Starting phenix.real_space_refine on Sat Mar 7 12:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0f_66433/03_2026/9x0f_66433.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 198 5.16 5 C 27036 2.51 5 N 7326 2.21 5 O 7992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42552 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "E" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "F" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "G" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "H" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "I" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "J" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "K" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "L" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "M" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "N" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "O" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "P" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "Q" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Chain: "R" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2364 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 284} Chain breaks: 1 Time building chain proxies: 8.71, per 1000 atoms: 0.20 Number of scatterers: 42552 At special positions: 0 Unit cell: (136.9, 134.68, 233.84, 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 198 16.00 O 7992 8.00 N 7326 7.00 C 27036 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9936 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 13 sheets defined 82.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 418 through 430 Proline residue: A 424 - end of helix Processing helix chain 'A' and resid 435 through 449 removed outlier: 3.714A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 494 through 516 removed outlier: 4.090A pdb=" N ILE A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 544 removed outlier: 3.786A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.847A pdb=" N PHE A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 611 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.654A pdb=" N MET A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.762A pdb=" N ARG A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 670 through 698 removed outlier: 4.318A pdb=" N PHE A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 Processing helix chain 'B' and resid 418 through 429 Proline residue: B 424 - end of helix Processing helix chain 'B' and resid 435 through 449 removed outlier: 3.838A pdb=" N VAL B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 478 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 513 removed outlier: 4.145A pdb=" N ILE B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 545 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 561 through 576 removed outlier: 3.967A pdb=" N PHE B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 610 removed outlier: 4.014A pdb=" N GLU B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.725A pdb=" N ARG B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 670 through 698 removed outlier: 4.196A pdb=" N PHE B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 713 Processing helix chain 'C' and resid 418 through 430 Proline residue: C 424 - end of helix removed outlier: 3.502A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 449 removed outlier: 3.522A pdb=" N ASN C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 477 removed outlier: 3.745A pdb=" N GLU C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 removed outlier: 3.546A pdb=" N ILE C 491 " --> pdb=" O THR C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 495 through 514 removed outlier: 3.826A pdb=" N LEU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 545 Processing helix chain 'C' and resid 549 through 575 removed outlier: 3.815A pdb=" N GLY C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 564 " --> pdb=" O LYS C 560 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 569 " --> pdb=" O PHE C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 605 Processing helix chain 'C' and resid 605 through 610 removed outlier: 3.859A pdb=" N TYR C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.853A pdb=" N ARG C 642 " --> pdb=" O ASN C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.770A pdb=" N LYS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 698 removed outlier: 3.953A pdb=" N PHE C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 713 Processing helix chain 'D' and resid 418 through 430 Proline residue: D 424 - end of helix removed outlier: 3.726A pdb=" N ALA D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 449 removed outlier: 3.765A pdb=" N GLN D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 478 removed outlier: 3.531A pdb=" N GLY D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.626A pdb=" N ILE D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 514 removed outlier: 3.875A pdb=" N ILE D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 545 Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 562 through 575 removed outlier: 3.516A pdb=" N ARG D 566 " --> pdb=" O GLY D 562 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 606 Processing helix chain 'D' and resid 625 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.615A pdb=" N ARG D 642 " --> pdb=" O ASN D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 670 through 698 removed outlier: 3.830A pdb=" N PHE D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 713 removed outlier: 3.534A pdb=" N THR D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 430 Proline residue: E 424 - end of helix removed outlier: 3.647A pdb=" N ALA E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 445 removed outlier: 3.941A pdb=" N GLN E 439 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 478 Processing helix chain 'E' and resid 487 through 493 Processing helix chain 'E' and resid 494 through 513 removed outlier: 3.978A pdb=" N ILE E 498 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 505 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 506 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN E 513 " --> pdb=" O LEU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 544 removed outlier: 3.737A pdb=" N VAL E 523 " --> pdb=" O ARG E 519 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 576 removed outlier: 4.209A pdb=" N LEU E 564 " --> pdb=" O LYS E 560 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE E 565 " --> pdb=" O THR E 561 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE E 568 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 605 removed outlier: 3.773A pdb=" N THR E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 removed outlier: 4.239A pdb=" N GLU E 621 " --> pdb=" O ASP E 618 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY E 622 " --> pdb=" O PHE E 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 618 through 622' Processing helix chain 'E' and resid 625 through 635 Processing helix chain 'E' and resid 639 through 652 Processing helix chain 'E' and resid 655 through 667 removed outlier: 3.979A pdb=" N LYS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 698 Processing helix chain 'E' and resid 704 through 713 Processing helix chain 'F' and resid 418 through 427 Proline residue: F 424 - end of helix removed outlier: 4.243A pdb=" N TYR F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 449 removed outlier: 4.159A pdb=" N VAL F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 478 Processing helix chain 'F' and resid 487 through 493 removed outlier: 3.593A pdb=" N ILE F 491 " --> pdb=" O ALA F 487 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 493 " --> pdb=" O HIS F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 514 removed outlier: 3.911A pdb=" N ILE F 498 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU F 505 " --> pdb=" O ALA F 501 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL F 506 " --> pdb=" O ASN F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 545 removed outlier: 3.572A pdb=" N VAL F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 575 removed outlier: 3.785A pdb=" N GLY F 563 " --> pdb=" O HIS F 559 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU F 564 " --> pdb=" O LYS F 560 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE F 565 " --> pdb=" O THR F 561 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE F 568 " --> pdb=" O LEU F 564 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 606 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 625 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.998A pdb=" N ARG F 642 " --> pdb=" O ASN F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 670 removed outlier: 3.829A pdb=" N LYS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 698 removed outlier: 4.426A pdb=" N PHE F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 713 removed outlier: 3.638A pdb=" N THR F 713 " --> pdb=" O GLU F 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 430 Proline residue: G 424 - end of helix Processing helix chain 'G' and resid 435 through 449 removed outlier: 3.794A pdb=" N VAL G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 478 Processing helix chain 'G' and resid 495 through 516 removed outlier: 3.820A pdb=" N LEU G 505 " --> pdb=" O ALA G 501 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL G 506 " --> pdb=" O ASN G 502 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 515 " --> pdb=" O GLU G 511 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 516 " --> pdb=" O LEU G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 545 removed outlier: 4.517A pdb=" N LEU G 522 " --> pdb=" O ALA G 518 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL G 523 " --> pdb=" O ARG G 519 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN G 544 " --> pdb=" O TYR G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 575 removed outlier: 3.527A pdb=" N GLY G 563 " --> pdb=" O HIS G 559 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU G 564 " --> pdb=" O LYS G 560 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE G 565 " --> pdb=" O THR G 561 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE G 568 " --> pdb=" O LEU G 564 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 611 Processing helix chain 'G' and resid 618 through 622 Processing helix chain 'G' and resid 625 through 635 removed outlier: 3.555A pdb=" N MET G 635 " --> pdb=" O LEU G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 652 removed outlier: 3.513A pdb=" N ARG G 642 " --> pdb=" O ASN G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 670 Processing helix chain 'G' and resid 670 through 698 removed outlier: 4.316A pdb=" N PHE G 674 " --> pdb=" O GLY G 670 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 713 Processing helix chain 'H' and resid 418 through 430 Proline residue: H 424 - end of helix Processing helix chain 'H' and resid 435 through 449 removed outlier: 4.087A pdb=" N VAL H 446 " --> pdb=" O ASP H 442 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 478 Processing helix chain 'H' and resid 487 through 492 removed outlier: 3.743A pdb=" N ILE H 491 " --> pdb=" O ALA H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 514 removed outlier: 3.703A pdb=" N ILE H 498 " --> pdb=" O LEU H 494 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU H 505 " --> pdb=" O ALA H 501 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 506 " --> pdb=" O ASN H 502 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS H 514 " --> pdb=" O GLN H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 545 Processing helix chain 'H' and resid 549 through 561 Processing helix chain 'H' and resid 561 through 576 removed outlier: 3.659A pdb=" N PHE H 565 " --> pdb=" O THR H 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE H 568 " --> pdb=" O LEU H 564 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 570 " --> pdb=" O ARG H 566 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET H 572 " --> pdb=" O PHE H 568 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA H 573 " --> pdb=" O GLY H 569 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL H 574 " --> pdb=" O ARG H 570 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS H 575 " --> pdb=" O LEU H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 610 removed outlier: 3.799A pdb=" N SER H 606 " --> pdb=" O GLN H 602 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA H 607 " --> pdb=" O ASN H 603 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU H 608 " --> pdb=" O LEU H 604 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 609 " --> pdb=" O VAL H 605 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 610 " --> pdb=" O SER H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 635 Processing helix chain 'H' and resid 638 through 652 removed outlier: 3.680A pdb=" N ARG H 642 " --> pdb=" O ASN H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 655 through 670 Processing helix chain 'H' and resid 670 through 698 removed outlier: 4.401A pdb=" N PHE H 674 " --> pdb=" O GLY H 670 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN H 676 " --> pdb=" O LEU H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 713 Processing helix chain 'I' and resid 418 through 430 Proline residue: I 424 - end of helix Processing helix chain 'I' and resid 435 through 449 removed outlier: 3.641A pdb=" N ASN I 445 " --> pdb=" O ILE I 441 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL I 446 " --> pdb=" O ASP I 442 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP I 447 " --> pdb=" O ALA I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 477 removed outlier: 3.814A pdb=" N GLU I 476 " --> pdb=" O LEU I 472 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP I 477 " --> pdb=" O ASP I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 514 removed outlier: 3.843A pdb=" N LEU I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL I 506 " --> pdb=" O ASN I 502 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS I 514 " --> pdb=" O GLN I 510 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 545 Processing helix chain 'I' and resid 549 through 575 removed outlier: 3.657A pdb=" N GLY I 563 " --> pdb=" O HIS I 559 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU I 564 " --> pdb=" O LYS I 560 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE I 565 " --> pdb=" O THR I 561 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE I 568 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY I 569 " --> pdb=" O PHE I 565 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS I 575 " --> pdb=" O LEU I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 605 Processing helix chain 'I' and resid 605 through 610 removed outlier: 4.185A pdb=" N TYR I 609 " --> pdb=" O VAL I 605 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR I 610 " --> pdb=" O SER I 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 605 through 610' Processing helix chain 'I' and resid 625 through 635 removed outlier: 3.513A pdb=" N MET I 635 " --> pdb=" O LEU I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 652 removed outlier: 4.032A pdb=" N ARG I 642 " --> pdb=" O ASN I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 655 through 670 removed outlier: 3.602A pdb=" N LYS I 659 " --> pdb=" O THR I 655 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 698 removed outlier: 3.858A pdb=" N PHE I 674 " --> pdb=" O GLY I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 713 Processing helix chain 'J' and resid 418 through 430 Proline residue: J 424 - end of helix Processing helix chain 'J' and resid 435 through 449 removed outlier: 3.994A pdb=" N GLN J 439 " --> pdb=" O GLY J 435 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 478 Processing helix chain 'J' and resid 487 through 491 removed outlier: 3.512A pdb=" N ILE J 491 " --> pdb=" O THR J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 514 removed outlier: 3.777A pdb=" N ILE J 498 " --> pdb=" O LEU J 494 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU J 505 " --> pdb=" O ALA J 501 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL J 506 " --> pdb=" O ASN J 502 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS J 514 " --> pdb=" O GLN J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 545 Processing helix chain 'J' and resid 549 through 561 Processing helix chain 'J' and resid 561 through 575 removed outlier: 4.317A pdb=" N PHE J 565 " --> pdb=" O THR J 561 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU J 567 " --> pdb=" O GLY J 563 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE J 568 " --> pdb=" O LEU J 564 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS J 575 " --> pdb=" O LEU J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 584 through 605 Processing helix chain 'J' and resid 625 through 635 Processing helix chain 'J' and resid 638 through 652 removed outlier: 3.748A pdb=" N ARG J 642 " --> pdb=" O ASN J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 655 through 670 removed outlier: 3.531A pdb=" N GLY J 670 " --> pdb=" O MET J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 670 through 698 removed outlier: 3.765A pdb=" N PHE J 674 " --> pdb=" O GLY J 670 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN J 676 " --> pdb=" O LEU J 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 713 removed outlier: 3.589A pdb=" N THR J 713 " --> pdb=" O GLU J 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 418 through 430 Proline residue: K 424 - end of helix removed outlier: 3.541A pdb=" N ILE K 428 " --> pdb=" O PRO K 424 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA K 430 " --> pdb=" O GLU K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 444 removed outlier: 3.956A pdb=" N GLN K 439 " --> pdb=" O GLY K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 447 No H-bonds generated for 'chain 'K' and resid 445 through 447' Processing helix chain 'K' and resid 451 through 478 Processing helix chain 'K' and resid 487 through 493 Processing helix chain 'K' and resid 495 through 513 removed outlier: 3.858A pdb=" N LEU K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL K 506 " --> pdb=" O ASN K 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN K 513 " --> pdb=" O LEU K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 545 removed outlier: 3.969A pdb=" N ASN K 530 " --> pdb=" O GLU K 526 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR K 532 " --> pdb=" O LEU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 576 removed outlier: 4.116A pdb=" N LEU K 564 " --> pdb=" O LYS K 560 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE K 565 " --> pdb=" O THR K 561 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE K 568 " --> pdb=" O LEU K 564 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL K 574 " --> pdb=" O ARG K 570 " (cutoff:3.500A) Processing helix chain 'K' and resid 584 through 605 removed outlier: 3.555A pdb=" N THR K 588 " --> pdb=" O LEU K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 635 Processing helix chain 'K' and resid 639 through 652 removed outlier: 3.617A pdb=" N ASN K 643 " --> pdb=" O LEU K 639 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY K 652 " --> pdb=" O ARG K 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 655 through 667 removed outlier: 3.931A pdb=" N LYS K 659 " --> pdb=" O THR K 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 670 through 698 removed outlier: 3.598A pdb=" N PHE K 674 " --> pdb=" O GLY K 670 " (cutoff:3.500A) Processing helix chain 'K' and resid 704 through 713 Processing helix chain 'L' and resid 418 through 423 removed outlier: 3.517A pdb=" N GLN L 422 " --> pdb=" O PRO L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 425 through 430 removed outlier: 3.609A pdb=" N THR L 429 " --> pdb=" O TYR L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 449 removed outlier: 4.055A pdb=" N VAL L 446 " --> pdb=" O ASP L 442 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP L 447 " --> pdb=" O ALA L 443 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 478 Processing helix chain 'L' and resid 487 through 493 Processing helix chain 'L' and resid 494 through 516 removed outlier: 3.897A pdb=" N ILE L 498 " --> pdb=" O LEU L 494 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU L 505 " --> pdb=" O ALA L 501 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL L 506 " --> pdb=" O ASN L 502 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU L 515 " --> pdb=" O GLU L 511 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY L 516 " --> pdb=" O LEU L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 545 removed outlier: 4.348A pdb=" N LEU L 521 " --> pdb=" O ASP L 517 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU L 522 " --> pdb=" O ALA L 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR L 532 " --> pdb=" O LEU L 528 " (cutoff:3.500A) Processing helix chain 'L' and resid 549 through 575 removed outlier: 3.754A pdb=" N GLY L 563 " --> pdb=" O HIS L 559 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU L 564 " --> pdb=" O LYS L 560 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE L 565 " --> pdb=" O THR L 561 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE L 568 " --> pdb=" O LEU L 564 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY L 569 " --> pdb=" O PHE L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 607 removed outlier: 3.824A pdb=" N ALA L 607 " --> pdb=" O ASN L 603 " (cutoff:3.500A) Processing helix chain 'L' and resid 625 through 635 Processing helix chain 'L' and resid 638 through 652 removed outlier: 3.842A pdb=" N ARG L 642 " --> pdb=" O ASN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 670 removed outlier: 3.598A pdb=" N LYS L 659 " --> pdb=" O THR L 655 " (cutoff:3.500A) Processing helix chain 'L' and resid 670 through 698 removed outlier: 4.452A pdb=" N PHE L 674 " --> pdb=" O GLY L 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 702 through 713 removed outlier: 3.653A pdb=" N THR L 713 " --> pdb=" O GLU L 709 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 429 Proline residue: M 424 - end of helix Processing helix chain 'M' and resid 435 through 449 removed outlier: 3.747A pdb=" N GLN M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL M 446 " --> pdb=" O ASP M 442 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP M 447 " --> pdb=" O ALA M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 477 Processing helix chain 'M' and resid 488 through 491 removed outlier: 3.537A pdb=" N ILE M 491 " --> pdb=" O THR M 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 488 through 491' Processing helix chain 'M' and resid 495 through 516 removed outlier: 3.986A pdb=" N LEU M 505 " --> pdb=" O ALA M 501 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL M 506 " --> pdb=" O ASN M 502 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU M 515 " --> pdb=" O GLU M 511 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY M 516 " --> pdb=" O LEU M 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 545 removed outlier: 3.578A pdb=" N VAL M 523 " --> pdb=" O ARG M 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN M 544 " --> pdb=" O TYR M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 549 through 561 removed outlier: 3.546A pdb=" N PHE M 554 " --> pdb=" O MET M 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 575 removed outlier: 3.936A pdb=" N PHE M 565 " --> pdb=" O THR M 561 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE M 568 " --> pdb=" O LEU M 564 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA M 573 " --> pdb=" O GLY M 569 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS M 575 " --> pdb=" O LEU M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 584 through 611 removed outlier: 3.604A pdb=" N LYS M 611 " --> pdb=" O ALA M 607 " (cutoff:3.500A) Processing helix chain 'M' and resid 625 through 635 Processing helix chain 'M' and resid 638 through 652 Processing helix chain 'M' and resid 655 through 670 Processing helix chain 'M' and resid 670 through 698 removed outlier: 4.165A pdb=" N PHE M 674 " --> pdb=" O GLY M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 713 Processing helix chain 'N' and resid 418 through 429 Proline residue: N 424 - end of helix Processing helix chain 'N' and resid 435 through 449 removed outlier: 4.059A pdb=" N VAL N 446 " --> pdb=" O ASP N 442 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP N 447 " --> pdb=" O ALA N 443 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 478 Processing helix chain 'N' and resid 487 through 492 Processing helix chain 'N' and resid 494 through 513 removed outlier: 4.219A pdb=" N ILE N 498 " --> pdb=" O LEU N 494 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU N 505 " --> pdb=" O ALA N 501 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL N 506 " --> pdb=" O ASN N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 545 Processing helix chain 'N' and resid 549 through 561 Processing helix chain 'N' and resid 561 through 575 removed outlier: 3.817A pdb=" N PHE N 565 " --> pdb=" O THR N 561 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE N 568 " --> pdb=" O LEU N 564 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET N 572 " --> pdb=" O PHE N 568 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA N 573 " --> pdb=" O GLY N 569 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS N 575 " --> pdb=" O LEU N 571 " (cutoff:3.500A) Processing helix chain 'N' and resid 584 through 610 removed outlier: 3.784A pdb=" N SER N 606 " --> pdb=" O GLN N 602 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA N 607 " --> pdb=" O ASN N 603 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR N 610 " --> pdb=" O SER N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 625 through 635 Processing helix chain 'N' and resid 638 through 652 removed outlier: 3.619A pdb=" N ARG N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 655 through 670 Processing helix chain 'N' and resid 670 through 698 removed outlier: 4.131A pdb=" N PHE N 674 " --> pdb=" O GLY N 670 " (cutoff:3.500A) Processing helix chain 'N' and resid 702 through 713 Processing helix chain 'O' and resid 418 through 430 Proline residue: O 424 - end of helix removed outlier: 3.559A pdb=" N ALA O 430 " --> pdb=" O GLU O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 449 removed outlier: 4.083A pdb=" N VAL O 446 " --> pdb=" O ASP O 442 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP O 447 " --> pdb=" O ALA O 443 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 477 removed outlier: 3.823A pdb=" N ASP O 477 " --> pdb=" O ASP O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 514 removed outlier: 3.987A pdb=" N ILE O 498 " --> pdb=" O LEU O 494 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU O 505 " --> pdb=" O ALA O 501 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL O 506 " --> pdb=" O ASN O 502 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS O 514 " --> pdb=" O GLN O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 545 Processing helix chain 'O' and resid 549 through 561 Processing helix chain 'O' and resid 561 through 576 removed outlier: 3.623A pdb=" N PHE O 565 " --> pdb=" O THR O 561 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE O 568 " --> pdb=" O LEU O 564 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY O 569 " --> pdb=" O PHE O 565 " (cutoff:3.500A) Processing helix chain 'O' and resid 584 through 609 removed outlier: 3.604A pdb=" N SER O 606 " --> pdb=" O GLN O 602 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA O 607 " --> pdb=" O ASN O 603 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU O 608 " --> pdb=" O LEU O 604 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR O 609 " --> pdb=" O VAL O 605 " (cutoff:3.500A) Processing helix chain 'O' and resid 625 through 635 Processing helix chain 'O' and resid 638 through 652 removed outlier: 3.753A pdb=" N ARG O 642 " --> pdb=" O ASN O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 655 through 670 Processing helix chain 'O' and resid 670 through 698 removed outlier: 3.905A pdb=" N PHE O 674 " --> pdb=" O GLY O 670 " (cutoff:3.500A) Processing helix chain 'O' and resid 702 through 713 Processing helix chain 'P' and resid 418 through 429 Proline residue: P 424 - end of helix Processing helix chain 'P' and resid 435 through 449 removed outlier: 4.131A pdb=" N GLN P 439 " --> pdb=" O GLY P 435 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP P 447 " --> pdb=" O ALA P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 451 through 477 Processing helix chain 'P' and resid 488 through 491 removed outlier: 3.562A pdb=" N ILE P 491 " --> pdb=" O THR P 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 488 through 491' Processing helix chain 'P' and resid 494 through 516 removed outlier: 4.011A pdb=" N ILE P 498 " --> pdb=" O LEU P 494 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU P 505 " --> pdb=" O ALA P 501 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL P 506 " --> pdb=" O ASN P 502 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS P 514 " --> pdb=" O GLN P 510 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY P 516 " --> pdb=" O LEU P 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 519 through 544 Processing helix chain 'P' and resid 549 through 561 Processing helix chain 'P' and resid 562 through 575 removed outlier: 3.683A pdb=" N ARG P 566 " --> pdb=" O GLY P 562 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU P 567 " --> pdb=" O GLY P 563 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE P 568 " --> pdb=" O LEU P 564 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA P 573 " --> pdb=" O GLY P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 584 through 606 Processing helix chain 'P' and resid 625 through 635 Processing helix chain 'P' and resid 638 through 652 removed outlier: 3.540A pdb=" N ARG P 642 " --> pdb=" O ASN P 638 " (cutoff:3.500A) Processing helix chain 'P' and resid 655 through 670 Processing helix chain 'P' and resid 670 through 698 removed outlier: 3.810A pdb=" N PHE P 674 " --> pdb=" O GLY P 670 " (cutoff:3.500A) Processing helix chain 'P' and resid 702 through 713 removed outlier: 3.608A pdb=" N THR P 713 " --> pdb=" O GLU P 709 " (cutoff:3.500A) Processing helix chain 'Q' and resid 418 through 430 Proline residue: Q 424 - end of helix Processing helix chain 'Q' and resid 435 through 444 removed outlier: 4.024A pdb=" N GLN Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 448 Processing helix chain 'Q' and resid 451 through 478 Processing helix chain 'Q' and resid 487 through 493 Processing helix chain 'Q' and resid 495 through 513 removed outlier: 4.076A pdb=" N LEU Q 505 " --> pdb=" O ALA Q 501 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL Q 506 " --> pdb=" O ASN Q 502 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN Q 513 " --> pdb=" O LEU Q 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 519 through 545 removed outlier: 3.784A pdb=" N ASN Q 530 " --> pdb=" O GLU Q 526 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU Q 531 " --> pdb=" O GLU Q 527 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR Q 532 " --> pdb=" O LEU Q 528 " (cutoff:3.500A) Processing helix chain 'Q' and resid 549 through 574 removed outlier: 4.675A pdb=" N LEU Q 564 " --> pdb=" O LYS Q 560 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE Q 565 " --> pdb=" O THR Q 561 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE Q 568 " --> pdb=" O LEU Q 564 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Q 573 " --> pdb=" O GLY Q 569 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 606 removed outlier: 4.093A pdb=" N THR Q 588 " --> pdb=" O LEU Q 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER Q 606 " --> pdb=" O GLN Q 602 " (cutoff:3.500A) Processing helix chain 'Q' and resid 625 through 635 Processing helix chain 'Q' and resid 638 through 652 removed outlier: 4.549A pdb=" N ARG Q 642 " --> pdb=" O ASN Q 638 " (cutoff:3.500A) Processing helix chain 'Q' and resid 655 through 667 removed outlier: 3.615A pdb=" N LYS Q 659 " --> pdb=" O THR Q 655 " (cutoff:3.500A) Processing helix chain 'Q' and resid 670 through 698 removed outlier: 3.688A pdb=" N PHE Q 674 " --> pdb=" O GLY Q 670 " (cutoff:3.500A) Processing helix chain 'Q' and resid 704 through 713 Processing helix chain 'R' and resid 418 through 423 Processing helix chain 'R' and resid 425 through 430 Processing helix chain 'R' and resid 436 through 449 removed outlier: 3.893A pdb=" N VAL R 446 " --> pdb=" O ASP R 442 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP R 447 " --> pdb=" O ALA R 443 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 451 through 478 Processing helix chain 'R' and resid 488 through 493 removed outlier: 3.561A pdb=" N GLY R 493 " --> pdb=" O HIS R 489 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 516 removed outlier: 3.887A pdb=" N ILE R 498 " --> pdb=" O LEU R 494 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL R 506 " --> pdb=" O ASN R 502 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 515 " --> pdb=" O GLU R 511 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY R 516 " --> pdb=" O LEU R 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 519 through 545 removed outlier: 3.827A pdb=" N ASN R 530 " --> pdb=" O GLU R 526 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 531 " --> pdb=" O GLU R 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR R 532 " --> pdb=" O LEU R 528 " (cutoff:3.500A) Processing helix chain 'R' and resid 549 through 561 Processing helix chain 'R' and resid 561 through 575 removed outlier: 3.943A pdb=" N PHE R 565 " --> pdb=" O THR R 561 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE R 568 " --> pdb=" O LEU R 564 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY R 569 " --> pdb=" O PHE R 565 " (cutoff:3.500A) Processing helix chain 'R' and resid 584 through 606 removed outlier: 3.624A pdb=" N THR R 588 " --> pdb=" O LEU R 584 " (cutoff:3.500A) Processing helix chain 'R' and resid 625 through 635 Processing helix chain 'R' and resid 638 through 652 removed outlier: 3.609A pdb=" N ARG R 642 " --> pdb=" O ASN R 638 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 670 removed outlier: 3.577A pdb=" N LYS R 659 " --> pdb=" O THR R 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 670 through 698 removed outlier: 4.397A pdb=" N PHE R 674 " --> pdb=" O GLY R 670 " (cutoff:3.500A) Processing helix chain 'R' and resid 702 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 481 through 482 Processing sheet with id=AA2, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AA4, first strand: chain 'D' and resid 481 through 482 Processing sheet with id=AA5, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AA6, first strand: chain 'G' and resid 481 through 482 Processing sheet with id=AA7, first strand: chain 'H' and resid 481 through 482 Processing sheet with id=AA8, first strand: chain 'I' and resid 481 through 482 Processing sheet with id=AA9, first strand: chain 'M' and resid 481 through 482 Processing sheet with id=AB1, first strand: chain 'N' and resid 481 through 482 Processing sheet with id=AB2, first strand: chain 'O' and resid 481 through 482 Processing sheet with id=AB3, first strand: chain 'P' and resid 481 through 482 Processing sheet with id=AB4, first strand: chain 'Q' and resid 481 through 482 3039 hydrogen bonds defined for protein. 9051 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: 10.15 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12530 1.34 - 1.46: 7741 1.46 - 1.58: 22703 1.58 - 1.70: 10 1.70 - 1.83: 378 Bond restraints: 43362 Sorted by residual: bond pdb=" N PRO H 418 " pdb=" CD PRO H 418 " ideal model delta sigma weight residual 1.473 1.609 -0.136 1.40e-02 5.10e+03 9.43e+01 bond pdb=" N PRO I 418 " pdb=" CD PRO I 418 " ideal model delta sigma weight residual 1.473 1.602 -0.129 1.40e-02 5.10e+03 8.44e+01 bond pdb=" N PRO L 636 " pdb=" CD PRO L 636 " ideal model delta sigma weight residual 1.473 1.387 0.086 1.40e-02 5.10e+03 3.78e+01 bond pdb=" CA GLU N 608 " pdb=" C GLU N 608 " ideal model delta sigma weight residual 1.524 1.603 -0.080 1.32e-02 5.74e+03 3.63e+01 bond pdb=" N PRO Q 451 " pdb=" CD PRO Q 451 " ideal model delta sigma weight residual 1.473 1.389 0.084 1.40e-02 5.10e+03 3.63e+01 ... (remaining 43357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.76: 58409 5.76 - 11.52: 245 11.52 - 17.28: 6 17.28 - 23.04: 1 23.04 - 28.80: 1 Bond angle restraints: 58662 Sorted by residual: angle pdb=" N THR C 588 " pdb=" CA THR C 588 " pdb=" C THR C 588 " ideal model delta sigma weight residual 111.28 123.61 -12.33 1.09e+00 8.42e-01 1.28e+02 angle pdb=" N ASP B 618 " pdb=" CA ASP B 618 " pdb=" CB ASP B 618 " ideal model delta sigma weight residual 110.50 129.41 -18.91 1.70e+00 3.46e-01 1.24e+02 angle pdb=" N GLN K 633 " pdb=" CA GLN K 633 " pdb=" C GLN K 633 " ideal model delta sigma weight residual 111.36 123.24 -11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N GLU B 476 " pdb=" CA GLU B 476 " pdb=" C GLU B 476 " ideal model delta sigma weight residual 111.36 122.73 -11.37 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N ASP B 618 " pdb=" CA ASP B 618 " pdb=" C ASP B 618 " ideal model delta sigma weight residual 111.00 82.20 28.80 2.80e+00 1.28e-01 1.06e+02 ... (remaining 58657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 21931 18.01 - 36.03: 3166 36.03 - 54.04: 757 54.04 - 72.06: 148 72.06 - 90.07: 80 Dihedral angle restraints: 26082 sinusoidal: 10710 harmonic: 15372 Sorted by residual: dihedral pdb=" C ASP B 618 " pdb=" N ASP B 618 " pdb=" CA ASP B 618 " pdb=" CB ASP B 618 " ideal model delta harmonic sigma weight residual -122.60 -109.52 -13.08 0 2.50e+00 1.60e-01 2.74e+01 dihedral pdb=" C ASP C 586 " pdb=" N ASP C 586 " pdb=" CA ASP C 586 " pdb=" CB ASP C 586 " ideal model delta harmonic sigma weight residual -122.60 -111.41 -11.19 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" N ASN N 544 " pdb=" C ASN N 544 " pdb=" CA ASN N 544 " pdb=" CB ASN N 544 " ideal model delta harmonic sigma weight residual 122.80 133.90 -11.10 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 26079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 6402 0.103 - 0.207: 190 0.207 - 0.310: 41 0.310 - 0.413: 25 0.413 - 0.517: 2 Chirality restraints: 6660 Sorted by residual: chirality pdb=" CA LYS B 611 " pdb=" N LYS B 611 " pdb=" C LYS B 611 " pdb=" CB LYS B 611 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CA GLU N 608 " pdb=" N GLU N 608 " pdb=" C GLU N 608 " pdb=" CB GLU N 608 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CA ASP C 586 " pdb=" N ASP C 586 " pdb=" C ASP C 586 " pdb=" CB ASP C 586 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 6657 not shown) Planarity restraints: 7542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 417 " 0.052 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO H 418 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 418 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 418 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 587 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C PHE C 587 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE C 587 " 0.019 2.00e-02 2.50e+03 pdb=" N THR C 588 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 554 " -0.023 2.00e-02 2.50e+03 2.09e-02 7.61e+00 pdb=" CG PHE C 554 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 554 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 554 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 554 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 554 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 554 " -0.004 2.00e-02 2.50e+03 ... (remaining 7539 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 55 2.58 - 3.16: 35515 3.16 - 3.74: 67475 3.74 - 4.32: 85100 4.32 - 4.90: 145382 Nonbonded interactions: 333527 Sorted by model distance: nonbonded pdb=" N ASP B 618 " pdb=" N PHE B 619 " model vdw 2.005 2.560 nonbonded pdb=" OD1 ASP O 586 " pdb=" N PHE O 587 " model vdw 2.052 3.120 nonbonded pdb=" OH TYR F 427 " pdb=" CG LYS F 485 " model vdw 2.126 3.440 nonbonded pdb=" OD1 ASP P 517 " pdb=" N ALA P 518 " model vdw 2.189 3.120 nonbonded pdb=" OD1 ASP N 517 " pdb=" N ALA N 518 " model vdw 2.192 3.120 ... (remaining 333522 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 38.080 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 : 0.004 0.275 43364 Z= 0.252 Angle : 0.855 28.802 58662 Z= 0.538 Chirality : 0.052 0.517 6660 Planarity : 0.004 0.073 7542 Dihedral : 18.037 90.072 16146 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.85 % Allowed : 24.18 % Favored : 74.97 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.12), residues: 5220 helix: 1.77 (0.08), residues: 4086 sheet: None (None), residues: 0 loop : -0.93 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 705 TYR 0.027 0.001 TYR B 532 PHE 0.048 0.001 PHE C 554 TRP 0.013 0.001 TRP I 447 HIS 0.008 0.001 HIS L 590 Details of bonding type rmsd covalent geometry : bond 0.00337 (43362) covalent geometry : angle 0.85495 (58662) hydrogen bonds : bond 0.13037 ( 3039) hydrogen bonds : angle 5.04368 ( 9051) Misc. bond : bond 0.23914 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 1051 time to evaluate : 1.482 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: A 539 LEU cc_start: 0.8038 (mm) cc_final: 0.7764 (mp) REVERT: A 632 MET cc_start: 0.6231 (mtp) cc_final: 0.5907 (mtp) REVERT: B 465 LEU cc_start: 0.5923 (mt) cc_final: 0.5580 (tp) REVERT: C 527 GLU cc_start: 0.5773 (mm-30) cc_final: 0.5486 (tp30) REVERT: C 543 SER cc_start: 0.6786 (t) cc_final: 0.6315 (p) REVERT: D 464 ILE cc_start: 0.7196 (mt) cc_final: 0.6931 (mm) REVERT: D 482 ARG cc_start: 0.4246 (ttt90) cc_final: 0.3646 (mmm160) REVERT: D 543 SER cc_start: 0.6388 (t) cc_final: 0.6089 (p) REVERT: E 666 MET cc_start: 0.2139 (mtt) cc_final: 0.1791 (mtp) REVERT: F 660 GLN cc_start: 0.6777 (tp-100) cc_final: 0.5687 (mm110) REVERT: F 687 GLU cc_start: 0.6464 (mm-30) cc_final: 0.5771 (mm-30) REVERT: F 701 ASN cc_start: 0.5691 (t0) cc_final: 0.5381 (m-40) REVERT: G 419 ARG cc_start: 0.5715 (tpp-160) cc_final: 0.4959 (tpt90) REVERT: G 586 ASP cc_start: 0.4176 (t0) cc_final: 0.3971 (p0) REVERT: H 608 GLU cc_start: 0.4808 (pt0) cc_final: 0.3454 (tt0) REVERT: H 632 MET cc_start: 0.5607 (mtp) cc_final: 0.5389 (mtp) REVERT: I 488 THR cc_start: 0.7445 (t) cc_final: 0.7101 (m) REVERT: I 491 ILE cc_start: 0.7397 (mm) cc_final: 0.7182 (mt) REVERT: I 701 ASN cc_start: 0.5973 (t0) cc_final: 0.5733 (m-40) REVERT: J 494 LEU cc_start: 0.6165 (tp) cc_final: 0.5928 (tp) REVERT: J 537 MET cc_start: 0.6010 (tpp) cc_final: 0.4886 (mtm) REVERT: J 635 MET cc_start: 0.3466 (mtt) cc_final: 0.3231 (mtp) REVERT: K 419 ARG cc_start: 0.5787 (tpp-160) cc_final: 0.5245 (tpt90) REVERT: K 543 SER cc_start: 0.7012 (t) cc_final: 0.6654 (p) REVERT: K 587 PHE cc_start: 0.3507 (t80) cc_final: 0.3266 (t80) REVERT: K 708 MET cc_start: 0.0395 (tpt) cc_final: 0.0123 (ttp) REVERT: K 710 LEU cc_start: 0.4314 (mt) cc_final: 0.4062 (pp) REVERT: L 464 ILE cc_start: 0.6817 (mm) cc_final: 0.6614 (mm) REVERT: L 514 LYS cc_start: 0.7019 (ttpp) cc_final: 0.6721 (tptt) REVERT: L 598 ARG cc_start: 0.6686 (tpt170) cc_final: 0.6481 (ttp-110) REVERT: L 632 MET cc_start: 0.3862 (mtp) cc_final: 0.3471 (mtp) REVERT: M 505 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (tt) REVERT: O 687 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7697 (mm-30) REVERT: P 428 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8182 (tt) REVERT: Q 473 ASP cc_start: 0.7672 (t0) cc_final: 0.7383 (t0) outliers start: 40 outliers final: 16 residues processed: 1074 average time/residue: 0.2472 time to fit residues: 435.1506 Evaluate side-chains 807 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 789 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain F residue 497 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 640 VAL Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 471 MET Chi-restraints excluded: chain M residue 505 LEU Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 537 MET Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 428 ILE Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 704 LEU Chi-restraints excluded: chain R residue 428 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 516 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 529 HIS A 559 HIS A 603 ASN A 656 HIS B 504 GLN ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 GLN D 638 ASN E 529 HIS E 630 HIS ** E 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 HIS F 555 GLN F 660 GLN H 529 HIS H 630 HIS I 656 HIS J 422 GLN J 510 GLN ** K 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 603 ASN O 535 GLN P 703 GLN Q 602 GLN Q 656 HIS R 603 ASN R 658 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.279224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.220295 restraints weight = 51964.379| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.13 r_work: 0.3760 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43364 Z= 0.149 Angle : 0.562 10.317 58662 Z= 0.283 Chirality : 0.039 0.200 6660 Planarity : 0.004 0.050 7542 Dihedral : 3.946 57.471 5755 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.11 % Allowed : 21.80 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.12), residues: 5220 helix: 2.04 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -0.76 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 598 TYR 0.022 0.001 TYR R 532 PHE 0.034 0.002 PHE D 568 TRP 0.013 0.001 TRP E 447 HIS 0.006 0.001 HIS R 529 Details of bonding type rmsd covalent geometry : bond 0.00349 (43362) covalent geometry : angle 0.56245 (58662) hydrogen bonds : bond 0.04387 ( 3039) hydrogen bonds : angle 3.72021 ( 9051) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 818 time to evaluate : 1.551 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 449 ARG cc_start: 0.7231 (mtt90) cc_final: 0.7020 (mtt-85) REVERT: A 477 ASP cc_start: 0.5082 (t70) cc_final: 0.4745 (p0) REVERT: A 632 MET cc_start: 0.5976 (mtp) cc_final: 0.5151 (mtp) REVERT: A 639 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6654 (mt) REVERT: A 648 ARG cc_start: 0.5712 (ttp80) cc_final: 0.5105 (ptt180) REVERT: B 561 THR cc_start: 0.8060 (m) cc_final: 0.7790 (p) REVERT: B 635 MET cc_start: 0.4228 (pmm) cc_final: 0.3011 (tpp) REVERT: C 445 ASN cc_start: 0.2652 (p0) cc_final: 0.1538 (t0) REVERT: C 543 SER cc_start: 0.7130 (t) cc_final: 0.6403 (p) REVERT: C 666 MET cc_start: 0.6687 (mmt) cc_final: 0.6474 (mmt) REVERT: C 708 MET cc_start: 0.4144 (tpp) cc_final: 0.2403 (ptm) REVERT: D 464 ILE cc_start: 0.6793 (mt) cc_final: 0.6460 (mm) REVERT: D 482 ARG cc_start: 0.4303 (ttt90) cc_final: 0.3559 (mmm160) REVERT: D 543 SER cc_start: 0.7305 (t) cc_final: 0.6554 (p) REVERT: E 456 GLU cc_start: 0.7526 (tp30) cc_final: 0.7205 (tp30) REVERT: E 502 ASN cc_start: 0.7354 (t0) cc_final: 0.6471 (m110) REVERT: E 537 MET cc_start: 0.5344 (tpp) cc_final: 0.4819 (tpp) REVERT: E 697 PHE cc_start: 0.4940 (m-80) cc_final: 0.4680 (m-80) REVERT: F 426 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: F 603 ASN cc_start: 0.7246 (m-40) cc_final: 0.6822 (m110) REVERT: F 687 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6131 (mm-30) REVERT: F 708 MET cc_start: 0.6650 (mtm) cc_final: 0.6304 (ttp) REVERT: G 482 ARG cc_start: 0.5171 (ttp80) cc_final: 0.3703 (mmm160) REVERT: G 628 MET cc_start: 0.4013 (mtt) cc_final: 0.3804 (mtp) REVERT: G 708 MET cc_start: 0.3114 (tpp) cc_final: 0.1542 (ptp) REVERT: H 426 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: H 456 GLU cc_start: 0.7695 (tp30) cc_final: 0.7417 (tp30) REVERT: H 568 PHE cc_start: 0.5994 (p90) cc_final: 0.5618 (p90) REVERT: H 580 VAL cc_start: 0.5429 (OUTLIER) cc_final: 0.5185 (p) REVERT: H 608 GLU cc_start: 0.3551 (pt0) cc_final: 0.2351 (tt0) REVERT: H 632 MET cc_start: 0.5339 (mtp) cc_final: 0.4968 (mtp) REVERT: H 639 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6665 (mt) REVERT: H 692 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6955 (mm-30) REVERT: H 700 GLU cc_start: 0.6777 (tt0) cc_final: 0.6409 (tt0) REVERT: I 456 GLU cc_start: 0.7620 (tp30) cc_final: 0.7269 (tp30) REVERT: I 488 THR cc_start: 0.7326 (t) cc_final: 0.6832 (m) REVERT: I 701 ASN cc_start: 0.6788 (t0) cc_final: 0.5787 (m-40) REVERT: J 537 MET cc_start: 0.5485 (tpp) cc_final: 0.4129 (mtm) REVERT: J 580 VAL cc_start: 0.4555 (OUTLIER) cc_final: 0.4261 (p) REVERT: J 608 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.1919 (mt-10) REVERT: J 692 GLU cc_start: 0.6974 (tp30) cc_final: 0.6210 (mt-10) REVERT: K 422 GLN cc_start: 0.6393 (mm-40) cc_final: 0.5560 (mp10) REVERT: K 543 SER cc_start: 0.7398 (t) cc_final: 0.6668 (p) REVERT: K 587 PHE cc_start: 0.5204 (t80) cc_final: 0.4185 (t80) REVERT: K 662 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7546 (mp) REVERT: K 708 MET cc_start: -0.0367 (tpt) cc_final: -0.1181 (ttp) REVERT: K 710 LEU cc_start: 0.5266 (mt) cc_final: 0.4576 (pp) REVERT: L 514 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7487 (ttpp) REVERT: L 556 MET cc_start: 0.5849 (ttp) cc_final: 0.4934 (ttp) REVERT: L 632 MET cc_start: 0.3453 (mtp) cc_final: 0.3172 (mtp) REVERT: M 505 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8410 (tt) REVERT: N 599 ASP cc_start: 0.8361 (t70) cc_final: 0.8090 (t0) REVERT: O 505 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8409 (tt) REVERT: O 598 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8038 (ttt90) REVERT: O 602 GLN cc_start: 0.8091 (mm110) cc_final: 0.7874 (mm110) REVERT: O 687 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8361 (tp30) REVERT: Q 473 ASP cc_start: 0.8166 (t0) cc_final: 0.7904 (t0) REVERT: Q 477 ASP cc_start: 0.7814 (m-30) cc_final: 0.7528 (m-30) REVERT: Q 567 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7902 (tp) outliers start: 146 outliers final: 67 residues processed: 911 average time/residue: 0.2328 time to fit residues: 354.3929 Evaluate side-chains 790 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 711 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 447 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 574 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 655 THR Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 603 ASN Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 505 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 595 PHE Chi-restraints excluded: chain O residue 420 VAL Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 598 ARG Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 711 LEU Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain Q residue 567 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 72 optimal weight: 2.9990 chunk 353 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 381 optimal weight: 0.7980 chunk 151 optimal weight: 30.0000 chunk 471 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 110 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 513 optimal weight: 1.9990 chunk 435 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS C 499 ASN C 555 GLN D 490 ASN D 502 ASN E 467 ASN ** E 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 GLN K 589 ASN ** K 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 603 ASN M 703 GLN N 638 ASN N 656 HIS N 660 GLN N 676 GLN Q 513 GLN Q 656 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.279943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.222427 restraints weight = 51870.174| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 2.97 r_work: 0.3857 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43364 Z= 0.114 Angle : 0.506 11.439 58662 Z= 0.251 Chirality : 0.037 0.228 6660 Planarity : 0.003 0.049 7542 Dihedral : 3.507 51.334 5731 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.43 % Allowed : 22.18 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.12), residues: 5220 helix: 2.31 (0.08), residues: 4122 sheet: None (None), residues: 0 loop : -0.75 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 449 TYR 0.015 0.001 TYR K 540 PHE 0.032 0.001 PHE D 568 TRP 0.018 0.001 TRP E 447 HIS 0.003 0.001 HIS R 529 Details of bonding type rmsd covalent geometry : bond 0.00256 (43362) covalent geometry : angle 0.50622 (58662) hydrogen bonds : bond 0.03598 ( 3039) hydrogen bonds : angle 3.47489 ( 9051) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 790 time to evaluate : 1.612 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 449 ARG cc_start: 0.7511 (mtt90) cc_final: 0.7291 (mtt-85) REVERT: A 459 LYS cc_start: 0.6344 (OUTLIER) cc_final: 0.6012 (mmtm) REVERT: A 632 MET cc_start: 0.6179 (mtp) cc_final: 0.5224 (mtp) REVERT: A 648 ARG cc_start: 0.5966 (ttp80) cc_final: 0.5287 (ptt180) REVERT: B 561 THR cc_start: 0.8333 (m) cc_final: 0.8041 (p) REVERT: B 572 MET cc_start: 0.5363 (mtt) cc_final: 0.5138 (mtt) REVERT: B 635 MET cc_start: 0.4478 (pmm) cc_final: 0.3077 (tpp) REVERT: C 445 ASN cc_start: 0.3059 (p0) cc_final: 0.1869 (t0) REVERT: C 543 SER cc_start: 0.7172 (t) cc_final: 0.6436 (p) REVERT: C 596 GLN cc_start: 0.6945 (tp-100) cc_final: 0.6682 (tp40) REVERT: D 482 ARG cc_start: 0.4549 (ttt90) cc_final: 0.3628 (mmm160) REVERT: D 514 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7384 (tmtt) REVERT: D 543 SER cc_start: 0.7246 (t) cc_final: 0.6555 (p) REVERT: E 449 ARG cc_start: 0.7007 (ptp-170) cc_final: 0.6630 (ptp-110) REVERT: E 456 GLU cc_start: 0.7624 (tp30) cc_final: 0.7282 (tp30) REVERT: E 537 MET cc_start: 0.5863 (tpp) cc_final: 0.5359 (tpp) REVERT: E 696 LYS cc_start: 0.7428 (tptt) cc_final: 0.6988 (mtpp) REVERT: F 502 ASN cc_start: 0.8019 (t0) cc_final: 0.7068 (m110) REVERT: F 632 MET cc_start: 0.5471 (mtp) cc_final: 0.5144 (mtp) REVERT: F 687 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6181 (mm-30) REVERT: F 697 PHE cc_start: 0.5891 (m-80) cc_final: 0.5490 (m-80) REVERT: F 708 MET cc_start: 0.6812 (mtm) cc_final: 0.6562 (ttp) REVERT: G 419 ARG cc_start: 0.4900 (tpp-160) cc_final: 0.4032 (tpt90) REVERT: G 482 ARG cc_start: 0.5540 (ttp80) cc_final: 0.4047 (mmm160) REVERT: G 708 MET cc_start: 0.2424 (tpp) cc_final: 0.1024 (ptp) REVERT: H 456 GLU cc_start: 0.7825 (tp30) cc_final: 0.7511 (tp30) REVERT: H 537 MET cc_start: 0.6278 (tpp) cc_final: 0.6009 (tpp) REVERT: H 568 PHE cc_start: 0.6407 (p90) cc_final: 0.6022 (p90) REVERT: H 608 GLU cc_start: 0.4106 (pt0) cc_final: 0.2731 (tt0) REVERT: H 632 MET cc_start: 0.5588 (mtp) cc_final: 0.5194 (mtp) REVERT: H 639 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6785 (mt) REVERT: H 692 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7137 (mm-30) REVERT: I 456 GLU cc_start: 0.7737 (tp30) cc_final: 0.7403 (tp30) REVERT: I 488 THR cc_start: 0.7556 (t) cc_final: 0.7086 (m) REVERT: I 538 ASP cc_start: 0.7741 (t70) cc_final: 0.7539 (t70) REVERT: J 608 GLU cc_start: 0.3336 (OUTLIER) cc_final: 0.1943 (mt-10) REVERT: J 648 ARG cc_start: 0.6144 (tmm-80) cc_final: 0.5146 (ptt180) REVERT: J 692 GLU cc_start: 0.7008 (tp30) cc_final: 0.6262 (mt-10) REVERT: K 499 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6838 (m-40) REVERT: K 543 SER cc_start: 0.7433 (t) cc_final: 0.6718 (p) REVERT: K 587 PHE cc_start: 0.4780 (t80) cc_final: 0.3773 (t80) REVERT: K 624 PHE cc_start: 0.4985 (m-80) cc_final: 0.4351 (m-80) REVERT: K 662 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7804 (mp) REVERT: K 672 LEU cc_start: 0.6883 (tp) cc_final: 0.6300 (pp) REVERT: K 708 MET cc_start: -0.0425 (tpt) cc_final: -0.1216 (ttp) REVERT: K 710 LEU cc_start: 0.5408 (mt) cc_final: 0.4586 (pp) REVERT: L 512 LEU cc_start: 0.6810 (pp) cc_final: 0.6358 (pp) REVERT: L 538 ASP cc_start: 0.5191 (t0) cc_final: 0.4927 (t0) REVERT: L 556 MET cc_start: 0.6102 (ttp) cc_final: 0.5737 (ttp) REVERT: L 572 MET cc_start: 0.5431 (tpp) cc_final: 0.5068 (tpt) REVERT: L 632 MET cc_start: 0.3769 (mtp) cc_final: 0.3489 (mtp) REVERT: M 473 ASP cc_start: 0.7688 (m-30) cc_final: 0.7149 (m-30) REVERT: N 599 ASP cc_start: 0.8274 (t70) cc_final: 0.8005 (t0) REVERT: O 505 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8349 (tt) REVERT: Q 428 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (tt) REVERT: Q 599 ASP cc_start: 0.8246 (t0) cc_final: 0.8013 (t0) outliers start: 161 outliers final: 77 residues processed: 895 average time/residue: 0.2368 time to fit residues: 353.1426 Evaluate side-chains 806 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 722 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 447 TRP Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain E residue 447 TRP Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 635 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 603 ASN Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 460 SER Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 499 ASN Chi-restraints excluded: chain K residue 606 SER Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 474 ASP Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 595 PHE Chi-restraints excluded: chain N residue 660 GLN Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 711 LEU Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 428 ILE Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain R residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 240 optimal weight: 5.9990 chunk 367 optimal weight: 0.0470 chunk 277 optimal weight: 20.0000 chunk 388 optimal weight: 0.8980 chunk 200 optimal weight: 40.0000 chunk 439 optimal weight: 0.5980 chunk 289 optimal weight: 6.9990 chunk 264 optimal weight: 0.0870 chunk 384 optimal weight: 0.7980 chunk 402 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 602 GLN C 499 ASN D 530 ASN E 422 GLN E 529 HIS ** E 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 589 ASN H 630 HIS J 422 GLN ** K 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN Q 513 GLN Q 656 HIS R 656 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.282126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.223815 restraints weight = 51901.982| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.03 r_work: 0.3839 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43364 Z= 0.095 Angle : 0.490 14.005 58662 Z= 0.241 Chirality : 0.036 0.223 6660 Planarity : 0.003 0.050 7542 Dihedral : 3.277 52.694 5726 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.60 % Allowed : 23.01 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.12), residues: 5220 helix: 2.41 (0.08), residues: 4176 sheet: None (None), residues: 0 loop : -0.50 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 649 TYR 0.015 0.001 TYR C 683 PHE 0.031 0.001 PHE D 568 TRP 0.013 0.001 TRP E 447 HIS 0.004 0.000 HIS J 529 Details of bonding type rmsd covalent geometry : bond 0.00199 (43362) covalent geometry : angle 0.48984 (58662) hydrogen bonds : bond 0.03002 ( 3039) hydrogen bonds : angle 3.32489 ( 9051) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 798 time to evaluate : 1.636 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: A 449 ARG cc_start: 0.7460 (mtt90) cc_final: 0.7241 (mtt-85) REVERT: A 459 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5833 (mmmm) REVERT: A 537 MET cc_start: 0.5873 (tpp) cc_final: 0.5076 (tpp) REVERT: A 552 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6892 (tt0) REVERT: A 559 HIS cc_start: 0.5854 (m90) cc_final: 0.5539 (m170) REVERT: A 632 MET cc_start: 0.6115 (mtp) cc_final: 0.5294 (mtp) REVERT: A 648 ARG cc_start: 0.5899 (ttp80) cc_final: 0.5270 (ptt180) REVERT: A 692 GLU cc_start: 0.7016 (tp30) cc_final: 0.6294 (mt-10) REVERT: B 561 THR cc_start: 0.8283 (m) cc_final: 0.8014 (p) REVERT: C 445 ASN cc_start: 0.2769 (p0) cc_final: 0.1723 (t0) REVERT: C 543 SER cc_start: 0.7118 (t) cc_final: 0.6383 (p) REVERT: C 596 GLN cc_start: 0.6824 (tp-100) cc_final: 0.6162 (tm-30) REVERT: D 464 ILE cc_start: 0.6836 (mt) cc_final: 0.6346 (mm) REVERT: D 482 ARG cc_start: 0.4641 (ttt90) cc_final: 0.4271 (mtp-110) REVERT: D 514 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7426 (pttp) REVERT: D 565 PHE cc_start: 0.6619 (m-80) cc_final: 0.6314 (m-80) REVERT: E 449 ARG cc_start: 0.6971 (ptp-170) cc_final: 0.6667 (ptp-110) REVERT: E 456 GLU cc_start: 0.7706 (tp30) cc_final: 0.7409 (tp30) REVERT: E 537 MET cc_start: 0.5843 (tpp) cc_final: 0.5385 (tpp) REVERT: E 696 LYS cc_start: 0.7387 (tptt) cc_final: 0.6966 (mtpp) REVERT: F 491 ILE cc_start: 0.7180 (tp) cc_final: 0.6971 (tp) REVERT: F 502 ASN cc_start: 0.8104 (t0) cc_final: 0.7131 (m110) REVERT: F 632 MET cc_start: 0.5558 (mtp) cc_final: 0.5223 (mtp) REVERT: F 687 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6182 (mm-30) REVERT: F 697 PHE cc_start: 0.5892 (m-80) cc_final: 0.5448 (m-80) REVERT: F 708 MET cc_start: 0.6637 (mtm) cc_final: 0.6381 (ttp) REVERT: G 419 ARG cc_start: 0.4702 (tpp-160) cc_final: 0.3854 (tpt90) REVERT: G 581 GLN cc_start: 0.2904 (OUTLIER) cc_final: 0.2446 (mt0) REVERT: G 598 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6731 (tpp80) REVERT: G 708 MET cc_start: 0.2459 (tpp) cc_final: 0.1062 (ptp) REVERT: H 537 MET cc_start: 0.6158 (tpp) cc_final: 0.5839 (tpp) REVERT: H 568 PHE cc_start: 0.6406 (p90) cc_final: 0.6033 (p90) REVERT: H 608 GLU cc_start: 0.4032 (pt0) cc_final: 0.2709 (tt0) REVERT: H 632 MET cc_start: 0.5489 (mtp) cc_final: 0.5058 (mtp) REVERT: H 639 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6771 (mt) REVERT: H 692 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7094 (mm-30) REVERT: I 441 ILE cc_start: 0.4610 (OUTLIER) cc_final: 0.4395 (mp) REVERT: I 456 GLU cc_start: 0.7798 (tp30) cc_final: 0.7481 (tp30) REVERT: I 488 THR cc_start: 0.7401 (t) cc_final: 0.6903 (m) REVERT: I 507 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.5923 (ttt-90) REVERT: I 537 MET cc_start: 0.6130 (tpp) cc_final: 0.5868 (tpp) REVERT: I 538 ASP cc_start: 0.7631 (t70) cc_final: 0.7412 (t70) REVERT: J 537 MET cc_start: 0.5695 (tpp) cc_final: 0.4325 (mtm) REVERT: J 608 GLU cc_start: 0.3305 (OUTLIER) cc_final: 0.2079 (mt-10) REVERT: J 648 ARG cc_start: 0.6087 (tmm-80) cc_final: 0.5111 (ptt180) REVERT: J 682 LEU cc_start: 0.7789 (mp) cc_final: 0.7547 (tp) REVERT: J 692 GLU cc_start: 0.7069 (tp30) cc_final: 0.6267 (mt-10) REVERT: K 543 SER cc_start: 0.7373 (t) cc_final: 0.6643 (p) REVERT: K 587 PHE cc_start: 0.4934 (t80) cc_final: 0.3927 (t80) REVERT: K 624 PHE cc_start: 0.4896 (m-80) cc_final: 0.4213 (m-80) REVERT: K 662 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7806 (mp) REVERT: K 672 LEU cc_start: 0.6816 (tp) cc_final: 0.6238 (pt) REVERT: K 708 MET cc_start: -0.0863 (tpt) cc_final: -0.1492 (ttp) REVERT: L 513 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6512 (pp30) REVERT: L 514 LYS cc_start: 0.8104 (ttpp) cc_final: 0.6988 (pttm) REVERT: L 556 MET cc_start: 0.6078 (ttp) cc_final: 0.5688 (ttp) REVERT: L 572 MET cc_start: 0.5318 (tpp) cc_final: 0.5030 (tpt) REVERT: L 632 MET cc_start: 0.3868 (mtp) cc_final: 0.3585 (mtp) REVERT: L 708 MET cc_start: 0.2633 (ptt) cc_final: 0.1799 (ppp) REVERT: M 473 ASP cc_start: 0.7699 (m-30) cc_final: 0.7273 (m-30) REVERT: M 505 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8332 (tt) REVERT: M 602 GLN cc_start: 0.7678 (mm110) cc_final: 0.7390 (mm110) REVERT: N 599 ASP cc_start: 0.8215 (t70) cc_final: 0.7974 (t0) REVERT: N 656 HIS cc_start: 0.6953 (t70) cc_final: 0.6468 (t70) REVERT: N 660 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: O 505 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (tt) REVERT: P 660 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7732 (mp10) REVERT: P 697 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: Q 599 ASP cc_start: 0.8257 (t0) cc_final: 0.8029 (t0) outliers start: 122 outliers final: 58 residues processed: 876 average time/residue: 0.2285 time to fit residues: 333.1136 Evaluate side-chains 789 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 721 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 539 LEU Chi-restraints excluded: chain G residue 581 GLN Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain I residue 697 PHE Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 472 LEU Chi-restraints excluded: chain M residue 474 ASP Chi-restraints excluded: chain M residue 505 LEU Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 595 PHE Chi-restraints excluded: chain N residue 660 GLN Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 441 ILE Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 605 VAL Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 697 PHE Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 27 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 409 optimal weight: 0.5980 chunk 398 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 391 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 HIS C 499 ASN D 656 HIS F 489 HIS G 602 GLN H 559 HIS H 590 HIS ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 ASN K 656 HIS ** K 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 656 HIS N 660 GLN Q 513 GLN Q 643 ASN Q 656 HIS ** R 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.278768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.218505 restraints weight = 51501.002| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.04 r_work: 0.3770 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43364 Z= 0.128 Angle : 0.520 11.895 58662 Z= 0.256 Chirality : 0.037 0.174 6660 Planarity : 0.004 0.070 7542 Dihedral : 3.357 54.962 5726 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.66 % Allowed : 23.41 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.12), residues: 5220 helix: 2.47 (0.08), residues: 4122 sheet: None (None), residues: 0 loop : -0.60 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 649 TYR 0.015 0.001 TYR N 532 PHE 0.024 0.001 PHE Q 702 TRP 0.014 0.001 TRP Q 447 HIS 0.009 0.001 HIS N 656 Details of bonding type rmsd covalent geometry : bond 0.00301 (43362) covalent geometry : angle 0.52027 (58662) hydrogen bonds : bond 0.03764 ( 3039) hydrogen bonds : angle 3.38396 ( 9051) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 742 time to evaluate : 1.638 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 449 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7204 (mtt-85) REVERT: A 459 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5794 (mmmm) REVERT: A 632 MET cc_start: 0.6030 (mtp) cc_final: 0.5127 (mtp) REVERT: A 648 ARG cc_start: 0.5913 (ttp80) cc_final: 0.5255 (ptt180) REVERT: A 692 GLU cc_start: 0.7082 (tp30) cc_final: 0.6274 (mt-10) REVERT: B 635 MET cc_start: 0.4237 (pmm) cc_final: 0.3007 (tpp) REVERT: C 445 ASN cc_start: 0.2801 (p0) cc_final: 0.1640 (t0) REVERT: C 543 SER cc_start: 0.7101 (t) cc_final: 0.6324 (p) REVERT: D 482 ARG cc_start: 0.4608 (ttt90) cc_final: 0.4119 (mtp-110) REVERT: D 514 LYS cc_start: 0.7768 (ttpt) cc_final: 0.7418 (pttp) REVERT: D 565 PHE cc_start: 0.6653 (m-80) cc_final: 0.6254 (m-80) REVERT: E 449 ARG cc_start: 0.7032 (ptp-170) cc_final: 0.6691 (ptp-110) REVERT: E 456 GLU cc_start: 0.7709 (tp30) cc_final: 0.7389 (tp30) REVERT: E 537 MET cc_start: 0.5852 (tpp) cc_final: 0.5353 (tpp) REVERT: E 696 LYS cc_start: 0.7363 (tptt) cc_final: 0.6765 (mtpp) REVERT: F 491 ILE cc_start: 0.7081 (tp) cc_final: 0.6841 (tp) REVERT: F 502 ASN cc_start: 0.8092 (t0) cc_final: 0.7180 (m110) REVERT: F 632 MET cc_start: 0.5624 (mtp) cc_final: 0.5294 (mtp) REVERT: F 697 PHE cc_start: 0.5788 (m-80) cc_final: 0.5568 (m-80) REVERT: G 456 GLU cc_start: 0.4223 (mm-30) cc_final: 0.3884 (tm-30) REVERT: G 635 MET cc_start: 0.2708 (pmm) cc_final: 0.2123 (tpp) REVERT: G 708 MET cc_start: 0.2462 (tpp) cc_final: 0.0927 (ptp) REVERT: H 426 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: H 456 GLU cc_start: 0.7878 (tp30) cc_final: 0.7591 (tp30) REVERT: H 537 MET cc_start: 0.6047 (tpp) cc_final: 0.5761 (tpp) REVERT: H 568 PHE cc_start: 0.6453 (p90) cc_final: 0.6014 (p90) REVERT: H 608 GLU cc_start: 0.4023 (pt0) cc_final: 0.2709 (tt0) REVERT: H 632 MET cc_start: 0.5440 (mtp) cc_final: 0.4933 (mtp) REVERT: H 639 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6822 (mt) REVERT: H 692 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7056 (mm-30) REVERT: I 441 ILE cc_start: 0.4581 (OUTLIER) cc_final: 0.4309 (mp) REVERT: I 456 GLU cc_start: 0.7741 (tp30) cc_final: 0.7442 (tp30) REVERT: I 488 THR cc_start: 0.7433 (t) cc_final: 0.6899 (m) REVERT: I 537 MET cc_start: 0.6047 (tpp) cc_final: 0.5801 (tpp) REVERT: I 538 ASP cc_start: 0.7618 (t70) cc_final: 0.7393 (t70) REVERT: J 608 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.2119 (mt-10) REVERT: J 648 ARG cc_start: 0.6060 (tmm-80) cc_final: 0.5113 (ptt180) REVERT: J 682 LEU cc_start: 0.7808 (mp) cc_final: 0.7572 (tp) REVERT: J 692 GLU cc_start: 0.7059 (tp30) cc_final: 0.6246 (mt-10) REVERT: K 543 SER cc_start: 0.7294 (t) cc_final: 0.6552 (p) REVERT: K 587 PHE cc_start: 0.5064 (t80) cc_final: 0.3974 (t80) REVERT: K 624 PHE cc_start: 0.4893 (m-80) cc_final: 0.4391 (m-80) REVERT: K 662 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (mp) REVERT: K 672 LEU cc_start: 0.6876 (tp) cc_final: 0.6354 (pt) REVERT: K 708 MET cc_start: -0.0812 (tpt) cc_final: -0.1642 (ttp) REVERT: L 482 ARG cc_start: 0.5307 (tpt170) cc_final: 0.3292 (ttp80) REVERT: L 513 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6670 (pp30) REVERT: L 514 LYS cc_start: 0.8057 (ttpp) cc_final: 0.6875 (pttm) REVERT: L 517 ASP cc_start: 0.4146 (t0) cc_final: 0.3691 (m-30) REVERT: L 556 MET cc_start: 0.6076 (ttp) cc_final: 0.5613 (ttp) REVERT: L 596 GLN cc_start: 0.6937 (tp40) cc_final: 0.5290 (pt0) REVERT: L 632 MET cc_start: 0.4006 (mtp) cc_final: 0.3731 (mtp) REVERT: M 473 ASP cc_start: 0.8067 (m-30) cc_final: 0.7653 (m-30) REVERT: M 483 ARG cc_start: 0.6382 (ttm170) cc_final: 0.6024 (mtm-85) REVERT: M 505 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8368 (tt) REVERT: M 602 GLN cc_start: 0.7721 (mm110) cc_final: 0.7431 (mm110) REVERT: N 599 ASP cc_start: 0.8261 (t70) cc_final: 0.7992 (t0) REVERT: O 505 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8336 (tt) REVERT: O 709 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7333 (tm-30) REVERT: Q 599 ASP cc_start: 0.8455 (t0) cc_final: 0.8195 (t0) outliers start: 125 outliers final: 85 residues processed: 820 average time/residue: 0.2214 time to fit residues: 304.7941 Evaluate side-chains 787 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 694 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 528 LEU Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain I residue 697 PHE Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 538 ASP Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 641 LEU Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 472 LEU Chi-restraints excluded: chain M residue 505 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 595 PHE Chi-restraints excluded: chain N residue 660 GLN Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 605 VAL Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 511 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 256 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 191 optimal weight: 30.0000 chunk 457 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 501 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 589 ASN F 590 HIS ** G 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 559 HIS H 603 ASN J 422 GLN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 HIS K 701 ASN ** M 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 603 ASN O 513 GLN P 575 HIS P 660 GLN Q 513 GLN R 603 ASN R 638 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.278253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205726 restraints weight = 51190.520| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.86 r_work: 0.3684 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 43364 Z= 0.193 Angle : 0.584 13.675 58662 Z= 0.288 Chirality : 0.040 0.237 6660 Planarity : 0.004 0.090 7542 Dihedral : 3.616 58.408 5726 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.28 % Allowed : 23.46 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.12), residues: 5220 helix: 2.20 (0.08), residues: 4158 sheet: None (None), residues: 0 loop : -0.60 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 642 TYR 0.018 0.001 TYR N 532 PHE 0.033 0.002 PHE D 568 TRP 0.020 0.001 TRP Q 447 HIS 0.006 0.001 HIS Q 529 Details of bonding type rmsd covalent geometry : bond 0.00472 (43362) covalent geometry : angle 0.58446 (58662) hydrogen bonds : bond 0.04758 ( 3039) hydrogen bonds : angle 3.55401 ( 9051) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 735 time to evaluate : 1.419 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: A 449 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7243 (mtt-85) REVERT: A 552 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6813 (tt0) REVERT: A 632 MET cc_start: 0.6030 (mtp) cc_final: 0.5227 (mtp) REVERT: A 648 ARG cc_start: 0.5947 (ttp80) cc_final: 0.5278 (ptt180) REVERT: A 692 GLU cc_start: 0.6981 (tp30) cc_final: 0.6335 (mt-10) REVERT: B 572 MET cc_start: 0.5918 (mtt) cc_final: 0.5533 (mtt) REVERT: B 632 MET cc_start: 0.2925 (OUTLIER) cc_final: 0.2160 (mtt) REVERT: B 635 MET cc_start: 0.4073 (pmm) cc_final: 0.3232 (tpp) REVERT: B 689 SER cc_start: 0.6547 (m) cc_final: 0.6041 (t) REVERT: C 445 ASN cc_start: 0.2592 (p0) cc_final: 0.1623 (t0) REVERT: C 596 GLN cc_start: 0.6771 (tp-100) cc_final: 0.6066 (tm-30) REVERT: C 712 LYS cc_start: 0.4432 (tppt) cc_final: 0.3282 (mtpp) REVERT: D 482 ARG cc_start: 0.4522 (ttt90) cc_final: 0.3919 (mtp-110) REVERT: D 514 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7490 (pttp) REVERT: D 543 SER cc_start: 0.6870 (t) cc_final: 0.6224 (p) REVERT: D 565 PHE cc_start: 0.6670 (m-80) cc_final: 0.6339 (m-80) REVERT: E 449 ARG cc_start: 0.6963 (ptp-170) cc_final: 0.6613 (ptp-110) REVERT: E 456 GLU cc_start: 0.7754 (tp30) cc_final: 0.7472 (tp30) REVERT: E 537 MET cc_start: 0.5949 (tpp) cc_final: 0.5509 (tpp) REVERT: F 426 GLU cc_start: 0.7601 (mp0) cc_final: 0.7180 (mp0) REVERT: F 464 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6928 (mp) REVERT: F 491 ILE cc_start: 0.7184 (tp) cc_final: 0.6958 (tp) REVERT: F 502 ASN cc_start: 0.8091 (t0) cc_final: 0.7152 (m110) REVERT: F 632 MET cc_start: 0.5516 (mtp) cc_final: 0.5227 (mtp) REVERT: F 635 MET cc_start: 0.4749 (mmm) cc_final: 0.4167 (ttt) REVERT: F 642 ARG cc_start: 0.5945 (mtp85) cc_final: 0.5691 (mtp85) REVERT: F 697 PHE cc_start: 0.5814 (m-80) cc_final: 0.5568 (m-80) REVERT: G 635 MET cc_start: 0.2744 (pmm) cc_final: 0.2253 (tpp) REVERT: G 660 GLN cc_start: 0.4896 (mm-40) cc_final: 0.4360 (mp10) REVERT: G 708 MET cc_start: 0.2299 (tpp) cc_final: 0.0688 (ptp) REVERT: H 426 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: H 456 GLU cc_start: 0.7984 (tp30) cc_final: 0.7698 (tp30) REVERT: H 537 MET cc_start: 0.6055 (tpp) cc_final: 0.5801 (tpp) REVERT: H 568 PHE cc_start: 0.6306 (p90) cc_final: 0.5929 (p90) REVERT: H 632 MET cc_start: 0.5556 (mtp) cc_final: 0.4952 (mtp) REVERT: H 639 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6970 (mt) REVERT: H 692 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6958 (mm-30) REVERT: I 441 ILE cc_start: 0.4425 (OUTLIER) cc_final: 0.4190 (mp) REVERT: I 449 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.7018 (mtt-85) REVERT: I 456 GLU cc_start: 0.7820 (tp30) cc_final: 0.7435 (tp30) REVERT: I 537 MET cc_start: 0.6073 (tpp) cc_final: 0.5869 (tpp) REVERT: I 538 ASP cc_start: 0.7570 (t70) cc_final: 0.7357 (t70) REVERT: I 682 LEU cc_start: 0.7478 (mp) cc_final: 0.7089 (tp) REVERT: J 550 MET cc_start: 0.7670 (mmt) cc_final: 0.7469 (mmt) REVERT: J 608 GLU cc_start: 0.3444 (OUTLIER) cc_final: 0.2132 (mt-10) REVERT: J 648 ARG cc_start: 0.6177 (tmm-80) cc_final: 0.5128 (ptt180) REVERT: J 682 LEU cc_start: 0.7764 (mp) cc_final: 0.7503 (tp) REVERT: J 692 GLU cc_start: 0.6929 (tp30) cc_final: 0.6243 (mt-10) REVERT: K 543 SER cc_start: 0.7292 (t) cc_final: 0.6545 (p) REVERT: K 587 PHE cc_start: 0.5130 (t80) cc_final: 0.3865 (t80) REVERT: K 624 PHE cc_start: 0.5147 (m-80) cc_final: 0.4674 (m-80) REVERT: K 642 ARG cc_start: 0.6274 (tpt-90) cc_final: 0.5758 (tpt-90) REVERT: K 662 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7772 (mp) REVERT: K 672 LEU cc_start: 0.7015 (tp) cc_final: 0.6437 (pt) REVERT: K 708 MET cc_start: -0.0722 (tpt) cc_final: -0.1841 (ptm) REVERT: L 482 ARG cc_start: 0.5274 (tpt170) cc_final: 0.3357 (ttp80) REVERT: L 513 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6563 (pp30) REVERT: L 514 LYS cc_start: 0.8041 (ttpp) cc_final: 0.6790 (pttm) REVERT: L 517 ASP cc_start: 0.4397 (t0) cc_final: 0.4170 (t0) REVERT: L 556 MET cc_start: 0.6097 (ttp) cc_final: 0.5320 (ttp) REVERT: L 572 MET cc_start: 0.5313 (tpp) cc_final: 0.5011 (tpt) REVERT: L 632 MET cc_start: 0.4119 (mtp) cc_final: 0.3879 (mtp) REVERT: M 473 ASP cc_start: 0.8199 (m-30) cc_final: 0.7798 (m-30) REVERT: M 688 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7892 (ttmm) REVERT: N 428 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (tt) REVERT: N 599 ASP cc_start: 0.8401 (t70) cc_final: 0.8103 (t0) REVERT: O 505 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8323 (tt) REVERT: O 709 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7564 (tm-30) REVERT: Q 599 ASP cc_start: 0.8572 (t0) cc_final: 0.8291 (t0) outliers start: 154 outliers final: 101 residues processed: 832 average time/residue: 0.2260 time to fit residues: 313.0325 Evaluate side-chains 801 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 690 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 506 VAL Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 462 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 655 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain I residue 697 PHE Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 511 GLU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 538 ASP Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain M residue 688 LYS Chi-restraints excluded: chain M residue 699 ILE Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 595 PHE Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 605 VAL Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 639 LEU Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 542 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Chi-restraints excluded: chain R residue 606 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 373 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 348 optimal weight: 1.9990 chunk 309 optimal weight: 30.0000 chunk 289 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 ASN C 596 GLN D 499 ASN F 603 ASN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 504 GLN J 422 GLN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 HIS ** M 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 638 ASN N 638 ASN P 638 ASN Q 513 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.274087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.217036 restraints weight = 51020.195| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.21 r_work: 0.3954 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 43364 Z= 0.211 Angle : 0.599 12.257 58662 Z= 0.297 Chirality : 0.040 0.231 6660 Planarity : 0.004 0.086 7542 Dihedral : 3.776 53.594 5726 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.32 % Allowed : 23.80 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.12), residues: 5220 helix: 2.02 (0.08), residues: 4194 sheet: None (None), residues: 0 loop : -0.52 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 649 TYR 0.019 0.002 TYR N 540 PHE 0.032 0.002 PHE K 568 TRP 0.047 0.002 TRP D 447 HIS 0.006 0.001 HIS R 529 Details of bonding type rmsd covalent geometry : bond 0.00521 (43362) covalent geometry : angle 0.59909 (58662) hydrogen bonds : bond 0.04899 ( 3039) hydrogen bonds : angle 3.62598 ( 9051) Misc. bond : bond 0.00088 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 728 time to evaluate : 1.285 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 480 GLU cc_start: 0.7637 (pm20) cc_final: 0.7111 (mp0) REVERT: A 632 MET cc_start: 0.6179 (mtp) cc_final: 0.5636 (mtp) REVERT: A 648 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5508 (ptt180) REVERT: A 692 GLU cc_start: 0.6990 (tp30) cc_final: 0.6552 (mt-10) REVERT: B 632 MET cc_start: 0.3200 (OUTLIER) cc_final: 0.2282 (mtt) REVERT: B 635 MET cc_start: 0.4022 (pmm) cc_final: 0.3467 (mmm) REVERT: C 419 ARG cc_start: 0.5111 (OUTLIER) cc_final: 0.4612 (tpt90) REVERT: C 445 ASN cc_start: 0.3655 (p0) cc_final: 0.2021 (t0) REVERT: C 454 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.4066 (mmtp) REVERT: C 633 GLN cc_start: 0.4737 (OUTLIER) cc_final: 0.4296 (mt0) REVERT: D 433 SER cc_start: 0.4133 (p) cc_final: 0.3682 (t) REVERT: D 482 ARG cc_start: 0.4566 (ttt90) cc_final: 0.4248 (mtp-110) REVERT: D 543 SER cc_start: 0.6832 (t) cc_final: 0.6315 (p) REVERT: D 668 GLU cc_start: 0.4542 (tm-30) cc_final: 0.4236 (mt-10) REVERT: D 708 MET cc_start: 0.2240 (ppp) cc_final: 0.0707 (tpt) REVERT: E 456 GLU cc_start: 0.7520 (tp30) cc_final: 0.7308 (tp30) REVERT: E 537 MET cc_start: 0.6461 (tpp) cc_final: 0.6128 (tpp) REVERT: E 696 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7011 (mtpp) REVERT: F 464 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7629 (mp) REVERT: F 488 THR cc_start: 0.8248 (t) cc_final: 0.7854 (m) REVERT: F 502 ASN cc_start: 0.8097 (t0) cc_final: 0.7377 (m110) REVERT: F 632 MET cc_start: 0.5888 (mtp) cc_final: 0.5673 (mtp) REVERT: F 642 ARG cc_start: 0.5894 (mtp85) cc_final: 0.5512 (mtp85) REVERT: F 677 ASP cc_start: 0.6837 (m-30) cc_final: 0.6611 (m-30) REVERT: F 697 PHE cc_start: 0.5980 (m-80) cc_final: 0.5764 (m-80) REVERT: F 708 MET cc_start: 0.7158 (mtp) cc_final: 0.6652 (ttp) REVERT: G 419 ARG cc_start: 0.5369 (tpp-160) cc_final: 0.4542 (tpt90) REVERT: G 635 MET cc_start: 0.2620 (pmm) cc_final: 0.2106 (tpp) REVERT: G 708 MET cc_start: 0.2438 (tpp) cc_final: 0.0904 (ptp) REVERT: H 426 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: H 456 GLU cc_start: 0.7914 (tp30) cc_final: 0.7681 (tp30) REVERT: H 568 PHE cc_start: 0.6802 (p90) cc_final: 0.6428 (p90) REVERT: H 608 GLU cc_start: 0.5297 (pt0) cc_final: 0.3199 (tt0) REVERT: H 632 MET cc_start: 0.5955 (mtp) cc_final: 0.5706 (mtp) REVERT: H 639 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7022 (mt) REVERT: H 692 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7254 (mm-30) REVERT: I 441 ILE cc_start: 0.5418 (OUTLIER) cc_final: 0.5190 (mp) REVERT: I 449 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.7146 (mtt-85) REVERT: I 464 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7479 (mp) REVERT: I 538 ASP cc_start: 0.7905 (t70) cc_final: 0.7676 (t70) REVERT: I 682 LEU cc_start: 0.7176 (mp) cc_final: 0.6937 (tp) REVERT: J 608 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.2563 (mt-10) REVERT: J 648 ARG cc_start: 0.6266 (tmm-80) cc_final: 0.5366 (ptt180) REVERT: J 692 GLU cc_start: 0.6901 (tp30) cc_final: 0.6375 (mt-10) REVERT: J 700 GLU cc_start: 0.6948 (mt-10) cc_final: 0.5933 (mt-10) REVERT: K 543 SER cc_start: 0.7347 (t) cc_final: 0.6724 (p) REVERT: K 587 PHE cc_start: 0.4519 (t80) cc_final: 0.3288 (t80) REVERT: K 642 ARG cc_start: 0.6363 (tpt-90) cc_final: 0.5994 (tpt-90) REVERT: K 662 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7526 (mp) REVERT: K 666 MET cc_start: 0.5958 (mmm) cc_final: 0.4624 (mmm) REVERT: K 672 LEU cc_start: 0.6718 (tp) cc_final: 0.6268 (pt) REVERT: K 708 MET cc_start: -0.0287 (tpt) cc_final: -0.1303 (ptm) REVERT: L 513 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6546 (pp30) REVERT: L 514 LYS cc_start: 0.7798 (ttpp) cc_final: 0.6815 (pttm) REVERT: L 556 MET cc_start: 0.6278 (ttp) cc_final: 0.5785 (ttp) REVERT: M 434 LYS cc_start: 0.7878 (mttp) cc_final: 0.7656 (mmtm) REVERT: M 473 ASP cc_start: 0.7918 (m-30) cc_final: 0.7559 (m-30) REVERT: M 602 GLN cc_start: 0.7843 (mm110) cc_final: 0.7634 (mm110) REVERT: N 428 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8281 (tt) REVERT: N 599 ASP cc_start: 0.8290 (t70) cc_final: 0.8013 (t0) REVERT: O 505 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8216 (tt) REVERT: O 709 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7361 (tm-30) REVERT: P 660 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7273 (mp-120) REVERT: Q 599 ASP cc_start: 0.8114 (t0) cc_final: 0.7849 (t0) REVERT: Q 664 ASN cc_start: 0.7883 (t0) cc_final: 0.7552 (m-40) outliers start: 156 outliers final: 112 residues processed: 828 average time/residue: 0.2266 time to fit residues: 311.7150 Evaluate side-chains 802 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 675 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 633 GLN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain D residue 662 ILE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 696 LYS Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 462 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 655 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 441 ILE Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 603 ASN Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain I residue 697 PHE Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 511 GLU Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 460 SER Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 608 GLU Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 638 ASN Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 542 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 660 GLN Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Chi-restraints excluded: chain R residue 606 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 106 optimal weight: 20.0000 chunk 236 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 507 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN B 643 ASN D 559 HIS G 422 GLN G 504 GLN G 602 GLN H 643 ASN J 496 GLN J 575 HIS J 638 ASN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 HIS ** M 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 656 HIS P 638 ASN P 656 HIS P 660 GLN Q 513 GLN Q 589 ASN ** R 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 638 ASN R 660 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.275780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.206159 restraints weight = 51028.513| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 4.20 r_work: 0.3599 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 43364 Z= 0.258 Angle : 0.661 12.525 58662 Z= 0.327 Chirality : 0.042 0.220 6660 Planarity : 0.004 0.093 7542 Dihedral : 4.026 51.454 5726 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.72 % Allowed : 24.03 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.12), residues: 5220 helix: 1.87 (0.08), residues: 4158 sheet: None (None), residues: 0 loop : -0.73 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 642 TYR 0.022 0.002 TYR N 540 PHE 0.031 0.002 PHE K 568 TRP 0.023 0.002 TRP Q 447 HIS 0.007 0.001 HIS Q 529 Details of bonding type rmsd covalent geometry : bond 0.00640 (43362) covalent geometry : angle 0.66147 (58662) hydrogen bonds : bond 0.05478 ( 3039) hydrogen bonds : angle 3.76726 ( 9051) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 704 time to evaluate : 1.856 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: A 449 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.7114 (mtm-85) REVERT: A 632 MET cc_start: 0.5689 (mtp) cc_final: 0.5085 (mtp) REVERT: A 648 ARG cc_start: 0.5649 (ttp80) cc_final: 0.5285 (ptt180) REVERT: B 459 LYS cc_start: 0.6764 (ttmt) cc_final: 0.6439 (pttt) REVERT: B 632 MET cc_start: 0.3241 (OUTLIER) cc_final: 0.2479 (mtt) REVERT: B 635 MET cc_start: 0.4093 (pmm) cc_final: 0.3447 (mmm) REVERT: C 419 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.4103 (tpt90) REVERT: C 445 ASN cc_start: 0.2504 (p0) cc_final: 0.1581 (t0) REVERT: C 454 LYS cc_start: 0.3620 (OUTLIER) cc_final: 0.3369 (mmtm) REVERT: C 633 GLN cc_start: 0.3828 (OUTLIER) cc_final: 0.3515 (mt0) REVERT: C 708 MET cc_start: 0.3723 (tpp) cc_final: 0.1823 (ptp) REVERT: D 433 SER cc_start: 0.3949 (p) cc_final: 0.3527 (t) REVERT: D 482 ARG cc_start: 0.4425 (ttt90) cc_final: 0.3509 (ttp-110) REVERT: D 514 LYS cc_start: 0.6885 (tmtt) cc_final: 0.6502 (pttm) REVERT: D 543 SER cc_start: 0.6890 (t) cc_final: 0.6187 (p) REVERT: D 668 GLU cc_start: 0.5241 (tm-30) cc_final: 0.4776 (mt-10) REVERT: E 456 GLU cc_start: 0.7773 (tp30) cc_final: 0.7422 (tp30) REVERT: E 537 MET cc_start: 0.5764 (tpp) cc_final: 0.5318 (tpp) REVERT: E 696 LYS cc_start: 0.7071 (tttm) cc_final: 0.6352 (mtpp) REVERT: F 426 GLU cc_start: 0.7316 (mp0) cc_final: 0.7085 (mp0) REVERT: F 464 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7097 (mp) REVERT: F 502 ASN cc_start: 0.8065 (t0) cc_final: 0.7145 (m110) REVERT: F 603 ASN cc_start: 0.7373 (m-40) cc_final: 0.7082 (m110) REVERT: F 632 MET cc_start: 0.5274 (mtp) cc_final: 0.5051 (mtp) REVERT: F 635 MET cc_start: 0.4840 (mmm) cc_final: 0.4257 (ttt) REVERT: F 642 ARG cc_start: 0.5889 (mtp85) cc_final: 0.5587 (mtp85) REVERT: F 659 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6712 (mttp) REVERT: F 677 ASP cc_start: 0.7173 (m-30) cc_final: 0.6772 (m-30) REVERT: F 696 LYS cc_start: 0.7492 (tptm) cc_final: 0.7160 (ttmm) REVERT: F 697 PHE cc_start: 0.5757 (m-80) cc_final: 0.5538 (m-80) REVERT: F 708 MET cc_start: 0.6550 (mtp) cc_final: 0.6265 (ttp) REVERT: G 419 ARG cc_start: 0.4743 (tpp-160) cc_final: 0.3908 (tpt90) REVERT: G 635 MET cc_start: 0.2552 (pmm) cc_final: 0.2053 (tpp) REVERT: G 662 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7122 (mm) REVERT: G 708 MET cc_start: 0.2385 (tpp) cc_final: 0.0546 (ptp) REVERT: H 456 GLU cc_start: 0.7989 (tp30) cc_final: 0.7703 (tp30) REVERT: H 632 MET cc_start: 0.5576 (mtp) cc_final: 0.5272 (mtp) REVERT: H 639 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7154 (mt) REVERT: H 692 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6910 (mm-30) REVERT: I 449 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.7022 (mtt-85) REVERT: I 464 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7223 (mp) REVERT: I 682 LEU cc_start: 0.7558 (mp) cc_final: 0.7219 (tp) REVERT: J 608 GLU cc_start: 0.3421 (OUTLIER) cc_final: 0.2230 (mt-10) REVERT: J 648 ARG cc_start: 0.6185 (tmm-80) cc_final: 0.5090 (ptt180) REVERT: J 692 GLU cc_start: 0.6768 (tp30) cc_final: 0.6074 (mt-10) REVERT: K 543 SER cc_start: 0.7066 (t) cc_final: 0.6418 (p) REVERT: K 587 PHE cc_start: 0.5236 (t80) cc_final: 0.3861 (t80) REVERT: K 662 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7434 (mp) REVERT: K 666 MET cc_start: 0.6024 (mmm) cc_final: 0.5065 (mmm) REVERT: K 672 LEU cc_start: 0.6925 (tp) cc_final: 0.6388 (pt) REVERT: K 708 MET cc_start: -0.0553 (tpt) cc_final: -0.1650 (ptm) REVERT: L 513 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6681 (pp30) REVERT: L 514 LYS cc_start: 0.8076 (ttpp) cc_final: 0.6854 (pttm) REVERT: L 517 ASP cc_start: 0.4004 (t0) cc_final: 0.3777 (m-30) REVERT: L 556 MET cc_start: 0.6339 (ttp) cc_final: 0.5745 (ttp) REVERT: M 434 LYS cc_start: 0.7983 (mttp) cc_final: 0.7623 (mmtm) REVERT: M 473 ASP cc_start: 0.8350 (m-30) cc_final: 0.7953 (m-30) REVERT: M 602 GLN cc_start: 0.7952 (mm110) cc_final: 0.7677 (mm110) REVERT: N 428 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (tt) REVERT: N 599 ASP cc_start: 0.8561 (t70) cc_final: 0.8250 (t0) REVERT: O 505 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8498 (tt) REVERT: O 709 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7660 (tm-30) REVERT: P 660 GLN cc_start: 0.8372 (mp10) cc_final: 0.8099 (mp10) REVERT: Q 599 ASP cc_start: 0.8622 (t0) cc_final: 0.8300 (t0) REVERT: Q 664 ASN cc_start: 0.8095 (t0) cc_final: 0.7605 (m-40) outliers start: 175 outliers final: 120 residues processed: 814 average time/residue: 0.2398 time to fit residues: 322.5065 Evaluate side-chains 802 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 670 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 633 GLN Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 475 VAL Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 475 VAL Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 506 VAL Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 662 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 462 THR Chi-restraints excluded: chain H residue 471 MET Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 543 SER Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 580 VAL Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain H residue 655 THR Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 603 ASN Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain I residue 697 PHE Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 511 GLU Chi-restraints excluded: chain J residue 538 ASP Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain J residue 595 PHE Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain J residue 708 MET Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 460 SER Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 471 MET Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 420 VAL Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 608 GLU Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 635 MET Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 542 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 580 VAL Chi-restraints excluded: chain R residue 606 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 369 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 404 optimal weight: 4.9990 chunk 480 optimal weight: 0.0570 chunk 255 optimal weight: 10.0000 chunk 472 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 375 optimal weight: 2.9990 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 ASN H 544 ASN J 676 GLN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 643 ASN ** M 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 638 ASN P 656 HIS Q 513 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.274940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216280 restraints weight = 51156.798| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 3.25 r_work: 0.3705 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43364 Z= 0.153 Angle : 0.582 14.085 58662 Z= 0.285 Chirality : 0.039 0.236 6660 Planarity : 0.004 0.071 7542 Dihedral : 3.769 52.472 5726 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.70 % Allowed : 24.93 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.12), residues: 5220 helix: 2.07 (0.08), residues: 4176 sheet: None (None), residues: 0 loop : -0.63 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 648 TYR 0.021 0.001 TYR L 425 PHE 0.031 0.002 PHE K 568 TRP 0.019 0.001 TRP D 447 HIS 0.006 0.001 HIS K 590 Details of bonding type rmsd covalent geometry : bond 0.00368 (43362) covalent geometry : angle 0.58201 (58662) hydrogen bonds : bond 0.04283 ( 3039) hydrogen bonds : angle 3.55667 ( 9051) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 721 time to evaluate : 1.485 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: A 449 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.7123 (mtm-85) REVERT: A 480 GLU cc_start: 0.7304 (pm20) cc_final: 0.7022 (mp0) REVERT: A 552 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6892 (tt0) REVERT: A 632 MET cc_start: 0.5761 (mtp) cc_final: 0.5179 (mtp) REVERT: A 648 ARG cc_start: 0.5760 (ttp80) cc_final: 0.5291 (ptt180) REVERT: A 692 GLU cc_start: 0.6766 (tp30) cc_final: 0.6185 (mt-10) REVERT: B 441 ILE cc_start: 0.4229 (OUTLIER) cc_final: 0.3868 (mt) REVERT: B 459 LYS cc_start: 0.6716 (ttmt) cc_final: 0.6303 (pttt) REVERT: B 572 MET cc_start: 0.5843 (mtt) cc_final: 0.5211 (mtt) REVERT: B 632 MET cc_start: 0.2758 (OUTLIER) cc_final: 0.1989 (mtt) REVERT: B 635 MET cc_start: 0.4036 (pmm) cc_final: 0.3400 (mmm) REVERT: C 419 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.4214 (tpt90) REVERT: C 633 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.3370 (mt0) REVERT: D 433 SER cc_start: 0.4187 (p) cc_final: 0.3793 (t) REVERT: D 482 ARG cc_start: 0.4363 (ttt90) cc_final: 0.3849 (mtp-110) REVERT: D 514 LYS cc_start: 0.6827 (tmtt) cc_final: 0.6414 (pttm) REVERT: D 668 GLU cc_start: 0.5258 (tm-30) cc_final: 0.4732 (mt-10) REVERT: D 708 MET cc_start: 0.1416 (ppp) cc_final: 0.0730 (tpt) REVERT: E 456 GLU cc_start: 0.7754 (tp30) cc_final: 0.7405 (tp30) REVERT: E 537 MET cc_start: 0.5747 (tpp) cc_final: 0.5194 (tpp) REVERT: E 696 LYS cc_start: 0.7154 (tttm) cc_final: 0.6407 (mtpp) REVERT: F 426 GLU cc_start: 0.7447 (mp0) cc_final: 0.7230 (mp0) REVERT: F 464 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7020 (mp) REVERT: F 502 ASN cc_start: 0.8054 (t0) cc_final: 0.7101 (m110) REVERT: F 603 ASN cc_start: 0.7400 (m-40) cc_final: 0.6940 (m110) REVERT: F 632 MET cc_start: 0.5385 (mtp) cc_final: 0.5161 (mtp) REVERT: F 642 ARG cc_start: 0.5902 (mtp85) cc_final: 0.5589 (mtp85) REVERT: F 677 ASP cc_start: 0.7085 (m-30) cc_final: 0.6728 (m-30) REVERT: F 697 PHE cc_start: 0.5703 (m-80) cc_final: 0.5489 (m-80) REVERT: F 708 MET cc_start: 0.6459 (mtp) cc_final: 0.6180 (ttp) REVERT: G 419 ARG cc_start: 0.4787 (tpp-160) cc_final: 0.3949 (tpt90) REVERT: G 635 MET cc_start: 0.2529 (pmm) cc_final: 0.1974 (tpp) REVERT: G 648 ARG cc_start: 0.4998 (tmm-80) cc_final: 0.4647 (ptm160) REVERT: G 708 MET cc_start: 0.1898 (tpp) cc_final: 0.0045 (ptp) REVERT: H 456 GLU cc_start: 0.7982 (tp30) cc_final: 0.7673 (tp30) REVERT: H 632 MET cc_start: 0.5533 (mtp) cc_final: 0.5253 (mtp) REVERT: H 639 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7104 (mt) REVERT: H 692 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6912 (mm-30) REVERT: I 449 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6980 (mtt-85) REVERT: I 464 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7127 (mp) REVERT: J 608 GLU cc_start: 0.3366 (OUTLIER) cc_final: 0.2373 (mt-10) REVERT: J 626 LEU cc_start: 0.5669 (mt) cc_final: 0.5469 (mt) REVERT: J 648 ARG cc_start: 0.6150 (tmm-80) cc_final: 0.5098 (ptt180) REVERT: J 692 GLU cc_start: 0.6690 (tp30) cc_final: 0.5961 (mt-10) REVERT: K 543 SER cc_start: 0.7076 (t) cc_final: 0.6354 (p) REVERT: K 587 PHE cc_start: 0.5195 (t80) cc_final: 0.3856 (t80) REVERT: K 662 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7349 (mp) REVERT: K 666 MET cc_start: 0.5989 (mmm) cc_final: 0.4909 (mmm) REVERT: K 672 LEU cc_start: 0.6871 (tp) cc_final: 0.6299 (pt) REVERT: K 708 MET cc_start: -0.0712 (tpt) cc_final: -0.1721 (ptm) REVERT: L 513 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6612 (pp30) REVERT: L 514 LYS cc_start: 0.8129 (ttpp) cc_final: 0.6932 (pttm) REVERT: L 517 ASP cc_start: 0.4058 (t0) cc_final: 0.3595 (m-30) REVERT: L 556 MET cc_start: 0.6279 (ttp) cc_final: 0.5683 (ttp) REVERT: M 434 LYS cc_start: 0.7915 (mttp) cc_final: 0.7601 (mmtm) REVERT: M 599 ASP cc_start: 0.8326 (t0) cc_final: 0.7971 (t0) REVERT: M 602 GLN cc_start: 0.7811 (mm110) cc_final: 0.7547 (mm110) REVERT: N 599 ASP cc_start: 0.8345 (t70) cc_final: 0.8061 (t0) REVERT: O 709 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7540 (tm-30) REVERT: P 660 GLN cc_start: 0.8237 (mp10) cc_final: 0.7991 (mp10) REVERT: Q 599 ASP cc_start: 0.8524 (t0) cc_final: 0.8228 (t0) outliers start: 127 outliers final: 93 residues processed: 802 average time/residue: 0.2272 time to fit residues: 302.1186 Evaluate side-chains 784 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 682 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 633 GLN Chi-restraints excluded: chain D residue 447 TRP Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 462 THR Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 511 GLU Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 460 SER Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain K residue 471 MET Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 608 GLU Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 638 ASN Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain O residue 635 MET Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 542 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 444 LEU Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 484 optimal weight: 0.9980 chunk 407 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS K 467 ASN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 ASN ** M 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 656 HIS Q 513 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.272000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.213869 restraints weight = 51012.392| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.34 r_work: 0.3858 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 43364 Z= 0.255 Angle : 0.672 14.638 58662 Z= 0.330 Chirality : 0.042 0.231 6660 Planarity : 0.004 0.093 7542 Dihedral : 4.035 53.127 5726 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 24.73 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.12), residues: 5220 helix: 1.85 (0.08), residues: 4158 sheet: None (None), residues: 0 loop : -0.71 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 642 TYR 0.022 0.002 TYR N 540 PHE 0.025 0.002 PHE O 568 TRP 0.023 0.002 TRP Q 447 HIS 0.008 0.001 HIS K 590 Details of bonding type rmsd covalent geometry : bond 0.00633 (43362) covalent geometry : angle 0.67203 (58662) hydrogen bonds : bond 0.05443 ( 3039) hydrogen bonds : angle 3.77522 ( 9051) Misc. bond : bond 0.00098 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10440 Ramachandran restraints generated. 5220 Oldfield, 0 Emsley, 5220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 702 time to evaluate : 1.633 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 480 GLU cc_start: 0.7719 (pm20) cc_final: 0.7411 (mp0) REVERT: A 632 MET cc_start: 0.6094 (mtp) cc_final: 0.5535 (mtp) REVERT: A 648 ARG cc_start: 0.5947 (ttp80) cc_final: 0.5502 (ptt180) REVERT: B 441 ILE cc_start: 0.4455 (OUTLIER) cc_final: 0.4072 (mt) REVERT: B 459 LYS cc_start: 0.6712 (ttmt) cc_final: 0.6335 (pttt) REVERT: B 572 MET cc_start: 0.5819 (mtt) cc_final: 0.5215 (mtt) REVERT: B 632 MET cc_start: 0.3368 (OUTLIER) cc_final: 0.2420 (mtt) REVERT: B 635 MET cc_start: 0.3811 (pmm) cc_final: 0.3216 (mmm) REVERT: C 419 ARG cc_start: 0.5073 (OUTLIER) cc_final: 0.4618 (tpt90) REVERT: C 445 ASN cc_start: 0.3510 (p0) cc_final: 0.1906 (t0) REVERT: C 633 GLN cc_start: 0.4471 (OUTLIER) cc_final: 0.3822 (mt0) REVERT: D 433 SER cc_start: 0.4020 (p) cc_final: 0.3653 (t) REVERT: D 482 ARG cc_start: 0.4496 (ttt90) cc_final: 0.3788 (ttp-110) REVERT: D 543 SER cc_start: 0.6947 (t) cc_final: 0.6343 (p) REVERT: D 708 MET cc_start: 0.2155 (ppp) cc_final: 0.0729 (tpt) REVERT: D 712 LYS cc_start: 0.5006 (tptm) cc_final: 0.4726 (ttpt) REVERT: E 456 GLU cc_start: 0.7644 (tp30) cc_final: 0.7397 (tp30) REVERT: E 537 MET cc_start: 0.6368 (tpp) cc_final: 0.5932 (tpp) REVERT: E 673 LYS cc_start: 0.6493 (tptp) cc_final: 0.5858 (pptt) REVERT: E 696 LYS cc_start: 0.7587 (tttm) cc_final: 0.6845 (mtpp) REVERT: F 426 GLU cc_start: 0.7626 (mp0) cc_final: 0.7391 (mp0) REVERT: F 464 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7567 (mp) REVERT: F 502 ASN cc_start: 0.8203 (t0) cc_final: 0.7378 (m110) REVERT: F 603 ASN cc_start: 0.7399 (m-40) cc_final: 0.7032 (m110) REVERT: F 635 MET cc_start: 0.4492 (mmm) cc_final: 0.3936 (ttt) REVERT: F 642 ARG cc_start: 0.5977 (mtp85) cc_final: 0.5591 (mtp85) REVERT: F 677 ASP cc_start: 0.7024 (m-30) cc_final: 0.6719 (m-30) REVERT: F 697 PHE cc_start: 0.5939 (m-80) cc_final: 0.5736 (m-80) REVERT: F 708 MET cc_start: 0.7088 (mtp) cc_final: 0.6862 (ttp) REVERT: G 419 ARG cc_start: 0.5196 (tpp-160) cc_final: 0.4343 (tpt90) REVERT: G 635 MET cc_start: 0.2407 (pmm) cc_final: 0.1833 (tpp) REVERT: G 708 MET cc_start: 0.1953 (tpp) cc_final: -0.0013 (ptp) REVERT: H 632 MET cc_start: 0.5984 (mtp) cc_final: 0.5738 (mtp) REVERT: H 639 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7117 (mt) REVERT: H 692 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7258 (mm-30) REVERT: I 449 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7111 (mtt-85) REVERT: I 464 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7603 (mp) REVERT: I 682 LEU cc_start: 0.7390 (mp) cc_final: 0.7151 (tp) REVERT: J 603 ASN cc_start: 0.6780 (m-40) cc_final: 0.6499 (m-40) REVERT: J 608 GLU cc_start: 0.4202 (OUTLIER) cc_final: 0.2851 (mt-10) REVERT: J 648 ARG cc_start: 0.6388 (tmm-80) cc_final: 0.5305 (ptt180) REVERT: J 692 GLU cc_start: 0.6792 (tp30) cc_final: 0.6197 (mt-10) REVERT: K 543 SER cc_start: 0.7157 (t) cc_final: 0.6584 (p) REVERT: K 662 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7455 (mp) REVERT: K 666 MET cc_start: 0.6093 (mmm) cc_final: 0.4816 (mmm) REVERT: K 672 LEU cc_start: 0.6807 (tp) cc_final: 0.6287 (pt) REVERT: K 708 MET cc_start: -0.0373 (tpt) cc_final: -0.1386 (ptm) REVERT: L 513 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6645 (pp30) REVERT: L 514 LYS cc_start: 0.7945 (ttpp) cc_final: 0.6886 (pttm) REVERT: L 517 ASP cc_start: 0.4555 (t0) cc_final: 0.3793 (m-30) REVERT: L 538 ASP cc_start: 0.5227 (t0) cc_final: 0.5000 (t0) REVERT: L 556 MET cc_start: 0.6613 (ttp) cc_final: 0.6078 (ttp) REVERT: M 434 LYS cc_start: 0.7987 (mttp) cc_final: 0.7745 (mmtm) REVERT: M 473 ASP cc_start: 0.8000 (m-30) cc_final: 0.7637 (m-30) REVERT: M 599 ASP cc_start: 0.7974 (t0) cc_final: 0.7706 (t0) REVERT: M 602 GLN cc_start: 0.7920 (mm110) cc_final: 0.7720 (mm110) REVERT: N 428 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8422 (tt) REVERT: N 599 ASP cc_start: 0.8436 (t70) cc_final: 0.8166 (t0) REVERT: O 505 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8259 (tt) REVERT: O 688 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8182 (mttp) REVERT: O 709 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7597 (tm-30) REVERT: P 660 GLN cc_start: 0.8121 (mp10) cc_final: 0.7920 (mp10) REVERT: Q 599 ASP cc_start: 0.8176 (t0) cc_final: 0.7891 (t0) outliers start: 123 outliers final: 101 residues processed: 781 average time/residue: 0.2304 time to fit residues: 298.0613 Evaluate side-chains 794 residues out of total 4698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 682 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 489 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 633 GLN Chi-restraints excluded: chain D residue 447 TRP Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 587 PHE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 655 THR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 471 MET Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 489 HIS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 452 THR Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 543 SER Chi-restraints excluded: chain H residue 571 LEU Chi-restraints excluded: chain H residue 585 THR Chi-restraints excluded: chain H residue 631 LEU Chi-restraints excluded: chain H residue 639 LEU Chi-restraints excluded: chain I residue 420 VAL Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 462 THR Chi-restraints excluded: chain I residue 464 ILE Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 655 THR Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 511 GLU Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain J residue 595 PHE Chi-restraints excluded: chain J residue 608 GLU Chi-restraints excluded: chain J residue 697 PHE Chi-restraints excluded: chain K residue 436 LEU Chi-restraints excluded: chain K residue 460 SER Chi-restraints excluded: chain K residue 471 MET Chi-restraints excluded: chain K residue 477 ASP Chi-restraints excluded: chain K residue 662 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 474 ASP Chi-restraints excluded: chain L residue 476 GLU Chi-restraints excluded: chain L residue 489 HIS Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain M residue 450 VAL Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain M residue 608 GLU Chi-restraints excluded: chain M residue 625 SER Chi-restraints excluded: chain M residue 666 MET Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 442 ASP Chi-restraints excluded: chain N residue 452 THR Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 438 GLU Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 505 LEU Chi-restraints excluded: chain O residue 564 LEU Chi-restraints excluded: chain O residue 580 VAL Chi-restraints excluded: chain O residue 586 ASP Chi-restraints excluded: chain O residue 666 MET Chi-restraints excluded: chain P residue 446 VAL Chi-restraints excluded: chain P residue 542 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 653 THR Chi-restraints excluded: chain P residue 699 ILE Chi-restraints excluded: chain P residue 710 LEU Chi-restraints excluded: chain Q residue 580 VAL Chi-restraints excluded: chain Q residue 584 LEU Chi-restraints excluded: chain Q residue 641 LEU Chi-restraints excluded: chain Q residue 699 ILE Chi-restraints excluded: chain R residue 442 ASP Chi-restraints excluded: chain R residue 580 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 50 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 461 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 443 optimal weight: 0.6980 chunk 383 optimal weight: 6.9990 chunk 413 optimal weight: 0.0980 chunk 294 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 575 HIS M 638 ASN ** P 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 513 GLN ** Q 656 HIS ** 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 = 0.4895 r_free = 0.4895 target = 0.273686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.213043 restraints weight = 51320.192| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.28 r_work: 0.3715 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43364 Z= 0.191 Angle : 0.620 14.681 58662 Z= 0.304 Chirality : 0.040 0.239 6660 Planarity : 0.004 0.080 7542 Dihedral : 3.902 53.610 5726 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.49 % Allowed : 25.01 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.12), residues: 5220 helix: 1.98 (0.08), residues: 4158 sheet: None (None), residues: 0 loop : -0.66 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 642 TYR 0.021 0.001 TYR L 425 PHE 0.023 0.002 PHE P 568 TRP 0.019 0.001 TRP Q 447 HIS 0.006 0.001 HIS K 590 Details of bonding type rmsd covalent geometry : bond 0.00468 (43362) covalent geometry : angle 0.61974 (58662) hydrogen bonds : bond 0.04693 ( 3039) hydrogen bonds : angle 3.65597 ( 9051) Misc. bond : bond 0.00083 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11282.13 seconds wall clock time: 193 minutes 45.46 seconds (11625.46 seconds total)