Starting phenix.real_space_refine on Fri Jun 13 20:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2m_47457/06_2025/9e2m_47457.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 94 5.16 5 C 9708 2.51 5 N 2658 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15412 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2289 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 1 Chain: "B" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4556 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 540} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2058 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 11, 'TRANS': 246} Chain breaks: 2 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "F" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.61, per 1000 atoms: 0.62 Number of scatterers: 15412 At special positions: 0 Unit cell: (129.6, 125.28, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 2 15.00 O 2950 8.00 N 2658 7.00 C 9708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 80.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.547A pdb=" N ILE A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.816A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.525A pdb=" N ILE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 503 through 523 removed outlier: 3.720A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 removed outlier: 6.354A pdb=" N ASP A 527 " --> pdb=" O GLN A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 527' Processing helix chain 'A' and resid 528 through 555 removed outlier: 4.100A pdb=" N ASP A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.680A pdb=" N ARG A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.510A pdb=" N LEU A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 removed outlier: 3.557A pdb=" N HIS A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.733A pdb=" N ARG A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 685 through 710 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.603A pdb=" N HIS A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 58 through 77 removed outlier: 3.722A pdb=" N ALA B 62 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 150 through 167 removed outlier: 3.613A pdb=" N LEU B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 190 removed outlier: 3.648A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.558A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 228 through 265 removed outlier: 3.771A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Proline residue: B 237 - end of helix Proline residue: B 241 - end of helix removed outlier: 4.806A pdb=" N ASP B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 285 through 308 removed outlier: 3.675A pdb=" N TYR B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.865A pdb=" N GLY B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.900A pdb=" N LEU B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.541A pdb=" N TYR B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.729A pdb=" N ILE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 503 through 525 removed outlier: 3.554A pdb=" N THR B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 4.292A pdb=" N ASP B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.742A pdb=" N GLN B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.542A pdb=" N GLN B 584 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 619 removed outlier: 3.844A pdb=" N LEU B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 619 " --> pdb=" O LYS B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.629A pdb=" N GLN B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 4.038A pdb=" N ARG B 654 " --> pdb=" O ASN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 Processing helix chain 'B' and resid 684 through 698 Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 445 through 455 removed outlier: 3.630A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.701A pdb=" N ILE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 503 through 522 removed outlier: 3.693A pdb=" N LEU C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.064A pdb=" N ASP C 526 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP C 527 " --> pdb=" O GLN C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 523 through 527' Processing helix chain 'C' and resid 528 through 554 removed outlier: 4.051A pdb=" N ASP C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.716A pdb=" N ARG C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 569 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 571 " --> pdb=" O ILE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 4.640A pdb=" N PHE C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 619 removed outlier: 3.530A pdb=" N GLN C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 removed outlier: 3.622A pdb=" N HIS C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 644 " --> pdb=" O LEU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.845A pdb=" N GLN C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 681 removed outlier: 3.510A pdb=" N ALA C 681 " --> pdb=" O HIS C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 709 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 461 through 486 removed outlier: 3.762A pdb=" N ILE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 501 Processing helix chain 'D' and resid 503 through 524 Processing helix chain 'D' and resid 527 through 555 removed outlier: 4.127A pdb=" N MET D 531 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.513A pdb=" N GLN D 584 " --> pdb=" O ARG D 580 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 615 Processing helix chain 'D' and resid 637 through 647 Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.984A pdb=" N ARG D 654 " --> pdb=" O ASN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 682 Processing helix chain 'D' and resid 682 through 701 removed outlier: 3.534A pdb=" N GLU D 688 " --> pdb=" O ILE D 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.841A pdb=" N VAL E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 486 removed outlier: 3.591A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 503 through 522 removed outlier: 3.635A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 520 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 555 removed outlier: 4.171A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR E 534 " --> pdb=" O CYS E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.662A pdb=" N GLN E 569 " --> pdb=" O ASP E 565 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 571 " --> pdb=" O ILE E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 586 removed outlier: 4.608A pdb=" N PHE E 575 " --> pdb=" O THR E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 619 Processing helix chain 'E' and resid 637 through 647 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.626A pdb=" N ARG E 654 " --> pdb=" O ASN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 682 Processing helix chain 'E' and resid 682 through 709 removed outlier: 3.558A pdb=" N LYS E 697 " --> pdb=" O GLU E 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.680A pdb=" N SER F 439 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 454 through 459 Processing helix chain 'F' and resid 461 through 486 removed outlier: 3.689A pdb=" N ILE F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 501 Processing helix chain 'F' and resid 503 through 524 removed outlier: 3.709A pdb=" N LEU F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 555 removed outlier: 4.023A pdb=" N MET F 531 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 571 removed outlier: 3.564A pdb=" N GLN F 569 " --> pdb=" O ASP F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 586 Processing helix chain 'F' and resid 594 through 619 Processing helix chain 'F' and resid 637 through 647 removed outlier: 3.510A pdb=" N HIS F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.629A pdb=" N ARG F 654 " --> pdb=" O ASN F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 679 Processing helix chain 'F' and resid 684 through 708 removed outlier: 3.544A pdb=" N GLU F 688 " --> pdb=" O ILE F 684 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS F 690 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 708 " --> pdb=" O SER F 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.358A pdb=" N LEU B 53 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AA5, first strand: chain 'D' and resid 491 through 492 Processing sheet with id=AA6, first strand: chain 'E' and resid 491 through 492 Processing sheet with id=AA7, first strand: chain 'F' and resid 491 through 492 1056 hydrogen bonds defined for protein. 3135 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: 4.47 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 - 1.33: 3207 1.33 - 1.45: 3426 1.45 - 1.57: 8891 1.57 - 1.69: 2 1.69 - 1.81: 162 Bond restraints: 15688 Sorted by residual: bond pdb=" N ILE B 308 " pdb=" CA ILE B 308 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.36e+00 bond pdb=" N ARG B 345 " pdb=" CA ARG B 345 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.31e-02 5.83e+03 8.22e+00 bond pdb=" O POP B 801 " pdb=" P1 POP B 801 " ideal model delta sigma weight residual 1.660 1.605 0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" C GLY B 78 " pdb=" N PRO B 79 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.25e-02 6.40e+03 6.95e+00 ... (remaining 15683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 20752 2.16 - 4.31: 349 4.31 - 6.47: 70 6.47 - 8.62: 11 8.62 - 10.78: 2 Bond angle restraints: 21184 Sorted by residual: angle pdb=" C ASP A 428 " pdb=" CA ASP A 428 " pdb=" CB ASP A 428 " ideal model delta sigma weight residual 115.79 110.32 5.47 1.19e+00 7.06e-01 2.11e+01 angle pdb=" N ILE A 684 " pdb=" CA ILE A 684 " pdb=" C ILE A 684 " ideal model delta sigma weight residual 112.90 108.71 4.19 9.60e-01 1.09e+00 1.90e+01 angle pdb=" C ASN B 319 " pdb=" N ILE B 320 " pdb=" CA ILE B 320 " ideal model delta sigma weight residual 120.42 114.53 5.89 1.42e+00 4.96e-01 1.72e+01 angle pdb=" N ASN D 616 " pdb=" CA ASN D 616 " pdb=" C ASN D 616 " ideal model delta sigma weight residual 114.75 109.54 5.21 1.26e+00 6.30e-01 1.71e+01 angle pdb=" N GLU A 685 " pdb=" CA GLU A 685 " pdb=" C GLU A 685 " ideal model delta sigma weight residual 113.88 108.92 4.96 1.23e+00 6.61e-01 1.63e+01 ... (remaining 21179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7879 17.99 - 35.98: 1143 35.98 - 53.97: 442 53.97 - 71.96: 84 71.96 - 89.95: 34 Dihedral angle restraints: 9582 sinusoidal: 4007 harmonic: 5575 Sorted by residual: dihedral pdb=" CA ASP E 667 " pdb=" C ASP E 667 " pdb=" N VAL E 668 " pdb=" CA VAL E 668 " ideal model delta harmonic sigma weight residual 180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ARG B 234 " pdb=" C ARG B 234 " pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LYS B 444 " pdb=" C LYS B 444 " pdb=" N GLY B 445 " pdb=" CA GLY B 445 " ideal model delta harmonic sigma weight residual 180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 9579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1819 0.047 - 0.093: 476 0.093 - 0.140: 60 0.140 - 0.186: 5 0.186 - 0.233: 2 Chirality restraints: 2362 Sorted by residual: chirality pdb=" CA ILE B 80 " pdb=" N ILE B 80 " pdb=" C ILE B 80 " pdb=" CB ILE B 80 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU B 350 " pdb=" CB LEU B 350 " pdb=" CD1 LEU B 350 " pdb=" CD2 LEU B 350 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA LEU E 577 " pdb=" N LEU E 577 " pdb=" C LEU E 577 " pdb=" CB LEU E 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 2359 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 433 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO C 434 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 434 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 434 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 433 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 434 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 586 " 0.035 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 587 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 587 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 587 " 0.030 5.00e-02 4.00e+02 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2901 2.77 - 3.30: 15023 3.30 - 3.83: 26364 3.83 - 4.37: 30633 4.37 - 4.90: 52452 Nonbonded interactions: 127373 Sorted by model distance: nonbonded pdb=" N GLU A 448 " pdb=" OE1 GLU A 448 " model vdw 2.235 3.120 nonbonded pdb=" N GLU B 619 " pdb=" OE1 GLU B 619 " model vdw 2.242 3.120 nonbonded pdb=" OE2 GLU E 536 " pdb=" NH2 ARG E 580 " model vdw 2.275 3.120 nonbonded pdb=" N GLU B 287 " pdb=" OE1 GLU B 287 " model vdw 2.278 3.120 nonbonded pdb=" NH1 ARG C 576 " pdb=" OD1 ASP C 602 " model vdw 2.288 3.120 ... (remaining 127368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 427 through 451 or resid 458 through 701)) selection = (chain 'C' and (resid 427 through 451 or resid 458 through 701)) selection = chain 'D' selection = (chain 'E' and (resid 427 through 451 or resid 458 through 701)) selection = (chain 'F' and (resid 427 through 451 or resid 458 through 701)) } 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: 3.440 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 35.700 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 0.055 15688 Z= 0.206 Angle : 0.744 10.779 21184 Z= 0.448 Chirality : 0.040 0.233 2362 Planarity : 0.005 0.061 2757 Dihedral : 19.896 89.949 5972 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.90 % Allowed : 3.70 % Favored : 95.41 % Rotamer: Outliers : 5.31 % Allowed : 31.91 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1894 helix: 1.44 (0.14), residues: 1423 sheet: -0.99 (1.80), residues: 10 loop : -2.36 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 180 HIS 0.005 0.001 HIS B 463 PHE 0.011 0.001 PHE B 547 TYR 0.026 0.002 TYR A 614 ARG 0.009 0.001 ARG F 679 Details of bonding type rmsd hydrogen bonds : bond 0.18691 ( 1056) hydrogen bonds : angle 5.98085 ( 3135) covalent geometry : bond 0.00386 (15688) covalent geometry : angle 0.74418 (21184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 534 time to evaluate : 1.948 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 452 ASP cc_start: 0.8100 (t0) cc_final: 0.7876 (t0) REVERT: A 466 ASN cc_start: 0.8616 (m-40) cc_final: 0.8095 (m110) REVERT: A 495 ARG cc_start: 0.7508 (mmm-85) cc_final: 0.7082 (mtm-85) REVERT: A 504 THR cc_start: 0.8434 (p) cc_final: 0.7909 (m) REVERT: A 517 ASP cc_start: 0.7776 (t0) cc_final: 0.7555 (t0) REVERT: A 520 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6935 (mp0) REVERT: A 672 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 68 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7863 (mtp85) REVERT: B 105 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6849 (mtt90) REVERT: B 155 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8183 (ttmm) REVERT: B 182 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7617 (tm-30) REVERT: B 220 ARG cc_start: 0.8083 (mpp80) cc_final: 0.7863 (mpt-90) REVERT: B 262 PHE cc_start: 0.6160 (t80) cc_final: 0.5822 (t80) REVERT: B 282 GLU cc_start: 0.7425 (mp0) cc_final: 0.7151 (pm20) REVERT: B 317 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7635 (ptpp) REVERT: B 466 ASN cc_start: 0.8509 (m-40) cc_final: 0.8296 (m110) REVERT: B 470 SER cc_start: 0.8483 (t) cc_final: 0.8244 (p) REVERT: B 548 ASP cc_start: 0.7902 (t70) cc_final: 0.7614 (t0) REVERT: B 568 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7902 (mtm180) REVERT: B 594 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: B 608 PHE cc_start: 0.8630 (m-80) cc_final: 0.8352 (m-80) REVERT: B 661 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7216 (ttp80) REVERT: B 668 VAL cc_start: 0.8606 (t) cc_final: 0.8374 (t) REVERT: B 671 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8055 (mtmm) REVERT: B 684 ILE cc_start: 0.8561 (mm) cc_final: 0.8146 (tt) REVERT: B 685 GLU cc_start: 0.7486 (mp0) cc_final: 0.7162 (mp0) REVERT: C 436 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7479 (mt-10) REVERT: C 448 GLU cc_start: 0.8025 (mp0) cc_final: 0.7702 (mp0) REVERT: C 483 ASP cc_start: 0.7522 (m-30) cc_final: 0.7285 (m-30) REVERT: C 548 ASP cc_start: 0.8255 (t0) cc_final: 0.7670 (t70) REVERT: C 582 MET cc_start: 0.8593 (ttt) cc_final: 0.8267 (ttp) REVERT: C 593 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7949 (pp) REVERT: C 635 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7260 (mmtt) REVERT: C 654 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (mtt-85) REVERT: C 657 LEU cc_start: 0.8489 (mt) cc_final: 0.8179 (mt) REVERT: C 659 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8374 (tp40) REVERT: C 661 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7610 (ttm-80) REVERT: C 672 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 703 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8281 (m) REVERT: D 436 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7674 (mp0) REVERT: D 444 LYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4378 (mppt) REVERT: D 469 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8302 (mtpt) REVERT: D 500 MET cc_start: 0.8019 (mmm) cc_final: 0.7812 (mmm) REVERT: D 504 THR cc_start: 0.8319 (m) cc_final: 0.8023 (p) REVERT: D 525 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6824 (tp) REVERT: D 541 LEU cc_start: 0.8221 (tt) cc_final: 0.7964 (mt) REVERT: D 667 ASP cc_start: 0.7605 (p0) cc_final: 0.7343 (p0) REVERT: D 671 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7963 (mtmt) REVERT: D 675 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (mm) REVERT: D 676 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (m) REVERT: D 679 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8211 (ttp80) REVERT: D 695 MET cc_start: 0.6668 (tpt) cc_final: 0.6401 (tpt) REVERT: E 487 ASP cc_start: 0.7108 (m-30) cc_final: 0.6895 (m-30) REVERT: E 491 LEU cc_start: 0.8303 (mt) cc_final: 0.8031 (mt) REVERT: E 539 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8184 (mtp85) REVERT: E 561 GLU cc_start: 0.7637 (mp0) cc_final: 0.7280 (mp0) REVERT: E 582 MET cc_start: 0.8671 (mtp) cc_final: 0.8423 (mtp) REVERT: E 685 GLU cc_start: 0.7671 (mp0) cc_final: 0.7316 (mp0) REVERT: E 691 MET cc_start: 0.8254 (mtp) cc_final: 0.8040 (mtp) REVERT: F 447 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8080 (mmt180) REVERT: F 529 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7387 (mmm-85) REVERT: F 565 ASP cc_start: 0.7549 (m-30) cc_final: 0.7250 (m-30) REVERT: F 604 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8026 (tp) REVERT: F 611 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7904 (ttt-90) REVERT: F 645 THR cc_start: 0.8125 (m) cc_final: 0.7885 (p) REVERT: F 668 VAL cc_start: 0.8607 (t) cc_final: 0.7968 (t) REVERT: F 671 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7764 (mppt) REVERT: F 672 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7637 (mp0) REVERT: F 680 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7372 (mp-120) REVERT: F 699 THR cc_start: 0.7935 (m) cc_final: 0.7552 (p) outliers start: 91 outliers final: 56 residues processed: 589 average time/residue: 1.6317 time to fit residues: 1040.7272 Evaluate side-chains 590 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 517 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 529 ARG Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 671 LYS Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 532 ASP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 570 LYS Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0050 chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 110 optimal weight: 0.7980 chunk 172 optimal weight: 0.0270 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN A 658 GLN B 158 GLN B 178 ASN B 303 GLN B 347 HIS B 463 HIS B 477 ASN B 499 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN D 509 ASN D 569 GLN D 647 GLN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 569 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127378 restraints weight = 21952.587| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.78 r_work: 0.3525 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15688 Z= 0.141 Angle : 0.588 8.876 21184 Z= 0.301 Chirality : 0.038 0.145 2362 Planarity : 0.005 0.063 2757 Dihedral : 10.535 82.384 2279 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.74 % Allowed : 2.96 % Favored : 96.30 % Rotamer: Outliers : 6.36 % Allowed : 28.18 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1894 helix: 1.83 (0.14), residues: 1471 sheet: -0.65 (1.94), residues: 10 loop : -2.17 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 180 HIS 0.005 0.001 HIS B 463 PHE 0.022 0.001 PHE B 214 TYR 0.014 0.001 TYR A 686 ARG 0.009 0.001 ARG F 568 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 1056) hydrogen bonds : angle 4.02623 ( 3135) covalent geometry : bond 0.00303 (15688) covalent geometry : angle 0.58750 (21184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 528 time to evaluate : 1.696 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: A 466 ASN cc_start: 0.8631 (m-40) cc_final: 0.8126 (m110) REVERT: A 565 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7488 (p0) REVERT: A 658 GLN cc_start: 0.8306 (tp40) cc_final: 0.8079 (tp-100) REVERT: A 670 LEU cc_start: 0.8028 (mt) cc_final: 0.7731 (mp) REVERT: A 672 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 79 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.7176 (Cg_exo) REVERT: B 114 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8211 (tp30) REVERT: B 155 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8087 (ttmm) REVERT: B 181 LYS cc_start: 0.8424 (mttt) cc_final: 0.8090 (mmtt) REVERT: B 182 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 208 ILE cc_start: 0.8452 (tp) cc_final: 0.8155 (mm) REVERT: B 209 ASP cc_start: 0.6581 (t0) cc_final: 0.6336 (t0) REVERT: B 282 GLU cc_start: 0.7424 (mp0) cc_final: 0.6998 (pm20) REVERT: B 333 VAL cc_start: 0.8975 (t) cc_final: 0.8766 (m) REVERT: B 470 SER cc_start: 0.8467 (t) cc_final: 0.8233 (p) REVERT: B 506 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: B 520 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6961 (mt-10) REVERT: B 521 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8025 (mtmp) REVERT: B 524 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: B 538 MET cc_start: 0.8405 (mmm) cc_final: 0.8165 (mmt) REVERT: B 548 ASP cc_start: 0.7794 (t70) cc_final: 0.7535 (t0) REVERT: B 580 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8290 (mtm180) REVERT: B 661 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7629 (ttp-110) REVERT: B 668 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8019 (m) REVERT: B 671 LYS cc_start: 0.8328 (mtmm) cc_final: 0.8093 (mttm) REVERT: B 697 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7872 (mmmm) REVERT: C 436 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 448 GLU cc_start: 0.8042 (mp0) cc_final: 0.7751 (mp0) REVERT: C 483 ASP cc_start: 0.7583 (m-30) cc_final: 0.7320 (m-30) REVERT: C 492 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7853 (tpp-160) REVERT: C 548 ASP cc_start: 0.8267 (t0) cc_final: 0.7733 (t70) REVERT: C 582 MET cc_start: 0.8575 (ttt) cc_final: 0.8236 (ttp) REVERT: C 593 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (pp) REVERT: C 601 SER cc_start: 0.8353 (m) cc_final: 0.8059 (p) REVERT: C 635 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7569 (mmtt) REVERT: C 703 VAL cc_start: 0.8765 (p) cc_final: 0.8378 (m) REVERT: D 444 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.4278 (mppt) REVERT: D 500 MET cc_start: 0.7954 (mmm) cc_final: 0.7743 (mmm) REVERT: D 519 MET cc_start: 0.7699 (tpp) cc_final: 0.6927 (tpp) REVERT: D 541 LEU cc_start: 0.8187 (tt) cc_final: 0.7960 (mt) REVERT: D 667 ASP cc_start: 0.7372 (p0) cc_final: 0.7149 (p0) REVERT: D 675 LEU cc_start: 0.8621 (mp) cc_final: 0.8389 (mm) REVERT: D 676 SER cc_start: 0.8741 (t) cc_final: 0.8387 (m) REVERT: D 679 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8214 (ttp80) REVERT: D 695 MET cc_start: 0.6681 (tpt) cc_final: 0.6470 (tpt) REVERT: E 487 ASP cc_start: 0.7116 (m-30) cc_final: 0.6901 (m-30) REVERT: E 491 LEU cc_start: 0.8415 (mt) cc_final: 0.8118 (mt) REVERT: E 539 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8184 (mtp85) REVERT: E 561 GLU cc_start: 0.7637 (mp0) cc_final: 0.7318 (mp0) REVERT: E 704 SER cc_start: 0.7857 (t) cc_final: 0.7651 (p) REVERT: F 447 ARG cc_start: 0.8401 (mpp-170) cc_final: 0.8171 (mmt180) REVERT: F 581 MET cc_start: 0.8656 (mtt) cc_final: 0.8363 (mtp) REVERT: F 611 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7883 (ttt-90) REVERT: F 645 THR cc_start: 0.8168 (m) cc_final: 0.7857 (p) REVERT: F 668 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.7859 (t) REVERT: F 671 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8006 (mppt) REVERT: F 672 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7596 (mp0) REVERT: F 680 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: F 695 MET cc_start: 0.8225 (tpp) cc_final: 0.7854 (tpp) REVERT: F 699 THR cc_start: 0.7908 (m) cc_final: 0.7606 (p) outliers start: 109 outliers final: 54 residues processed: 589 average time/residue: 1.4807 time to fit residues: 946.5644 Evaluate side-chains 568 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 503 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 500 MET Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 701 SER Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 652 GLN B 302 GLN B 347 HIS B 463 HIS B 499 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 609 GLN C 652 GLN D 509 ASN D 680 GLN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 569 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126013 restraints weight = 21909.184| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.76 r_work: 0.3504 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15688 Z= 0.160 Angle : 0.586 15.943 21184 Z= 0.296 Chirality : 0.038 0.141 2362 Planarity : 0.005 0.058 2757 Dihedral : 8.629 81.910 2194 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.17 % Favored : 96.09 % Rotamer: Outliers : 6.24 % Allowed : 27.54 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1894 helix: 1.93 (0.14), residues: 1478 sheet: -0.64 (1.95), residues: 10 loop : -2.07 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 180 HIS 0.005 0.001 HIS D 430 PHE 0.011 0.001 PHE D 513 TYR 0.017 0.002 TYR C 686 ARG 0.010 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 1056) hydrogen bonds : angle 3.80393 ( 3135) covalent geometry : bond 0.00364 (15688) covalent geometry : angle 0.58566 (21184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 515 time to evaluate : 1.594 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 452 ASP cc_start: 0.8053 (t0) cc_final: 0.7678 (t0) REVERT: A 466 ASN cc_start: 0.8643 (m-40) cc_final: 0.8150 (m110) REVERT: A 495 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7365 (mmm-85) REVERT: A 565 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7457 (p0) REVERT: A 658 GLN cc_start: 0.8305 (tp40) cc_final: 0.8065 (tp-100) REVERT: A 670 LEU cc_start: 0.8056 (mt) cc_final: 0.7724 (mp) REVERT: A 672 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 59 GLU cc_start: 0.7439 (mp0) cc_final: 0.7172 (mp0) REVERT: B 109 ILE cc_start: 0.8892 (mm) cc_final: 0.8670 (mm) REVERT: B 114 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8192 (tp30) REVERT: B 118 LEU cc_start: 0.8590 (mt) cc_final: 0.8356 (mp) REVERT: B 155 LYS cc_start: 0.8453 (ttmm) cc_final: 0.7980 (ttmm) REVERT: B 181 LYS cc_start: 0.8387 (mttt) cc_final: 0.8058 (mmtt) REVERT: B 182 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 189 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7548 (mmpt) REVERT: B 209 ASP cc_start: 0.6799 (t0) cc_final: 0.6596 (t0) REVERT: B 215 VAL cc_start: 0.8871 (t) cc_final: 0.8665 (m) REVERT: B 220 ARG cc_start: 0.8129 (mpp80) cc_final: 0.7917 (mpp80) REVERT: B 273 ASN cc_start: 0.6729 (t0) cc_final: 0.6336 (t0) REVERT: B 282 GLU cc_start: 0.7439 (mp0) cc_final: 0.6952 (pm20) REVERT: B 315 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6281 (tt0) REVERT: B 327 LYS cc_start: 0.8198 (tttt) cc_final: 0.6774 (tttt) REVERT: B 470 SER cc_start: 0.8467 (t) cc_final: 0.8237 (p) REVERT: B 506 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: B 520 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6852 (mt-10) REVERT: B 524 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: B 538 MET cc_start: 0.8441 (mmm) cc_final: 0.8189 (mmt) REVERT: B 548 ASP cc_start: 0.7801 (t70) cc_final: 0.7538 (t0) REVERT: B 661 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7647 (ttp-110) REVERT: B 668 VAL cc_start: 0.8429 (t) cc_final: 0.8100 (m) REVERT: B 671 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8100 (mttm) REVERT: B 688 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7799 (mm-30) REVERT: C 436 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 448 GLU cc_start: 0.7991 (mp0) cc_final: 0.7710 (mp0) REVERT: C 480 LEU cc_start: 0.8305 (mt) cc_final: 0.7993 (mp) REVERT: C 483 ASP cc_start: 0.7624 (m-30) cc_final: 0.7379 (m-30) REVERT: C 495 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.7093 (mmm-85) REVERT: C 548 ASP cc_start: 0.8263 (t0) cc_final: 0.7726 (t70) REVERT: C 568 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7502 (ttm170) REVERT: C 582 MET cc_start: 0.8751 (ttt) cc_final: 0.8427 (ttp) REVERT: C 593 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7958 (pp) REVERT: C 601 SER cc_start: 0.8375 (m) cc_final: 0.8055 (p) REVERT: C 635 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7407 (mmtt) REVERT: C 685 GLU cc_start: 0.7663 (mp0) cc_final: 0.7271 (mp0) REVERT: C 703 VAL cc_start: 0.8770 (p) cc_final: 0.8352 (m) REVERT: D 436 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7347 (mp0) REVERT: D 444 LYS cc_start: 0.4858 (OUTLIER) cc_final: 0.4252 (mppt) REVERT: D 541 LEU cc_start: 0.8105 (tt) cc_final: 0.7884 (mt) REVERT: D 667 ASP cc_start: 0.7254 (p0) cc_final: 0.7027 (p0) REVERT: D 675 LEU cc_start: 0.8618 (mp) cc_final: 0.8378 (mm) REVERT: D 676 SER cc_start: 0.8708 (t) cc_final: 0.8412 (m) REVERT: D 679 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8256 (ttp80) REVERT: D 695 MET cc_start: 0.6626 (tpt) cc_final: 0.6422 (tpt) REVERT: E 487 ASP cc_start: 0.7185 (m-30) cc_final: 0.6965 (m-30) REVERT: E 491 LEU cc_start: 0.8423 (mt) cc_final: 0.8136 (mt) REVERT: E 539 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8134 (mtp85) REVERT: E 561 GLU cc_start: 0.7644 (mp0) cc_final: 0.7341 (mp0) REVERT: E 566 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8378 (tmt) REVERT: E 704 SER cc_start: 0.7906 (t) cc_final: 0.7686 (p) REVERT: F 447 ARG cc_start: 0.8391 (mpp-170) cc_final: 0.8154 (mmt180) REVERT: F 611 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: F 619 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: F 645 THR cc_start: 0.8135 (m) cc_final: 0.7818 (p) REVERT: F 668 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.7728 (t) REVERT: F 671 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7945 (mppt) REVERT: F 672 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7729 (mp0) REVERT: F 680 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: F 695 MET cc_start: 0.8286 (tpp) cc_final: 0.7876 (tpp) REVERT: F 699 THR cc_start: 0.7921 (m) cc_final: 0.7603 (p) outliers start: 107 outliers final: 61 residues processed: 575 average time/residue: 1.6206 time to fit residues: 1012.3657 Evaluate side-chains 576 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 502 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 589 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 6 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.0570 chunk 18 optimal weight: 0.2980 chunk 87 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN B 347 HIS B 463 HIS B 499 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 616 ASN D 509 ASN D 680 GLN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 545 GLN F 569 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127157 restraints weight = 21890.122| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.76 r_work: 0.3524 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15688 Z= 0.123 Angle : 0.561 13.191 21184 Z= 0.282 Chirality : 0.037 0.199 2362 Planarity : 0.005 0.061 2757 Dihedral : 8.264 78.336 2186 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.74 % Allowed : 2.69 % Favored : 96.57 % Rotamer: Outliers : 6.01 % Allowed : 27.65 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 1894 helix: 2.20 (0.14), residues: 1479 sheet: -0.52 (1.87), residues: 10 loop : -2.06 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 180 HIS 0.004 0.001 HIS B 463 PHE 0.024 0.001 PHE B 214 TYR 0.023 0.001 TYR B 331 ARG 0.009 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 1056) hydrogen bonds : angle 3.61686 ( 3135) covalent geometry : bond 0.00270 (15688) covalent geometry : angle 0.56137 (21184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 522 time to evaluate : 2.050 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 452 ASP cc_start: 0.8064 (t0) cc_final: 0.7739 (t0) REVERT: A 466 ASN cc_start: 0.8602 (m-40) cc_final: 0.8235 (m110) REVERT: A 495 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7407 (mmm-85) REVERT: A 658 GLN cc_start: 0.8284 (tp40) cc_final: 0.8070 (tp-100) REVERT: A 667 ASP cc_start: 0.7092 (p0) cc_final: 0.6738 (p0) REVERT: A 672 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 706 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6992 (mt-10) REVERT: B 59 GLU cc_start: 0.7485 (mp0) cc_final: 0.7245 (mp0) REVERT: B 114 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8124 (tp30) REVERT: B 155 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8079 (ttmm) REVERT: B 181 LYS cc_start: 0.8480 (mttt) cc_final: 0.8121 (mmtt) REVERT: B 182 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 183 MET cc_start: 0.8212 (tmm) cc_final: 0.7916 (tmm) REVERT: B 189 LYS cc_start: 0.7773 (mmpt) cc_final: 0.7442 (mmpt) REVERT: B 209 ASP cc_start: 0.6699 (t0) cc_final: 0.6493 (t0) REVERT: B 215 VAL cc_start: 0.8893 (t) cc_final: 0.8688 (m) REVERT: B 273 ASN cc_start: 0.6696 (t0) cc_final: 0.6292 (t0) REVERT: B 298 LYS cc_start: 0.7709 (tppt) cc_final: 0.7429 (tppp) REVERT: B 315 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: B 333 VAL cc_start: 0.9126 (m) cc_final: 0.8875 (p) REVERT: B 466 ASN cc_start: 0.8491 (m-40) cc_final: 0.8219 (m110) REVERT: B 506 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: B 520 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6863 (mt-10) REVERT: B 524 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: B 538 MET cc_start: 0.8400 (mmm) cc_final: 0.8162 (mmt) REVERT: B 548 ASP cc_start: 0.7921 (t70) cc_final: 0.7644 (t0) REVERT: B 633 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5454 (tm-30) REVERT: B 658 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: B 661 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7605 (ttp-110) REVERT: B 668 VAL cc_start: 0.8469 (t) cc_final: 0.8152 (m) REVERT: B 671 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8117 (mttm) REVERT: B 688 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7789 (mm-30) REVERT: C 436 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7408 (mt-10) REVERT: C 448 GLU cc_start: 0.8009 (mp0) cc_final: 0.7732 (mp0) REVERT: C 483 ASP cc_start: 0.7615 (m-30) cc_final: 0.7352 (m-30) REVERT: C 495 ARG cc_start: 0.7356 (mmm-85) cc_final: 0.7111 (mmm-85) REVERT: C 548 ASP cc_start: 0.8232 (t0) cc_final: 0.7552 (t70) REVERT: C 582 MET cc_start: 0.8745 (ttt) cc_final: 0.8451 (ttp) REVERT: C 593 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (pp) REVERT: C 601 SER cc_start: 0.8386 (m) cc_final: 0.8066 (p) REVERT: C 635 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7411 (mmtt) REVERT: C 672 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 685 GLU cc_start: 0.7664 (mp0) cc_final: 0.7255 (mp0) REVERT: C 703 VAL cc_start: 0.8780 (p) cc_final: 0.8347 (m) REVERT: D 444 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.4193 (mppt) REVERT: D 541 LEU cc_start: 0.8104 (tt) cc_final: 0.7871 (mt) REVERT: D 667 ASP cc_start: 0.7156 (p0) cc_final: 0.6912 (p0) REVERT: D 675 LEU cc_start: 0.8604 (mp) cc_final: 0.8361 (mm) REVERT: D 676 SER cc_start: 0.8714 (t) cc_final: 0.8415 (m) REVERT: D 679 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8238 (ttp80) REVERT: D 695 MET cc_start: 0.6612 (tpt) cc_final: 0.6410 (tpt) REVERT: E 487 ASP cc_start: 0.7215 (m-30) cc_final: 0.7004 (m-30) REVERT: E 491 LEU cc_start: 0.8410 (mt) cc_final: 0.8120 (mt) REVERT: E 539 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8190 (mtp85) REVERT: E 561 GLU cc_start: 0.7653 (mp0) cc_final: 0.7430 (mp0) REVERT: E 566 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8279 (tmt) REVERT: E 645 THR cc_start: 0.8434 (m) cc_final: 0.8214 (m) REVERT: E 685 GLU cc_start: 0.7732 (mp0) cc_final: 0.7299 (mp0) REVERT: F 447 ARG cc_start: 0.8327 (mpp-170) cc_final: 0.8108 (mmt180) REVERT: F 562 GLN cc_start: 0.8164 (mt0) cc_final: 0.7932 (mt0) REVERT: F 581 MET cc_start: 0.8709 (mtt) cc_final: 0.8428 (mtp) REVERT: F 611 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7890 (ttt-90) REVERT: F 619 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: F 645 THR cc_start: 0.8063 (m) cc_final: 0.7759 (p) REVERT: F 668 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.7714 (t) REVERT: F 672 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7699 (mp0) REVERT: F 680 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7297 (mp-120) REVERT: F 699 THR cc_start: 0.7928 (m) cc_final: 0.7609 (p) outliers start: 103 outliers final: 52 residues processed: 584 average time/residue: 1.4448 time to fit residues: 919.1271 Evaluate side-chains 583 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 518 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 619 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 60 HIS B 250 ASN B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 509 ASN E 545 GLN E 647 GLN F 477 ASN F 512 ASN F 545 GLN F 647 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124606 restraints weight = 22212.212| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.77 r_work: 0.3483 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15688 Z= 0.195 Angle : 0.602 9.906 21184 Z= 0.305 Chirality : 0.040 0.133 2362 Planarity : 0.005 0.057 2757 Dihedral : 7.993 76.488 2175 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.69 % Allowed : 3.22 % Favored : 96.09 % Rotamer: Outliers : 6.18 % Allowed : 27.77 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1894 helix: 2.02 (0.14), residues: 1482 sheet: -0.43 (1.83), residues: 10 loop : -2.11 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 180 HIS 0.004 0.001 HIS E 430 PHE 0.015 0.002 PHE B 214 TYR 0.021 0.002 TYR C 686 ARG 0.008 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.05448 ( 1056) hydrogen bonds : angle 3.74812 ( 3135) covalent geometry : bond 0.00457 (15688) covalent geometry : angle 0.60207 (21184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 519 time to evaluate : 1.697 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: A 436 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7302 (mp0) REVERT: A 452 ASP cc_start: 0.8028 (t0) cc_final: 0.7703 (t0) REVERT: A 466 ASN cc_start: 0.8711 (m-40) cc_final: 0.8348 (m110) REVERT: A 495 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7327 (mmm-85) REVERT: A 658 GLN cc_start: 0.8279 (tp40) cc_final: 0.8043 (tp-100) REVERT: A 672 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 675 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 706 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 155 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8114 (ttmm) REVERT: B 181 LYS cc_start: 0.8482 (mttt) cc_final: 0.8161 (mmtt) REVERT: B 183 MET cc_start: 0.8217 (tmm) cc_final: 0.7964 (tmm) REVERT: B 189 LYS cc_start: 0.7793 (mmpt) cc_final: 0.7471 (mmpt) REVERT: B 208 ILE cc_start: 0.8417 (tp) cc_final: 0.8060 (tp) REVERT: B 209 ASP cc_start: 0.6860 (t0) cc_final: 0.6578 (t0) REVERT: B 215 VAL cc_start: 0.8853 (t) cc_final: 0.8637 (m) REVERT: B 220 ARG cc_start: 0.8192 (mpp80) cc_final: 0.7727 (mtt180) REVERT: B 273 ASN cc_start: 0.6718 (t0) cc_final: 0.6321 (t0) REVERT: B 278 PHE cc_start: 0.7409 (m-80) cc_final: 0.7123 (m-80) REVERT: B 333 VAL cc_start: 0.9133 (m) cc_final: 0.8873 (p) REVERT: B 506 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: B 519 MET cc_start: 0.8252 (tpp) cc_final: 0.7963 (tpt) REVERT: B 520 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6886 (mt-10) REVERT: B 524 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: B 538 MET cc_start: 0.8485 (mmm) cc_final: 0.8251 (mmt) REVERT: B 548 ASP cc_start: 0.7802 (t70) cc_final: 0.7541 (t0) REVERT: B 633 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: B 661 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (ttp-110) REVERT: B 668 VAL cc_start: 0.8537 (t) cc_final: 0.8199 (m) REVERT: B 671 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8126 (mttm) REVERT: B 688 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7837 (mm-30) REVERT: C 436 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7415 (mt-10) REVERT: C 483 ASP cc_start: 0.7664 (m-30) cc_final: 0.7396 (m-30) REVERT: C 495 ARG cc_start: 0.7366 (mmm-85) cc_final: 0.7085 (mmm-85) REVERT: C 548 ASP cc_start: 0.8303 (t0) cc_final: 0.7746 (t70) REVERT: C 582 MET cc_start: 0.8810 (ttt) cc_final: 0.8458 (ttp) REVERT: C 593 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7963 (pp) REVERT: C 601 SER cc_start: 0.8403 (m) cc_final: 0.8067 (p) REVERT: C 635 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7384 (mmtt) REVERT: C 654 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8176 (mtt-85) REVERT: C 703 VAL cc_start: 0.8785 (p) cc_final: 0.8371 (m) REVERT: D 541 LEU cc_start: 0.8208 (tt) cc_final: 0.7964 (mt) REVERT: D 582 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8300 (mtp) REVERT: D 647 GLN cc_start: 0.8186 (mt0) cc_final: 0.7851 (mt0) REVERT: D 667 ASP cc_start: 0.7201 (p0) cc_final: 0.6969 (p0) REVERT: D 675 LEU cc_start: 0.8593 (mp) cc_final: 0.8334 (mm) REVERT: D 676 SER cc_start: 0.8731 (t) cc_final: 0.8447 (m) REVERT: D 679 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8255 (ttp80) REVERT: D 695 MET cc_start: 0.6713 (tpt) cc_final: 0.6506 (tpt) REVERT: E 491 LEU cc_start: 0.8411 (mt) cc_final: 0.8121 (mt) REVERT: E 539 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8113 (ttp80) REVERT: E 561 GLU cc_start: 0.7676 (mp0) cc_final: 0.7441 (mp0) REVERT: E 566 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8304 (tmt) REVERT: E 704 SER cc_start: 0.7925 (t) cc_final: 0.7695 (p) REVERT: F 447 ARG cc_start: 0.8424 (mpp-170) cc_final: 0.8191 (mmt180) REVERT: F 562 GLN cc_start: 0.8165 (mt0) cc_final: 0.7921 (mt0) REVERT: F 611 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7914 (ttt-90) REVERT: F 617 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8462 (tp) REVERT: F 619 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: F 645 THR cc_start: 0.8057 (m) cc_final: 0.7751 (p) REVERT: F 668 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.7753 (t) REVERT: F 672 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7688 (mp0) REVERT: F 680 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: F 699 THR cc_start: 0.7846 (m) cc_final: 0.7512 (p) outliers start: 106 outliers final: 70 residues processed: 581 average time/residue: 1.4311 time to fit residues: 904.3263 Evaluate side-chains 588 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 504 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 680 GLN Chi-restraints excluded: chain E residue 701 SER Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 619 GLU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 189 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 303 GLN B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 569 GLN C 466 ASN C 616 ASN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 545 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125000 restraints weight = 21959.145| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.76 r_work: 0.3490 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15688 Z= 0.182 Angle : 0.603 10.130 21184 Z= 0.305 Chirality : 0.040 0.139 2362 Planarity : 0.005 0.060 2757 Dihedral : 7.898 75.657 2172 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.74 % Allowed : 2.90 % Favored : 96.36 % Rotamer: Outliers : 6.24 % Allowed : 28.47 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1894 helix: 2.05 (0.14), residues: 1486 sheet: -0.21 (1.84), residues: 10 loop : -2.22 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 180 HIS 0.004 0.001 HIS C 476 PHE 0.027 0.002 PHE B 214 TYR 0.032 0.002 TYR B 331 ARG 0.011 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 1056) hydrogen bonds : angle 3.74015 ( 3135) covalent geometry : bond 0.00427 (15688) covalent geometry : angle 0.60285 (21184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 510 time to evaluate : 1.846 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 436 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7289 (mp0) REVERT: A 452 ASP cc_start: 0.8047 (t0) cc_final: 0.7799 (t0) REVERT: A 466 ASN cc_start: 0.8684 (m-40) cc_final: 0.8346 (m110) REVERT: A 495 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7316 (mmm-85) REVERT: A 504 THR cc_start: 0.8299 (p) cc_final: 0.7758 (m) REVERT: A 613 ASP cc_start: 0.8046 (m-30) cc_final: 0.7638 (m-30) REVERT: A 658 GLN cc_start: 0.8271 (tp40) cc_final: 0.8035 (tp-100) REVERT: A 672 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7414 (mt-10) REVERT: A 675 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 706 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 155 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8022 (ttmm) REVERT: B 181 LYS cc_start: 0.8461 (mttt) cc_final: 0.8116 (mmtt) REVERT: B 182 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 189 LYS cc_start: 0.7677 (mmpt) cc_final: 0.7375 (mmpt) REVERT: B 209 ASP cc_start: 0.6877 (t0) cc_final: 0.6665 (t0) REVERT: B 214 PHE cc_start: 0.7883 (t80) cc_final: 0.7596 (t80) REVERT: B 215 VAL cc_start: 0.8887 (t) cc_final: 0.8675 (m) REVERT: B 273 ASN cc_start: 0.6717 (t0) cc_final: 0.6356 (t0) REVERT: B 278 PHE cc_start: 0.7360 (m-80) cc_final: 0.7080 (m-80) REVERT: B 298 LYS cc_start: 0.7988 (tppt) cc_final: 0.7730 (tppp) REVERT: B 506 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 524 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: B 529 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7109 (ttm-80) REVERT: B 538 MET cc_start: 0.8453 (mmm) cc_final: 0.8216 (mmt) REVERT: B 548 ASP cc_start: 0.7810 (t70) cc_final: 0.7535 (t0) REVERT: B 633 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5519 (tm-30) REVERT: B 658 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7996 (tp40) REVERT: B 661 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7603 (ttp-110) REVERT: B 668 VAL cc_start: 0.8523 (t) cc_final: 0.8191 (m) REVERT: C 436 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 483 ASP cc_start: 0.7657 (m-30) cc_final: 0.7372 (m-30) REVERT: C 495 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.7108 (mmm-85) REVERT: C 548 ASP cc_start: 0.8287 (t0) cc_final: 0.7737 (t70) REVERT: C 582 MET cc_start: 0.8774 (ttt) cc_final: 0.8425 (ttp) REVERT: C 593 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7963 (pp) REVERT: C 601 SER cc_start: 0.8422 (m) cc_final: 0.8082 (p) REVERT: C 635 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7398 (mmtt) REVERT: C 654 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8189 (mtm-85) REVERT: C 672 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7509 (mt-10) REVERT: C 703 VAL cc_start: 0.8768 (p) cc_final: 0.8370 (m) REVERT: D 541 LEU cc_start: 0.8185 (tt) cc_final: 0.7953 (mt) REVERT: D 667 ASP cc_start: 0.7184 (p0) cc_final: 0.6787 (p0) REVERT: D 675 LEU cc_start: 0.8594 (mp) cc_final: 0.8333 (mm) REVERT: D 676 SER cc_start: 0.8722 (t) cc_final: 0.8434 (m) REVERT: D 679 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8291 (ttp80) REVERT: D 695 MET cc_start: 0.6665 (tpt) cc_final: 0.6461 (tpt) REVERT: E 491 LEU cc_start: 0.8413 (mt) cc_final: 0.8126 (mt) REVERT: E 539 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8167 (mtp85) REVERT: E 561 GLU cc_start: 0.7700 (mp0) cc_final: 0.7468 (mp0) REVERT: E 704 SER cc_start: 0.7935 (t) cc_final: 0.7706 (p) REVERT: F 447 ARG cc_start: 0.8369 (mpp-170) cc_final: 0.8146 (mmt180) REVERT: F 562 GLN cc_start: 0.8181 (mt0) cc_final: 0.7941 (mt0) REVERT: F 611 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7901 (ttt-90) REVERT: F 617 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8336 (mm) REVERT: F 619 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: F 645 THR cc_start: 0.8037 (m) cc_final: 0.7763 (p) REVERT: F 668 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.7719 (t) REVERT: F 672 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7731 (mp0) REVERT: F 680 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7326 (mp-120) REVERT: F 699 THR cc_start: 0.7848 (m) cc_final: 0.7520 (p) outliers start: 107 outliers final: 67 residues processed: 575 average time/residue: 1.5086 time to fit residues: 944.7056 Evaluate side-chains 586 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 505 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 619 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 121 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 616 ASN E 647 GLN E 658 GLN F 473 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125078 restraints weight = 22065.859| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.76 r_work: 0.3490 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15688 Z= 0.180 Angle : 0.615 10.460 21184 Z= 0.309 Chirality : 0.040 0.146 2362 Planarity : 0.005 0.059 2757 Dihedral : 7.835 75.348 2170 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.27 % Favored : 95.99 % Rotamer: Outliers : 6.18 % Allowed : 29.05 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.20), residues: 1894 helix: 2.05 (0.14), residues: 1489 sheet: -0.11 (1.85), residues: 10 loop : -2.25 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 180 HIS 0.004 0.001 HIS B 463 PHE 0.022 0.002 PHE B 214 TYR 0.030 0.002 TYR B 331 ARG 0.012 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 1056) hydrogen bonds : angle 3.73134 ( 3135) covalent geometry : bond 0.00421 (15688) covalent geometry : angle 0.61543 (21184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 510 time to evaluate : 1.651 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 436 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7271 (mp0) REVERT: A 452 ASP cc_start: 0.8049 (t0) cc_final: 0.7788 (t0) REVERT: A 495 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7459 (mmm-85) REVERT: A 504 THR cc_start: 0.8306 (p) cc_final: 0.7761 (m) REVERT: A 613 ASP cc_start: 0.8041 (m-30) cc_final: 0.7683 (m-30) REVERT: A 658 GLN cc_start: 0.8274 (tp40) cc_final: 0.7908 (tp-100) REVERT: A 672 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 706 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7097 (mt-10) REVERT: B 155 LYS cc_start: 0.8534 (ttmm) cc_final: 0.7999 (mttp) REVERT: B 181 LYS cc_start: 0.8411 (mttt) cc_final: 0.8035 (mmtp) REVERT: B 182 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 189 LYS cc_start: 0.7634 (mmpt) cc_final: 0.7328 (mmpt) REVERT: B 214 PHE cc_start: 0.7845 (t80) cc_final: 0.7543 (t80) REVERT: B 218 LEU cc_start: 0.8540 (mp) cc_final: 0.8280 (mp) REVERT: B 240 LYS cc_start: 0.8498 (tttt) cc_final: 0.8097 (tptt) REVERT: B 273 ASN cc_start: 0.6750 (t0) cc_final: 0.6532 (t0) REVERT: B 278 PHE cc_start: 0.7348 (m-80) cc_final: 0.7048 (m-80) REVERT: B 444 LYS cc_start: 0.6326 (pmtt) cc_final: 0.5832 (pmtt) REVERT: B 481 MET cc_start: 0.8421 (mtp) cc_final: 0.7910 (ttm) REVERT: B 506 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: B 520 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 524 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: B 529 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7081 (ttm-80) REVERT: B 538 MET cc_start: 0.8446 (mmm) cc_final: 0.8215 (mmt) REVERT: B 548 ASP cc_start: 0.7800 (t70) cc_final: 0.7525 (t0) REVERT: B 581 MET cc_start: 0.8628 (mtt) cc_final: 0.8387 (mtp) REVERT: B 658 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7976 (tp40) REVERT: B 661 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7605 (ttp-110) REVERT: B 668 VAL cc_start: 0.8531 (t) cc_final: 0.8204 (m) REVERT: B 671 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8150 (mttm) REVERT: C 436 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7331 (mt-10) REVERT: C 483 ASP cc_start: 0.7653 (m-30) cc_final: 0.7361 (m-30) REVERT: C 495 ARG cc_start: 0.7396 (mmm-85) cc_final: 0.7124 (mmm-85) REVERT: C 548 ASP cc_start: 0.8284 (t0) cc_final: 0.7730 (t70) REVERT: C 582 MET cc_start: 0.8815 (ttt) cc_final: 0.8491 (ttp) REVERT: C 593 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7940 (pp) REVERT: C 601 SER cc_start: 0.8410 (m) cc_final: 0.8071 (p) REVERT: C 611 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8195 (ttp-110) REVERT: C 635 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7392 (mmtt) REVERT: C 647 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: C 654 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8198 (mtt-85) REVERT: C 685 GLU cc_start: 0.7642 (mp0) cc_final: 0.7289 (mp0) REVERT: C 703 VAL cc_start: 0.8772 (p) cc_final: 0.8377 (m) REVERT: D 436 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7395 (mp0) REVERT: D 493 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6869 (mtt180) REVERT: D 541 LEU cc_start: 0.8186 (tt) cc_final: 0.7954 (mt) REVERT: D 675 LEU cc_start: 0.8573 (mp) cc_final: 0.8334 (mm) REVERT: D 676 SER cc_start: 0.8687 (t) cc_final: 0.8411 (m) REVERT: D 679 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8242 (ttp80) REVERT: E 491 LEU cc_start: 0.8411 (mt) cc_final: 0.8125 (mt) REVERT: E 539 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8226 (mtp85) REVERT: E 561 GLU cc_start: 0.7725 (mp0) cc_final: 0.7497 (mp0) REVERT: E 566 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8343 (tmt) REVERT: E 658 GLN cc_start: 0.8363 (tp40) cc_final: 0.7915 (tp-100) REVERT: E 704 SER cc_start: 0.7931 (t) cc_final: 0.7692 (p) REVERT: F 447 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8140 (mmt180) REVERT: F 562 GLN cc_start: 0.8179 (mt0) cc_final: 0.7935 (mt0) REVERT: F 611 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (ttt-90) REVERT: F 617 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8323 (mm) REVERT: F 619 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: F 645 THR cc_start: 0.8030 (m) cc_final: 0.7760 (p) REVERT: F 668 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.7733 (t) REVERT: F 672 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7688 (mp0) REVERT: F 699 THR cc_start: 0.7856 (m) cc_final: 0.7523 (p) outliers start: 106 outliers final: 71 residues processed: 569 average time/residue: 1.4229 time to fit residues: 881.5597 Evaluate side-chains 598 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 513 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 619 GLU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 680 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 18 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN A 506 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 616 ASN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 545 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125232 restraints weight = 21687.854| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.78 r_work: 0.3497 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15688 Z= 0.177 Angle : 0.638 10.929 21184 Z= 0.321 Chirality : 0.040 0.148 2362 Planarity : 0.005 0.060 2757 Dihedral : 7.721 74.869 2168 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.12 % Favored : 96.15 % Rotamer: Outliers : 6.07 % Allowed : 29.05 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.20), residues: 1894 helix: 2.04 (0.14), residues: 1486 sheet: -0.10 (1.92), residues: 10 loop : -2.22 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 180 HIS 0.004 0.001 HIS D 430 PHE 0.020 0.001 PHE B 214 TYR 0.032 0.002 TYR B 331 ARG 0.010 0.001 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 1056) hydrogen bonds : angle 3.74128 ( 3135) covalent geometry : bond 0.00415 (15688) covalent geometry : angle 0.63791 (21184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 513 time to evaluate : 1.731 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 436 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7298 (mp0) REVERT: A 452 ASP cc_start: 0.8075 (t0) cc_final: 0.7810 (t0) REVERT: A 466 ASN cc_start: 0.8662 (m-40) cc_final: 0.8166 (m110) REVERT: A 495 ARG cc_start: 0.7791 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: A 504 THR cc_start: 0.8248 (p) cc_final: 0.7722 (m) REVERT: A 577 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 613 ASP cc_start: 0.8039 (m-30) cc_final: 0.7676 (m-30) REVERT: A 672 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 706 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7044 (mt-10) REVERT: B 58 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.5554 (m90) REVERT: B 155 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8039 (mttp) REVERT: B 181 LYS cc_start: 0.8395 (mttt) cc_final: 0.8075 (mmtt) REVERT: B 182 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 189 LYS cc_start: 0.7667 (mmpt) cc_final: 0.7364 (mmpt) REVERT: B 208 ILE cc_start: 0.8308 (tp) cc_final: 0.8011 (tp) REVERT: B 214 PHE cc_start: 0.7832 (t80) cc_final: 0.7515 (t80) REVERT: B 218 LEU cc_start: 0.8547 (mp) cc_final: 0.8272 (mp) REVERT: B 240 LYS cc_start: 0.8495 (tttt) cc_final: 0.8121 (tptt) REVERT: B 278 PHE cc_start: 0.7375 (m-80) cc_final: 0.7097 (m-80) REVERT: B 298 LYS cc_start: 0.8054 (tppt) cc_final: 0.7056 (tppp) REVERT: B 305 LEU cc_start: 0.7992 (tm) cc_final: 0.7697 (mm) REVERT: B 350 LEU cc_start: 0.6952 (mm) cc_final: 0.6220 (mm) REVERT: B 444 LYS cc_start: 0.6390 (pmtt) cc_final: 0.5869 (pmtt) REVERT: B 506 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: B 520 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6751 (mt-10) REVERT: B 524 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: B 529 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7167 (ttm-80) REVERT: B 538 MET cc_start: 0.8457 (mmm) cc_final: 0.8233 (mmt) REVERT: B 548 ASP cc_start: 0.7852 (t70) cc_final: 0.7593 (t0) REVERT: B 633 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5527 (tm-30) REVERT: B 658 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (tp40) REVERT: B 661 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7624 (ttp-110) REVERT: B 668 VAL cc_start: 0.8547 (t) cc_final: 0.8233 (m) REVERT: B 671 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8124 (mttm) REVERT: C 436 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7324 (mt-10) REVERT: C 469 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8556 (mttp) REVERT: C 483 ASP cc_start: 0.7660 (m-30) cc_final: 0.7349 (m-30) REVERT: C 495 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7124 (mmm-85) REVERT: C 548 ASP cc_start: 0.8318 (t0) cc_final: 0.7772 (t70) REVERT: C 582 MET cc_start: 0.8751 (ttt) cc_final: 0.8382 (ttp) REVERT: C 593 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7895 (pp) REVERT: C 601 SER cc_start: 0.8419 (m) cc_final: 0.8073 (p) REVERT: C 611 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8132 (ttp-110) REVERT: C 635 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7464 (mmtt) REVERT: C 647 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: C 654 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8173 (mtt-85) REVERT: C 685 GLU cc_start: 0.7684 (mp0) cc_final: 0.7315 (mp0) REVERT: C 703 VAL cc_start: 0.8754 (p) cc_final: 0.8359 (m) REVERT: D 436 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7379 (mp0) REVERT: D 493 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6847 (mtt180) REVERT: D 541 LEU cc_start: 0.8206 (tt) cc_final: 0.7979 (mt) REVERT: D 566 MET cc_start: 0.8281 (tmm) cc_final: 0.8046 (tmm) REVERT: D 647 GLN cc_start: 0.8157 (mt0) cc_final: 0.7898 (mt0) REVERT: D 675 LEU cc_start: 0.8564 (mp) cc_final: 0.8313 (mm) REVERT: D 676 SER cc_start: 0.8701 (t) cc_final: 0.8411 (m) REVERT: D 679 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8244 (ttp80) REVERT: D 695 MET cc_start: 0.6591 (tpt) cc_final: 0.6151 (tpt) REVERT: E 491 LEU cc_start: 0.8405 (mt) cc_final: 0.8123 (mt) REVERT: E 519 MET cc_start: 0.7490 (mtp) cc_final: 0.7132 (mtm) REVERT: E 539 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8184 (mtp85) REVERT: E 561 GLU cc_start: 0.7654 (mp0) cc_final: 0.7439 (mp0) REVERT: E 566 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (tmt) REVERT: E 704 SER cc_start: 0.7952 (t) cc_final: 0.7723 (p) REVERT: F 447 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8105 (mmt180) REVERT: F 562 GLN cc_start: 0.8186 (mt0) cc_final: 0.7936 (mt0) REVERT: F 611 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7938 (ttt-90) REVERT: F 617 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8351 (mm) REVERT: F 645 THR cc_start: 0.8014 (m) cc_final: 0.7747 (p) REVERT: F 668 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.7705 (t) REVERT: F 672 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7741 (mt-10) REVERT: F 699 THR cc_start: 0.7848 (m) cc_final: 0.7524 (p) outliers start: 104 outliers final: 64 residues processed: 575 average time/residue: 1.4914 time to fit residues: 938.6836 Evaluate side-chains 588 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 508 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 529 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 701 SER Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 616 ASN E 647 GLN F 473 GLN F 477 ASN F 512 ASN F 647 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124557 restraints weight = 21881.041| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.78 r_work: 0.3489 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15688 Z= 0.192 Angle : 0.664 11.173 21184 Z= 0.332 Chirality : 0.041 0.155 2362 Planarity : 0.005 0.059 2757 Dihedral : 7.133 74.350 2160 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.17 % Favored : 96.09 % Rotamer: Outliers : 5.60 % Allowed : 29.87 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.20), residues: 1894 helix: 2.02 (0.14), residues: 1486 sheet: -0.21 (1.88), residues: 10 loop : -2.24 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 180 HIS 0.004 0.001 HIS F 499 PHE 0.015 0.002 PHE B 214 TYR 0.030 0.002 TYR B 331 ARG 0.013 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 1056) hydrogen bonds : angle 3.78643 ( 3135) covalent geometry : bond 0.00452 (15688) covalent geometry : angle 0.66384 (21184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 517 time to evaluate : 1.751 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 436 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7305 (mp0) REVERT: A 452 ASP cc_start: 0.8059 (t0) cc_final: 0.7806 (t0) REVERT: A 466 ASN cc_start: 0.8631 (m-40) cc_final: 0.8172 (m110) REVERT: A 495 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: A 504 THR cc_start: 0.8252 (p) cc_final: 0.7731 (m) REVERT: A 672 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 706 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 58 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.5617 (m90) REVERT: B 155 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8020 (ttmm) REVERT: B 181 LYS cc_start: 0.8390 (mttt) cc_final: 0.8092 (mmtt) REVERT: B 182 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 189 LYS cc_start: 0.7674 (mmpt) cc_final: 0.7370 (mmpt) REVERT: B 208 ILE cc_start: 0.8313 (tp) cc_final: 0.8024 (tp) REVERT: B 214 PHE cc_start: 0.7759 (t80) cc_final: 0.7473 (t80) REVERT: B 218 LEU cc_start: 0.8543 (mp) cc_final: 0.8269 (mp) REVERT: B 278 PHE cc_start: 0.7362 (m-80) cc_final: 0.7060 (m-80) REVERT: B 350 LEU cc_start: 0.6954 (mm) cc_final: 0.5932 (mm) REVERT: B 506 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: B 520 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 524 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: B 538 MET cc_start: 0.8487 (mmm) cc_final: 0.8247 (mmt) REVERT: B 548 ASP cc_start: 0.7849 (t70) cc_final: 0.7575 (t0) REVERT: B 615 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8347 (mtmm) REVERT: B 633 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5497 (tm-30) REVERT: B 658 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7950 (tp40) REVERT: B 661 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7652 (ttp-110) REVERT: B 668 VAL cc_start: 0.8574 (t) cc_final: 0.8073 (m) REVERT: C 436 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 469 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8573 (mttp) REVERT: C 483 ASP cc_start: 0.7652 (m-30) cc_final: 0.7335 (m-30) REVERT: C 495 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7122 (mmm-85) REVERT: C 548 ASP cc_start: 0.8316 (t0) cc_final: 0.7776 (t70) REVERT: C 582 MET cc_start: 0.8768 (ttt) cc_final: 0.8436 (ttp) REVERT: C 593 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7916 (pp) REVERT: C 601 SER cc_start: 0.8437 (m) cc_final: 0.8098 (p) REVERT: C 635 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7571 (mmtt) REVERT: C 647 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: C 654 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8196 (mtt-85) REVERT: C 685 GLU cc_start: 0.7655 (mp0) cc_final: 0.7320 (mp0) REVERT: C 703 VAL cc_start: 0.8769 (p) cc_final: 0.8380 (m) REVERT: D 436 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7368 (mp0) REVERT: D 493 ARG cc_start: 0.7073 (mtt180) cc_final: 0.6866 (mtt180) REVERT: D 541 LEU cc_start: 0.8199 (tt) cc_final: 0.7981 (mt) REVERT: D 561 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: D 566 MET cc_start: 0.8283 (tmm) cc_final: 0.8061 (tmm) REVERT: D 582 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: D 675 LEU cc_start: 0.8544 (mp) cc_final: 0.8298 (mm) REVERT: D 676 SER cc_start: 0.8672 (t) cc_final: 0.8394 (m) REVERT: D 679 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8228 (ttp80) REVERT: E 491 LEU cc_start: 0.8392 (mt) cc_final: 0.8123 (mt) REVERT: E 539 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8169 (mtp85) REVERT: E 561 GLU cc_start: 0.7653 (mp0) cc_final: 0.7440 (mp0) REVERT: E 566 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8236 (tmt) REVERT: E 704 SER cc_start: 0.7943 (t) cc_final: 0.7712 (p) REVERT: F 447 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8097 (mmt180) REVERT: F 562 GLN cc_start: 0.8172 (mt0) cc_final: 0.7921 (mt0) REVERT: F 611 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7973 (ttt-90) REVERT: F 645 THR cc_start: 0.8085 (m) cc_final: 0.7818 (p) REVERT: F 668 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.7713 (t) REVERT: F 672 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7742 (mt-10) REVERT: F 680 GLN cc_start: 0.7971 (mp-120) cc_final: 0.7469 (mp-120) REVERT: F 699 THR cc_start: 0.7843 (m) cc_final: 0.7509 (p) outliers start: 96 outliers final: 63 residues processed: 573 average time/residue: 1.4609 time to fit residues: 910.9818 Evaluate side-chains 585 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 507 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 667 ASP Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 594 GLU Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 701 SER Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 12 optimal weight: 0.2980 chunk 111 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 616 ASN E 647 GLN F 473 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125276 restraints weight = 21773.966| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.76 r_work: 0.3499 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15688 Z= 0.172 Angle : 0.672 11.426 21184 Z= 0.338 Chirality : 0.040 0.187 2362 Planarity : 0.006 0.102 2757 Dihedral : 7.042 74.096 2156 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.06 % Favored : 96.20 % Rotamer: Outliers : 4.78 % Allowed : 30.98 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 1894 helix: 2.12 (0.14), residues: 1477 sheet: -0.43 (1.81), residues: 10 loop : -2.12 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 180 HIS 0.003 0.001 HIS F 499 PHE 0.015 0.001 PHE B 214 TYR 0.030 0.002 TYR B 331 ARG 0.020 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 1056) hydrogen bonds : angle 3.78384 ( 3135) covalent geometry : bond 0.00403 (15688) covalent geometry : angle 0.67210 (21184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 511 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 452 ASP cc_start: 0.8063 (t0) cc_final: 0.7806 (t0) REVERT: A 466 ASN cc_start: 0.8614 (m-40) cc_final: 0.8148 (m110) REVERT: A 495 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7430 (mmm-85) REVERT: A 504 THR cc_start: 0.8296 (p) cc_final: 0.7775 (m) REVERT: A 568 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7669 (ttm-80) REVERT: A 661 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7813 (ttm-80) REVERT: A 672 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 706 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7035 (mt-10) REVERT: B 155 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8007 (mttp) REVERT: B 181 LYS cc_start: 0.8381 (mttt) cc_final: 0.8068 (mmtt) REVERT: B 182 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 189 LYS cc_start: 0.7620 (mmpt) cc_final: 0.7312 (mmpt) REVERT: B 208 ILE cc_start: 0.8282 (tp) cc_final: 0.7968 (tp) REVERT: B 214 PHE cc_start: 0.7805 (t80) cc_final: 0.7464 (t80) REVERT: B 218 LEU cc_start: 0.8523 (mp) cc_final: 0.8227 (mp) REVERT: B 240 LYS cc_start: 0.8514 (tttt) cc_final: 0.8162 (tptt) REVERT: B 278 PHE cc_start: 0.7351 (m-80) cc_final: 0.7126 (m-80) REVERT: B 350 LEU cc_start: 0.6637 (mm) cc_final: 0.5904 (mm) REVERT: B 353 GLU cc_start: 0.7382 (pm20) cc_final: 0.7125 (pm20) REVERT: B 444 LYS cc_start: 0.6374 (pmtt) cc_final: 0.5755 (pmtt) REVERT: B 506 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: B 519 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8092 (tpt) REVERT: B 524 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: B 538 MET cc_start: 0.8464 (mmm) cc_final: 0.8226 (mmt) REVERT: B 548 ASP cc_start: 0.7829 (t70) cc_final: 0.7542 (t0) REVERT: B 614 TYR cc_start: 0.8572 (t80) cc_final: 0.8333 (t80) REVERT: B 633 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5493 (tm-30) REVERT: B 658 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: B 661 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7653 (ttp-110) REVERT: B 668 VAL cc_start: 0.8523 (t) cc_final: 0.8313 (t) REVERT: B 688 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 436 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 469 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8571 (mttp) REVERT: C 483 ASP cc_start: 0.7633 (m-30) cc_final: 0.7322 (m-30) REVERT: C 495 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.7123 (mmm-85) REVERT: C 531 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7110 (mmp) REVERT: C 548 ASP cc_start: 0.8302 (t0) cc_final: 0.7761 (t70) REVERT: C 582 MET cc_start: 0.8704 (ttt) cc_final: 0.8377 (ttp) REVERT: C 593 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (pp) REVERT: C 601 SER cc_start: 0.8456 (m) cc_final: 0.8109 (p) REVERT: C 611 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8071 (ttp-110) REVERT: C 635 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7575 (mmtt) REVERT: C 647 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: C 654 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8167 (mtt-85) REVERT: C 672 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 685 GLU cc_start: 0.7598 (mp0) cc_final: 0.7247 (mp0) REVERT: C 703 VAL cc_start: 0.8775 (p) cc_final: 0.8381 (m) REVERT: D 436 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7384 (mp0) REVERT: D 481 MET cc_start: 0.8740 (mtp) cc_final: 0.8532 (mtp) REVERT: D 493 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6866 (mtt180) REVERT: D 541 LEU cc_start: 0.8205 (tt) cc_final: 0.7983 (mt) REVERT: D 561 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: D 566 MET cc_start: 0.8261 (tmm) cc_final: 0.8045 (tmm) REVERT: D 582 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: D 675 LEU cc_start: 0.8556 (mp) cc_final: 0.8320 (mm) REVERT: D 676 SER cc_start: 0.8680 (t) cc_final: 0.8393 (m) REVERT: D 679 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8165 (ttp80) REVERT: E 491 LEU cc_start: 0.8392 (mt) cc_final: 0.8118 (mt) REVERT: E 539 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8239 (mtp85) REVERT: E 561 GLU cc_start: 0.7632 (mp0) cc_final: 0.7425 (mp0) REVERT: E 704 SER cc_start: 0.7936 (t) cc_final: 0.7704 (p) REVERT: F 447 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8080 (mmt180) REVERT: F 562 GLN cc_start: 0.8182 (mt0) cc_final: 0.7934 (mt0) REVERT: F 611 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7966 (ttt-90) REVERT: F 645 THR cc_start: 0.7996 (m) cc_final: 0.7731 (p) REVERT: F 668 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.7688 (t) REVERT: F 672 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7735 (mt-10) REVERT: F 680 GLN cc_start: 0.7980 (mp-120) cc_final: 0.7460 (mp-120) REVERT: F 699 THR cc_start: 0.7817 (m) cc_final: 0.7496 (p) outliers start: 82 outliers final: 62 residues processed: 559 average time/residue: 1.4307 time to fit residues: 872.5113 Evaluate side-chains 583 residues out of total 1715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 506 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 680 GLN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 327 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 654 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain E residue 436 GLU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 505 GLU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 591 LYS Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 649 LYS Chi-restraints excluded: chain E residue 701 SER Chi-restraints excluded: chain F residue 447 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 611 ARG Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 164 optimal weight: 0.0170 chunk 175 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 155 optimal weight: 0.0980 chunk 147 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 616 ASN E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125992 restraints weight = 21728.502| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.77 r_work: 0.3512 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15688 Z= 0.150 Angle : 0.666 11.247 21184 Z= 0.334 Chirality : 0.039 0.162 2362 Planarity : 0.006 0.096 2757 Dihedral : 6.825 73.938 2153 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.74 % Allowed : 2.85 % Favored : 96.41 % Rotamer: Outliers : 4.61 % Allowed : 31.21 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1894 helix: 2.20 (0.14), residues: 1486 sheet: None (None), residues: 0 loop : -2.05 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 180 HIS 0.003 0.001 HIS C 476 PHE 0.013 0.001 PHE B 214 TYR 0.029 0.002 TYR B 331 ARG 0.020 0.001 ARG A 661 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 1056) hydrogen bonds : angle 3.72048 ( 3135) covalent geometry : bond 0.00346 (15688) covalent geometry : angle 0.66647 (21184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16660.25 seconds wall clock time: 288 minutes 8.04 seconds (17288.04 seconds total)