (48126) hydrogen bonds : bond 0.04009 ( 1098) hydrogen bonds : angle 5.21602 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 313 time to evaluate : 1.237 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0700 (mmp) cc_final: -0.0371 (tpt) REVERT: A 307 ASP cc_start: 0.9335 (p0) cc_final: 0.8631 (t0) REVERT: A 639 LEU cc_start: 0.9381 (mt) cc_final: 0.8932 (mp) REVERT: A 640 ASP cc_start: 0.8156 (p0) cc_final: 0.7583 (p0) REVERT: A 687 LEU cc_start: 0.9075 (pt) cc_final: 0.8814 (mp) REVERT: B 46 MET cc_start: 0.1260 (mmp) cc_final: -0.0087 (tpt) REVERT: B 242 LEU cc_start: 0.9454 (mt) cc_final: 0.9024 (tt) REVERT: B 332 MET cc_start: 0.8971 (ttt) cc_final: 0.8613 (tmm) REVERT: B 508 MET cc_start: 0.8042 (tpp) cc_final: 0.7616 (tpp) REVERT: B 639 LEU cc_start: 0.9300 (mt) cc_final: 0.8818 (mp) REVERT: B 640 ASP cc_start: 0.8069 (p0) cc_final: 0.7745 (p0) REVERT: B 687 LEU cc_start: 0.8728 (pt) cc_final: 0.8420 (mp) REVERT: B 764 GLN cc_start: 0.6999 (tt0) cc_final: 0.6283 (tp40) REVERT: C 46 MET cc_start: -0.0703 (mmp) cc_final: -0.1340 (tpt) REVERT: C 242 LEU cc_start: 0.9530 (mt) cc_final: 0.9192 (tt) REVERT: C 275 MET cc_start: 0.8780 (mmp) cc_final: 0.8561 (mmm) REVERT: C 332 MET cc_start: 0.9096 (tpp) cc_final: 0.8740 (tpp) REVERT: C 639 LEU cc_start: 0.9244 (mt) cc_final: 0.8694 (mp) REVERT: C 640 ASP cc_start: 0.8059 (p0) cc_final: 0.7739 (p0) REVERT: C 764 GLN cc_start: 0.7277 (tt0) cc_final: 0.7040 (tt0) REVERT: D 46 MET cc_start: 0.0911 (mmp) cc_final: -0.0029 (tpt) REVERT: D 307 ASP cc_start: 0.9353 (p0) cc_final: 0.8785 (m-30) REVERT: D 464 LEU cc_start: 0.7592 (tt) cc_final: 0.7276 (tp) REVERT: D 640 ASP cc_start: 0.8149 (p0) cc_final: 0.7694 (p0) REVERT: D 678 MET cc_start: 0.8088 (mmp) cc_final: 0.7664 (ttm) REVERT: E 46 MET cc_start: 0.0504 (mmp) cc_final: -0.0754 (tpt) REVERT: E 332 MET cc_start: 0.9114 (ttt) cc_final: 0.8568 (tmm) REVERT: E 547 LEU cc_start: 0.9500 (tp) cc_final: 0.9182 (tt) REVERT: E 639 LEU cc_start: 0.9204 (mt) cc_final: 0.8818 (mp) REVERT: E 640 ASP cc_start: 0.8129 (p0) cc_final: 0.7826 (p0) REVERT: E 740 MET cc_start: 0.9089 (tpp) cc_final: 0.8847 (tpp) REVERT: F 46 MET cc_start: -0.0246 (mmp) cc_final: -0.0973 (tpt) REVERT: F 275 MET cc_start: 0.8809 (mmp) cc_final: 0.8508 (mmm) REVERT: F 508 MET cc_start: 0.8199 (tpt) cc_final: 0.7958 (tpt) REVERT: F 640 ASP cc_start: 0.7976 (p0) cc_final: 0.7676 (p0) outliers start: 12 outliers final: 1 residues processed: 325 average time/residue: 0.1953 time to fit residues: 107.1794 Evaluate side-chains 214 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 74 optimal weight: 30.0000 chunk 331 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 chunk 312 optimal weight: 30.0000 chunk 131 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 320 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 760 GLN B 90 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 760 GLN E 337 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 760 GLN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 750 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.091285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058979 restraints weight = 162404.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060533 restraints weight = 100668.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061381 restraints weight = 73770.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062031 restraints weight = 60726.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062385 restraints weight = 53459.025| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35640 Z= 0.124 Angle : 0.617 10.964 48126 Z= 0.307 Chirality : 0.045 0.171 5406 Planarity : 0.004 0.046 6390 Dihedral : 4.790 24.692 4842 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.08 (0.12), residues: 4422 helix: -0.72 (0.13), residues: 1644 sheet: -2.19 (0.19), residues: 552 loop : -1.62 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 313 TYR 0.009 0.001 TYR B 203 PHE 0.020 0.001 PHE A 363 TRP 0.008 0.001 TRP B 454 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00276 (35640) covalent geometry : angle 0.61710 (48126) hydrogen bonds : bond 0.03457 ( 1098) hydrogen bonds : angle 4.70941 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 1.423 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0910 (mmp) cc_final: -0.0118 (tpt) REVERT: A 307 ASP cc_start: 0.9248 (p0) cc_final: 0.8628 (t0) REVERT: A 343 VAL cc_start: 0.9382 (t) cc_final: 0.9157 (m) REVERT: A 639 LEU cc_start: 0.9331 (mt) cc_final: 0.8861 (mp) REVERT: A 640 ASP cc_start: 0.8158 (p0) cc_final: 0.7776 (p0) REVERT: A 740 MET cc_start: 0.9018 (tpp) cc_final: 0.8501 (tpp) REVERT: B 46 MET cc_start: 0.1452 (mmp) cc_final: 0.0063 (tpt) REVERT: B 242 LEU cc_start: 0.9637 (mt) cc_final: 0.9157 (tp) REVERT: B 508 MET cc_start: 0.8311 (tpp) cc_final: 0.7907 (tpp) REVERT: B 550 MET cc_start: 0.9210 (mtm) cc_final: 0.8766 (mtt) REVERT: B 639 LEU cc_start: 0.9240 (mt) cc_final: 0.8824 (mp) REVERT: B 640 ASP cc_start: 0.8066 (p0) cc_final: 0.7841 (p0) REVERT: B 764 GLN cc_start: 0.6911 (tt0) cc_final: 0.6196 (tp40) REVERT: C 46 MET cc_start: -0.0365 (mmp) cc_final: -0.1298 (tpt) REVERT: C 242 LEU cc_start: 0.9581 (mt) cc_final: 0.9253 (tp) REVERT: C 639 LEU cc_start: 0.9076 (mt) cc_final: 0.8724 (mp) REVERT: C 640 ASP cc_start: 0.7836 (p0) cc_final: 0.7584 (p0) REVERT: C 740 MET cc_start: 0.9335 (tpp) cc_final: 0.9043 (tpp) REVERT: C 764 GLN cc_start: 0.7129 (tt0) cc_final: 0.6878 (tt0) REVERT: D 46 MET cc_start: 0.1181 (mmp) cc_final: 0.0248 (tpt) REVERT: D 307 ASP cc_start: 0.9303 (p0) cc_final: 0.8831 (m-30) REVERT: D 464 LEU cc_start: 0.7617 (tt) cc_final: 0.7292 (tp) REVERT: D 640 ASP cc_start: 0.8038 (p0) cc_final: 0.7722 (p0) REVERT: D 740 MET cc_start: 0.9157 (tpp) cc_final: 0.8704 (tpp) REVERT: E 46 MET cc_start: 0.0614 (mmp) cc_final: -0.0748 (tpt) REVERT: E 242 LEU cc_start: 0.9447 (mt) cc_final: 0.9017 (tp) REVERT: E 508 MET cc_start: 0.8504 (mmm) cc_final: 0.8218 (tpp) REVERT: E 564 ASP cc_start: 0.8401 (p0) cc_final: 0.8169 (t0) REVERT: E 639 LEU cc_start: 0.8989 (mt) cc_final: 0.8510 (mp) REVERT: E 640 ASP cc_start: 0.8102 (p0) cc_final: 0.7862 (p0) REVERT: E 687 LEU cc_start: 0.8871 (pt) cc_final: 0.8529 (mp) REVERT: E 740 MET cc_start: 0.9178 (tpp) cc_final: 0.8914 (tpp) REVERT: F 46 MET cc_start: 0.0102 (mmp) cc_final: -0.0781 (tpt) REVERT: F 242 LEU cc_start: 0.9580 (mt) cc_final: 0.9236 (tp) REVERT: F 275 MET cc_start: 0.8874 (mmp) cc_final: 0.8669 (mmm) REVERT: F 344 MET cc_start: 0.8989 (mtp) cc_final: 0.8666 (mtt) REVERT: F 640 ASP cc_start: 0.7971 (p0) cc_final: 0.7711 (p0) REVERT: F 740 MET cc_start: 0.9339 (tpp) cc_final: 0.9030 (tpp) outliers start: 3 outliers final: 0 residues processed: 261 average time/residue: 0.1883 time to fit residues: 84.6016 Evaluate side-chains 203 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 165 optimal weight: 0.0870 chunk 183 optimal weight: 0.9990 chunk 392 optimal weight: 0.0020 chunk 411 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 chunk 235 optimal weight: 50.0000 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.091654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059611 restraints weight = 162180.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061119 restraints weight = 100150.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062003 restraints weight = 73511.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.062652 restraints weight = 60444.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.063010 restraints weight = 53145.116| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35640 Z= 0.103 Angle : 0.593 10.295 48126 Z= 0.291 Chirality : 0.045 0.166 5406 Planarity : 0.004 0.043 6390 Dihedral : 4.601 22.548 4842 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.67 (0.12), residues: 4422 helix: -0.42 (0.13), residues: 1638 sheet: -2.08 (0.19), residues: 564 loop : -1.29 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.009 0.001 TYR F 244 PHE 0.018 0.001 PHE D 563 TRP 0.015 0.001 TRP D 476 HIS 0.002 0.000 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00232 (35640) covalent geometry : angle 0.59251 (48126) hydrogen bonds : bond 0.02989 ( 1098) hydrogen bonds : angle 4.49894 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 1.180 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.0805 (mmp) cc_final: -0.0242 (tpt) REVERT: A 307 ASP cc_start: 0.9190 (p0) cc_final: 0.8558 (t0) REVERT: A 512 LYS cc_start: 0.9015 (ptpp) cc_final: 0.8609 (mmtt) REVERT: A 639 LEU cc_start: 0.9222 (mt) cc_final: 0.8745 (mp) REVERT: A 640 ASP cc_start: 0.7957 (p0) cc_final: 0.7682 (p0) REVERT: A 740 MET cc_start: 0.9108 (tpp) cc_final: 0.8540 (tpp) REVERT: B 46 MET cc_start: 0.1339 (mmp) cc_final: -0.0079 (tpt) REVERT: B 242 LEU cc_start: 0.9669 (mt) cc_final: 0.9176 (tp) REVERT: B 275 MET cc_start: 0.8979 (mmm) cc_final: 0.8655 (mmm) REVERT: B 344 MET cc_start: 0.8719 (mtp) cc_final: 0.8509 (mtp) REVERT: B 508 MET cc_start: 0.8146 (tpp) cc_final: 0.7906 (tpp) REVERT: B 550 MET cc_start: 0.9242 (mtm) cc_final: 0.8796 (mtt) REVERT: B 639 LEU cc_start: 0.8993 (mt) cc_final: 0.8482 (mp) REVERT: B 764 GLN cc_start: 0.6789 (tt0) cc_final: 0.6084 (tp40) REVERT: C 46 MET cc_start: -0.0339 (mmp) cc_final: -0.1388 (tpt) REVERT: C 242 LEU cc_start: 0.9589 (mt) cc_final: 0.9285 (tp) REVERT: C 639 LEU cc_start: 0.9084 (mt) cc_final: 0.8642 (mp) REVERT: C 640 ASP cc_start: 0.7965 (p0) cc_final: 0.7725 (p0) REVERT: C 740 MET cc_start: 0.9337 (tpp) cc_final: 0.9008 (tpp) REVERT: C 764 GLN cc_start: 0.6997 (tt0) cc_final: 0.5729 (tp40) REVERT: D 46 MET cc_start: 0.0903 (mmp) cc_final: -0.0153 (tpt) REVERT: D 242 LEU cc_start: 0.9498 (mt) cc_final: 0.9022 (tt) REVERT: D 275 MET cc_start: 0.8955 (mmm) cc_final: 0.8688 (mmm) REVERT: D 307 ASP cc_start: 0.9256 (p0) cc_final: 0.8800 (m-30) REVERT: D 464 LEU cc_start: 0.7633 (tt) cc_final: 0.7305 (tp) REVERT: D 582 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8924 (tt) REVERT: D 640 ASP cc_start: 0.8001 (p0) cc_final: 0.7687 (p0) REVERT: D 740 MET cc_start: 0.9205 (tpp) cc_final: 0.8678 (tpp) REVERT: E 46 MET cc_start: 0.0532 (mmp) cc_final: -0.0849 (tpt) REVERT: E 242 LEU cc_start: 0.9493 (mt) cc_final: 0.8889 (tt) REVERT: E 332 MET cc_start: 0.8962 (ttt) cc_final: 0.8756 (tmm) REVERT: E 508 MET cc_start: 0.8523 (mmm) cc_final: 0.8147 (tpp) REVERT: E 582 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8856 (tt) REVERT: E 639 LEU cc_start: 0.9024 (mt) cc_final: 0.8330 (mp) REVERT: E 640 ASP cc_start: 0.8061 (p0) cc_final: 0.7806 (p0) REVERT: E 687 LEU cc_start: 0.8876 (pt) cc_final: 0.8634 (mp) REVERT: E 740 MET cc_start: 0.9187 (tpp) cc_final: 0.8969 (tpp) REVERT: F 46 MET cc_start: 0.0011 (mmp) cc_final: -0.0878 (tpt) REVERT: F 242 LEU cc_start: 0.9585 (mt) cc_final: 0.9336 (tp) REVERT: F 508 MET cc_start: 0.8173 (tpt) cc_final: 0.7663 (tpt) REVERT: F 640 ASP cc_start: 0.8115 (p0) cc_final: 0.7800 (p0) REVERT: F 740 MET cc_start: 0.9324 (tpp) cc_final: 0.9062 (tpp) REVERT: F 764 GLN cc_start: 0.6610 (tt0) cc_final: 0.5986 (tp40) outliers start: 7 outliers final: 0 residues processed: 275 average time/residue: 0.1854 time to fit residues: 87.5445 Evaluate side-chains 213 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 184 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 376 optimal weight: 20.0000 chunk 155 optimal weight: 40.0000 chunk 299 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.090956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057935 restraints weight = 155285.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059296 restraints weight = 98792.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060149 restraints weight = 73939.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060732 restraints weight = 61441.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061023 restraints weight = 55004.005| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35640 Z= 0.109 Angle : 0.579 10.251 48126 Z= 0.285 Chirality : 0.044 0.179 5406 Planarity : 0.004 0.044 6390 Dihedral : 4.469 22.329 4842 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.37 (0.13), residues: 4422 helix: -0.19 (0.13), residues: 1644 sheet: -1.94 (0.19), residues: 570 loop : -1.10 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 362 TYR 0.007 0.001 TYR F 244 PHE 0.013 0.001 PHE C 771 TRP 0.013 0.001 TRP F 551 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00241 (35640) covalent geometry : angle 0.57882 (48126) hydrogen bonds : bond 0.02825 ( 1098) hydrogen bonds : angle 4.35764 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 1.255 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1415 (mmp) cc_final: 0.0347 (tpt) REVERT: A 307 ASP cc_start: 0.9264 (p0) cc_final: 0.8620 (t0) REVERT: A 740 MET cc_start: 0.9220 (tpp) cc_final: 0.8824 (tpp) REVERT: B 46 MET cc_start: 0.1860 (mmp) cc_final: 0.0542 (tpt) REVERT: B 242 LEU cc_start: 0.9611 (mt) cc_final: 0.9071 (tp) REVERT: B 275 MET cc_start: 0.9094 (mmm) cc_final: 0.8824 (mmm) REVERT: B 344 MET cc_start: 0.8940 (mtp) cc_final: 0.8695 (mtp) REVERT: B 550 MET cc_start: 0.9192 (mtm) cc_final: 0.8715 (mtt) REVERT: B 740 MET cc_start: 0.6931 (ptt) cc_final: 0.6627 (ptt) REVERT: C 46 MET cc_start: 0.0390 (mmp) cc_final: -0.0505 (tpt) REVERT: C 242 LEU cc_start: 0.9548 (mt) cc_final: 0.9153 (tp) REVERT: C 344 MET cc_start: 0.8834 (mtp) cc_final: 0.8586 (mtt) REVERT: C 639 LEU cc_start: 0.9161 (mt) cc_final: 0.8680 (mp) REVERT: C 740 MET cc_start: 0.9392 (tpp) cc_final: 0.9052 (tpp) REVERT: C 764 GLN cc_start: 0.7151 (tt0) cc_final: 0.5820 (tp40) REVERT: D 46 MET cc_start: 0.1683 (mmp) cc_final: 0.0631 (tpt) REVERT: D 242 LEU cc_start: 0.9418 (mt) cc_final: 0.8857 (tt) REVERT: D 275 MET cc_start: 0.9017 (mmm) cc_final: 0.8651 (mmm) REVERT: D 307 ASP cc_start: 0.9310 (p0) cc_final: 0.8762 (m-30) REVERT: D 420 LEU cc_start: 0.9275 (tt) cc_final: 0.9056 (mm) REVERT: D 464 LEU cc_start: 0.7529 (tt) cc_final: 0.7232 (tp) REVERT: D 512 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8619 (mmtt) REVERT: D 640 ASP cc_start: 0.8015 (p0) cc_final: 0.7782 (p0) REVERT: D 740 MET cc_start: 0.9226 (tpp) cc_final: 0.8834 (tpp) REVERT: E 46 MET cc_start: 0.0926 (mmp) cc_final: -0.0346 (tpt) REVERT: E 242 LEU cc_start: 0.9468 (mt) cc_final: 0.9012 (tp) REVERT: E 508 MET cc_start: 0.8531 (mmm) cc_final: 0.8177 (tpp) REVERT: E 740 MET cc_start: 0.9316 (tpp) cc_final: 0.9102 (tpp) REVERT: F 46 MET cc_start: 0.0514 (mmp) cc_final: -0.0467 (tpt) REVERT: F 242 LEU cc_start: 0.9542 (mt) cc_final: 0.9171 (tp) REVERT: F 332 MET cc_start: 0.9260 (tmm) cc_final: 0.9054 (tmm) REVERT: F 564 ASP cc_start: 0.8504 (p0) cc_final: 0.8243 (t0) REVERT: F 640 ASP cc_start: 0.8136 (p0) cc_final: 0.7916 (p0) REVERT: F 740 MET cc_start: 0.9382 (tpp) cc_final: 0.9103 (tpp) REVERT: F 764 GLN cc_start: 0.6737 (tt0) cc_final: 0.6042 (tp40) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.1995 time to fit residues: 85.2448 Evaluate side-chains 206 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 431 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 254 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 384 HIS A 458 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 458 GLN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN C 215 GLN C 340 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 340 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 384 HIS E 458 GLN ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS F 384 HIS ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.086200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052395 restraints weight = 159987.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052288 restraints weight = 118840.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053040 restraints weight = 92063.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053576 restraints weight = 77015.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053782 restraints weight = 66433.779| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 35640 Z= 0.344 Angle : 0.817 12.489 48126 Z= 0.419 Chirality : 0.048 0.168 5406 Planarity : 0.006 0.049 6390 Dihedral : 5.149 24.561 4842 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.77 (0.12), residues: 4422 helix: -0.75 (0.12), residues: 1626 sheet: -2.24 (0.20), residues: 522 loop : -1.13 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 560 TYR 0.013 0.002 TYR A 755 PHE 0.035 0.003 PHE B 563 TRP 0.028 0.003 TRP F 476 HIS 0.010 0.003 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00706 (35640) covalent geometry : angle 0.81743 (48126) hydrogen bonds : bond 0.04172 ( 1098) hydrogen bonds : angle 5.28041 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 212 time to evaluate : 1.216 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1703 (mmp) cc_final: 0.0500 (tpt) REVERT: A 740 MET cc_start: 0.9277 (tpp) cc_final: 0.8910 (tpp) REVERT: B 46 MET cc_start: 0.1770 (mmp) cc_final: 0.0399 (tpt) REVERT: B 550 MET cc_start: 0.8937 (mtm) cc_final: 0.8658 (mtp) REVERT: B 640 ASP cc_start: 0.8068 (p0) cc_final: 0.7809 (p0) REVERT: B 740 MET cc_start: 0.7027 (ptt) cc_final: 0.6823 (ptt) REVERT: C 46 MET cc_start: 0.0103 (mmp) cc_final: -0.0835 (tpt) REVERT: C 740 MET cc_start: 0.9486 (tpp) cc_final: 0.9132 (tpp) REVERT: D 46 MET cc_start: 0.1894 (mmp) cc_final: 0.0714 (tpt) REVERT: D 740 MET cc_start: 0.9260 (tpp) cc_final: 0.8808 (tpp) REVERT: E 46 MET cc_start: 0.1076 (mmp) cc_final: -0.0238 (tpt) REVERT: E 508 MET cc_start: 0.8705 (mmm) cc_final: 0.8043 (tpp) REVERT: E 740 MET cc_start: 0.9340 (tpp) cc_final: 0.9035 (tpp) REVERT: F 46 MET cc_start: 0.0595 (mmp) cc_final: -0.0425 (tpt) REVERT: F 740 MET cc_start: 0.9504 (tpp) cc_final: 0.9105 (tpp) outliers start: 3 outliers final: 0 residues processed: 215 average time/residue: 0.2011 time to fit residues: 72.6414 Evaluate side-chains 177 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 218 optimal weight: 0.8980 chunk 369 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 398 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 391 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 458 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 384 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 764 GLN D 103 GLN D 384 HIS ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 103 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 GLN F 215 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.090332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057305 restraints weight = 163509.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058651 restraints weight = 105215.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059473 restraints weight = 79391.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059869 restraints weight = 66938.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060232 restraints weight = 61328.849| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35640 Z= 0.110 Angle : 0.616 10.567 48126 Z= 0.305 Chirality : 0.045 0.238 5406 Planarity : 0.004 0.042 6390 Dihedral : 4.631 23.893 4842 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.03 % Allowed : 1.80 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.19 (0.13), residues: 4422 helix: -0.14 (0.13), residues: 1644 sheet: -1.66 (0.21), residues: 498 loop : -0.99 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 693 TYR 0.015 0.001 TYR C 244 PHE 0.013 0.001 PHE E 563 TRP 0.009 0.001 TRP F 476 HIS 0.009 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00242 (35640) covalent geometry : angle 0.61598 (48126) hydrogen bonds : bond 0.02928 ( 1098) hydrogen bonds : angle 4.45986 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.234 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1740 (mmp) cc_final: 0.0682 (tpt) REVERT: A 242 LEU cc_start: 0.9476 (mt) cc_final: 0.9060 (tp) REVERT: A 275 MET cc_start: 0.9111 (mmm) cc_final: 0.8870 (mmm) REVERT: A 411 LEU cc_start: 0.9353 (mt) cc_final: 0.9081 (pp) REVERT: A 740 MET cc_start: 0.9133 (tpp) cc_final: 0.8764 (tpp) REVERT: B 46 MET cc_start: 0.2212 (mmp) cc_final: 0.0910 (tpt) REVERT: B 242 LEU cc_start: 0.9608 (mt) cc_final: 0.9020 (tp) REVERT: B 550 MET cc_start: 0.9021 (mtm) cc_final: 0.8670 (mtt) REVERT: C 46 MET cc_start: 0.0608 (mmp) cc_final: -0.0421 (tpt) REVERT: C 242 LEU cc_start: 0.9553 (mt) cc_final: 0.9131 (tp) REVERT: C 740 MET cc_start: 0.9354 (tpp) cc_final: 0.8991 (tpp) REVERT: D 46 MET cc_start: 0.2346 (mmp) cc_final: 0.1328 (tpt) REVERT: D 242 LEU cc_start: 0.9510 (mt) cc_final: 0.8979 (tt) REVERT: D 420 LEU cc_start: 0.9261 (tt) cc_final: 0.9060 (mm) REVERT: D 460 ASN cc_start: 0.8500 (p0) cc_final: 0.8192 (p0) REVERT: D 740 MET cc_start: 0.9276 (tpp) cc_final: 0.9014 (tpp) REVERT: E 46 MET cc_start: 0.1410 (mmp) cc_final: 0.0173 (tpt) REVERT: E 242 LEU cc_start: 0.9599 (mt) cc_final: 0.9053 (tp) REVERT: E 508 MET cc_start: 0.8555 (mmm) cc_final: 0.7975 (tpp) REVERT: F 46 MET cc_start: 0.1065 (mmp) cc_final: 0.0054 (tpt) REVERT: F 242 LEU cc_start: 0.9582 (mt) cc_final: 0.9243 (tp) REVERT: F 332 MET cc_start: 0.9546 (ttp) cc_final: 0.8502 (tmm) REVERT: F 411 LEU cc_start: 0.9149 (mt) cc_final: 0.8915 (pp) REVERT: F 460 ASN cc_start: 0.8152 (p0) cc_final: 0.7829 (p0) REVERT: F 508 MET cc_start: 0.7483 (tpt) cc_final: 0.5794 (tpt) REVERT: F 640 ASP cc_start: 0.8071 (p0) cc_final: 0.7842 (p0) REVERT: F 740 MET cc_start: 0.9328 (tpp) cc_final: 0.9029 (tpp) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2303 time to fit residues: 88.9482 Evaluate side-chains 196 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 443 optimal weight: 0.0070 chunk 83 optimal weight: 50.0000 chunk 413 optimal weight: 3.9990 chunk 356 optimal weight: 0.6980 chunk 344 optimal weight: 0.0770 chunk 433 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 110 optimal weight: 0.0060 chunk 305 optimal weight: 40.0000 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 458 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 458 GLN C 538 ASN D 103 GLN D 458 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.090687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057986 restraints weight = 164045.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059190 restraints weight = 108729.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060055 restraints weight = 80325.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060652 restraints weight = 66720.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060887 restraints weight = 59019.663| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35640 Z= 0.103 Angle : 0.597 9.844 48126 Z= 0.292 Chirality : 0.044 0.184 5406 Planarity : 0.004 0.042 6390 Dihedral : 4.397 23.249 4842 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 1.23 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.96 (0.13), residues: 4422 helix: 0.07 (0.13), residues: 1650 sheet: -1.41 (0.21), residues: 498 loop : -0.92 (0.14), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 766 TYR 0.011 0.001 TYR C 244 PHE 0.014 0.001 PHE E 563 TRP 0.007 0.001 TRP C 476 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00230 (35640) covalent geometry : angle 0.59694 (48126) hydrogen bonds : bond 0.02768 ( 1098) hydrogen bonds : angle 4.36595 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 1.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.1427 (mmp) cc_final: 0.0229 (tpt) REVERT: A 242 LEU cc_start: 0.9450 (mt) cc_final: 0.9041 (tp) REVERT: A 275 MET cc_start: 0.9155 (mmm) cc_final: 0.8897 (mmm) REVERT: A 411 LEU cc_start: 0.9331 (mt) cc_final: 0.9117 (pp) REVERT: A 740 MET cc_start: 0.9134 (tpp) cc_final: 0.8907 (tpp) REVERT: B 46 MET cc_start: 0.1512 (mmp) cc_final: 0.0340 (tpt) REVERT: B 242 LEU cc_start: 0.9610 (mt) cc_final: 0.9016 (tp) REVERT: B 550 MET cc_start: 0.9060 (mtm) cc_final: 0.8753 (mtt) REVERT: C 46 MET cc_start: 0.0501 (mmp) cc_final: -0.0523 (tpt) REVERT: C 242 LEU cc_start: 0.9601 (mt) cc_final: 0.9200 (tp) REVERT: C 332 MET cc_start: 0.9302 (tmm) cc_final: 0.8988 (tmm) REVERT: C 458 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8091 (pp30) REVERT: C 460 ASN cc_start: 0.8141 (p0) cc_final: 0.7801 (p0) REVERT: C 740 MET cc_start: 0.9318 (tpp) cc_final: 0.8985 (tpp) REVERT: D 46 MET cc_start: 0.1717 (mmp) cc_final: 0.0613 (tpt) REVERT: D 242 LEU cc_start: 0.9492 (mt) cc_final: 0.8944 (tt) REVERT: D 411 LEU cc_start: 0.9334 (mt) cc_final: 0.9036 (pp) REVERT: D 420 LEU cc_start: 0.9217 (tt) cc_final: 0.9016 (mm) REVERT: D 460 ASN cc_start: 0.8398 (p0) cc_final: 0.8097 (p0) REVERT: D 512 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8750 (mmtm) REVERT: E 46 MET cc_start: 0.0952 (mmp) cc_final: -0.0356 (tpt) REVERT: E 242 LEU cc_start: 0.9607 (mt) cc_final: 0.9039 (tp) REVERT: E 508 MET cc_start: 0.8481 (mmm) cc_final: 0.7937 (tpp) REVERT: F 46 MET cc_start: 0.0696 (mmp) cc_final: -0.0310 (tpt) REVERT: F 242 LEU cc_start: 0.9608 (mt) cc_final: 0.9307 (tp) REVERT: F 332 MET cc_start: 0.9527 (ttp) cc_final: 0.8494 (tmm) REVERT: F 460 ASN cc_start: 0.8096 (p0) cc_final: 0.7717 (p0) REVERT: F 640 ASP cc_start: 0.8010 (p0) cc_final: 0.7771 (p0) REVERT: F 740 MET cc_start: 0.9302 (tpp) cc_final: 0.9008 (tpp) outliers start: 3 outliers final: 0 residues processed: 240 average time/residue: 0.2214 time to fit residues: 88.7751 Evaluate side-chains 197 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 301 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 405 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 458 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 458 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 317 HIS D 458 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 317 HIS ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.086745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051904 restraints weight = 159719.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053036 restraints weight = 116861.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052799 restraints weight = 90504.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053465 restraints weight = 78263.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053456 restraints weight = 68582.391| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 35640 Z= 0.268 Angle : 0.726 10.243 48126 Z= 0.372 Chirality : 0.047 0.244 5406 Planarity : 0.005 0.043 6390 Dihedral : 4.798 23.942 4842 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.08 % Allowed : 0.94 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.25 (0.12), residues: 4422 helix: -0.14 (0.13), residues: 1614 sheet: -1.78 (0.21), residues: 516 loop : -1.04 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.010 0.002 TYR F 495 PHE 0.018 0.002 PHE D 768 TRP 0.024 0.003 TRP B 476 HIS 0.008 0.002 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00561 (35640) covalent geometry : angle 0.72603 (48126) hydrogen bonds : bond 0.03477 ( 1098) hydrogen bonds : angle 4.93018 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 1.079 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 46 MET cc_start: 0.2334 (mmp) cc_final: 0.1112 (tpt) REVERT: A 740 MET cc_start: 0.9106 (tpp) cc_final: 0.8899 (tpp) REVERT: B 46 MET cc_start: 0.2016 (mmp) cc_final: 0.0886 (tpt) REVERT: B 740 MET cc_start: 0.9284 (tpp) cc_final: 0.8770 (ptt) REVERT: C 46 MET cc_start: 0.0883 (mmp) cc_final: 0.0001 (tpt) REVERT: C 332 MET cc_start: 0.9281 (tmm) cc_final: 0.8954 (tmm) REVERT: C 458 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8148 (pp30) REVERT: C 740 MET cc_start: 0.9370 (tpp) cc_final: 0.9093 (tpp) REVERT: D 46 MET cc_start: 0.2619 (mmp) cc_final: 0.1517 (tpt) REVERT: D 242 LEU cc_start: 0.9544 (mt) cc_final: 0.9000 (tp) REVERT: D 460 ASN cc_start: 0.8647 (p0) cc_final: 0.8180 (p0) REVERT: E 46 MET cc_start: 0.1752 (mmp) cc_final: 0.0496 (tpt) REVERT: E 508 MET cc_start: 0.8698 (mmm) cc_final: 0.8408 (tpp) REVERT: F 46 MET cc_start: 0.1479 (mmp) cc_final: 0.0400 (tpt) REVERT: F 332 MET cc_start: 0.9482 (ttp) cc_final: 0.8461 (tmm) REVERT: F 460 ASN cc_start: 0.8473 (p0) cc_final: 0.8021 (p0) REVERT: F 740 MET cc_start: 0.9352 (tpp) cc_final: 0.8874 (tpp) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.1998 time to fit residues: 69.1882 Evaluate side-chains 186 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 342 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 441 optimal weight: 3.9990 chunk 375 optimal weight: 40.0000 chunk 96 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 306 optimal weight: 10.0000 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 458 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 317 HIS D 458 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN D 760 GLN D 764 GLN E 103 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 760 GLN E 764 GLN F 103 GLN ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.088582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055789 restraints weight = 160607.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056801 restraints weight = 107159.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057602 restraints weight = 80339.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058199 restraints weight = 66727.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.058506 restraints weight = 59534.298| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35640 Z= 0.123 Angle : 0.624 10.155 48126 Z= 0.311 Chirality : 0.045 0.264 5406 Planarity : 0.004 0.040 6390 Dihedral : 4.560 22.796 4842 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.00 (0.13), residues: 4422 helix: 0.06 (0.13), residues: 1656 sheet: -1.56 (0.21), residues: 510 loop : -0.93 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.010 0.001 TYR C 244 PHE 0.013 0.001 PHE E 563 TRP 0.014 0.002 TRP B 476 HIS 0.003 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00277 (35640) covalent geometry : angle 0.62417 (48126) hydrogen bonds : bond 0.02907 ( 1098) hydrogen bonds : angle 4.58733 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8844 Ramachandran restraints generated. 4422 Oldfield, 0 Emsley, 4422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 1.268 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: symmetry clash REVERT: A 46 MET cc_start: 0.1811 (mmp) cc_final: 0.0548 (tpt) REVERT: A 242 LEU cc_start: 0.9446 (mt) cc_final: 0.9011 (tp) REVERT: A 411 LEU cc_start: 0.9386 (mt) cc_final: 0.9065 (pp) REVERT: A 740 MET cc_start: 0.9184 (tpp) cc_final: 0.8967 (tpp) REVERT: B 46 MET cc_start: 0.1678 (mmp) cc_final: 0.0520 (tpt) REVERT: B 242 LEU cc_start: 0.9586 (mt) cc_final: 0.8952 (tp) REVERT: B 550 MET cc_start: 0.8963 (mtm) cc_final: 0.8713 (mtt) REVERT: B 740 MET cc_start: 0.9354 (tpp) cc_final: 0.8898 (ptt) REVERT: C 46 MET cc_start: 0.0499 (mmp) cc_final: -0.0385 (tpt) REVERT: C 242 LEU cc_start: 0.9571 (mt) cc_final: 0.9155 (tp) REVERT: C 332 MET cc_start: 0.9413 (tmm) cc_final: 0.9120 (tmm) REVERT: C 458 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: C 740 MET cc_start: 0.9343 (tpp) cc_final: 0.8997 (tpp) REVERT: D 46 MET cc_start: 0.2126 (mmp) cc_final: 0.0978 (tpt) REVERT: D 242 LEU cc_start: 0.9491 (mt) cc_final: 0.9025 (tp) REVERT: D 411 LEU cc_start: 0.9384 (mt) cc_final: 0.8984 (pp) REVERT: D 420 LEU cc_start: 0.9331 (tt) cc_final: 0.9054 (mm) REVERT: D 460 ASN cc_start: 0.8552 (p0) cc_final: 0.8264 (p0) REVERT: E 46 MET cc_start: 0.1383 (mmp) cc_final: 0.0108 (tpt) REVERT: E 242 LEU cc_start: 0.9571 (mt) cc_final: 0.8960 (tp) REVERT: E 508 MET cc_start: 0.8619 (mmm) cc_final: 0.8073 (tpp) REVERT: F 46 MET cc_start: 0.0916 (mmp) cc_final: -0.0149 (tpt) REVERT: F 242 LEU cc_start: 0.9573 (mt) cc_final: 0.9169 (tp) REVERT: F 332 MET cc_start: 0.9504 (ttp) cc_final: 0.8462 (tmm) REVERT: F 420 LEU cc_start: 0.9336 (tt) cc_final: 0.9129 (mm) REVERT: F 460 ASN cc_start: 0.8232 (p0) cc_final: 0.7838 (p0) REVERT: F 740 MET cc_start: 0.9350 (tpp) cc_final: 0.8863 (tpp) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1891 time to fit residues: 71.1465 Evaluate side-chains 191 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 165 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 288 optimal weight: 0.9980 chunk 412 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 344 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 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 103 GLN A 317 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 317 HIS C 458 GLN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 458 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.089191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055567 restraints weight = 163080.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056479 restraints weight = 108152.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057263 restraints weight = 82041.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057698 restraints weight = 69476.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058040 restraints weight = 61998.559| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35640 Z= 0.113 Angle : 0.614 10.682 48126 Z= 0.303 Chirality : 0.045 0.255 5406 Planarity : 0.004 0.040 6390 Dihedral : 4.438 22.240 4842 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.05 % Allowed : 0.50 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.87 (0.13), residues: 4422 helix: 0.16 (0.13), residues: 1650 sheet: -1.41 (0.21), residues: 510 loop : -0.86 (0.14), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 766 TYR 0.010 0.001 TYR C 244 PHE 0.011 0.001 PHE D 563 TRP 0.012 0.001 TRP B 476 HIS 0.002 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00256 (35640) covalent geometry : angle 0.61352 (48126) hydrogen bonds : bond 0.02779 ( 1098) hydrogen bonds : angle 4.47669 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5808.12 seconds wall clock time: 100 minutes 59.59 seconds (6059.59 seconds total)