Starting phenix.real_space_refine on Fri Jun 13 21:03:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2l_47456/06_2025/9e2l_47456.cif" } resolution = 3.08 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= 0.016 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 9721 2.51 5 N 2666 2.21 5 O 2953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15436 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: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4580 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 23, 'TRANS': 542} Chain breaks: 4 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: 9.78, per 1000 atoms: 0.63 Number of scatterers: 15436 At special positions: 0 Unit cell: (133.92, 126.36, 125.28, 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 2953 8.00 N 2666 7.00 C 9721 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: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 79.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.883A pdb=" N VAL A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.661A pdb=" N ILE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 523 removed outlier: 3.652A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 removed outlier: 6.344A 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: 4.297A pdb=" N ASP A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.824A 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: 3.649A pdb=" N ARG A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.500A pdb=" N ASP A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.695A pdb=" N ARG A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.825A pdb=" N ALA A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 710 Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.500A pdb=" N LEU A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 77 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 105 through 121 removed outlier: 3.664A pdb=" N ILE B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.745A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 189 removed outlier: 4.240A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.612A pdb=" N ILE B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.869A pdb=" N PHE B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.787A pdb=" N PHE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.975A pdb=" N GLU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 298 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.879A pdb=" N THR B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.819A pdb=" N ALA B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.545A 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: 3.747A 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: 4.189A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 554 removed outlier: 4.435A pdb=" N ASP B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.629A pdb=" N GLN B 584 " --> pdb=" O ARG B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 619 removed outlier: 3.919A pdb=" N LEU B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.521A pdb=" N HIS B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 4.183A 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 682 through 698 removed outlier: 3.734A pdb=" N TYR B 686 " --> pdb=" O GLY B 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 445 through 455 removed outlier: 3.698A pdb=" N ILE C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.554A pdb=" N ASP C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 3.982A 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 523 removed outlier: 3.726A pdb=" N LEU C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 523 " --> pdb=" O MET C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 527 removed outlier: 6.374A pdb=" N ASP C 527 " --> pdb=" O GLN C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 527' Processing helix chain 'C' and resid 528 through 554 removed outlier: 4.138A pdb=" N ASP C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.515A pdb=" N ARG C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 569 " --> pdb=" O ASP C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 583 Processing helix chain 'C' and resid 594 through 619 removed outlier: 3.734A pdb=" N ASP C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 removed outlier: 3.526A pdb=" N HIS C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 664 removed outlier: 3.565A pdb=" N ARG C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 682 removed outlier: 3.563A 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: 3.732A 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 removed outlier: 3.536A pdb=" N GLN D 524 " --> pdb=" O GLU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 526 No H-bonds generated for 'chain 'D' and resid 525 through 526' Processing helix chain 'D' and resid 527 through 528 No H-bonds generated for 'chain 'D' and resid 527 through 528' Processing helix chain 'D' and resid 529 through 555 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.687A pdb=" N ARG D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D 569 " --> pdb=" O ASP D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.588A pdb=" N GLN D 584 " --> pdb=" O ARG D 580 " (cutoff:3.500A) removed outlier: 3.735A 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: 3.880A 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: 3.706A pdb=" N GLU D 688 " --> pdb=" O ILE D 684 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 690 " --> pdb=" O TYR D 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.714A pdb=" N VAL E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TRP E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 486 removed outlier: 3.615A pdb=" N ILE E 485 " --> pdb=" O MET E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 501 Processing helix chain 'E' and resid 503 through 523 removed outlier: 3.775A pdb=" N MET E 519 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU E 520 " --> pdb=" O ILE E 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 555 removed outlier: 4.194A pdb=" N ASP E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 534 " --> pdb=" O CYS E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 3.542A pdb=" N THR E 571 " --> pdb=" O ILE E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 586 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: 3.592A 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 Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.774A 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: 3.538A 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 502 through 524 removed outlier: 4.281A pdb=" N GLN F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 555 removed outlier: 4.010A pdb=" N MET F 531 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP F 532 " --> pdb=" O PRO F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 571 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: 3.580A pdb=" N HIS F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 647 " --> pdb=" O ALA F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.624A 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 683 through 705 removed outlier: 3.588A pdb=" N THR F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 688 " --> pdb=" O ILE F 684 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS F 690 " --> pdb=" O TYR F 686 " (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 36 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 1054 hydrogen bonds defined for protein. 3120 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: 4.61 Time building geometry restraints manager: 4.24 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: 3765 1.33 - 1.45: 2939 1.45 - 1.57: 8844 1.57 - 1.69: 2 1.69 - 1.81: 162 Bond restraints: 15712 Sorted by residual: bond pdb=" C ALA B 212 " pdb=" N PRO B 213 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.28e-02 6.10e+03 1.36e+01 bond pdb=" N GLU B 258 " pdb=" CA GLU B 258 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.32e-02 5.74e+03 5.57e+00 bond pdb=" O POP B 801 " pdb=" P2 POP B 801 " ideal model delta sigma weight residual 1.661 1.614 0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" O POP B 801 " pdb=" P1 POP B 801 " ideal model delta sigma weight residual 1.660 1.614 0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" N LEU C 593 " pdb=" CA LEU C 593 " ideal model delta sigma weight residual 1.463 1.492 -0.029 1.29e-02 6.01e+03 5.06e+00 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20883 2.52 - 5.04: 292 5.04 - 7.56: 33 7.56 - 10.08: 6 10.08 - 12.60: 1 Bond angle restraints: 21215 Sorted by residual: angle pdb=" N ALA B 264 " pdb=" CA ALA B 264 " pdb=" C ALA B 264 " ideal model delta sigma weight residual 114.64 107.36 7.28 1.52e+00 4.33e-01 2.30e+01 angle pdb=" N ILE B 501 " pdb=" CA ILE B 501 " pdb=" C ILE B 501 " ideal model delta sigma weight residual 113.53 108.86 4.67 9.80e-01 1.04e+00 2.27e+01 angle pdb=" N ILE F 501 " pdb=" CA ILE F 501 " pdb=" C ILE F 501 " ideal model delta sigma weight residual 113.53 109.08 4.45 9.80e-01 1.04e+00 2.06e+01 angle pdb=" CB MET D 531 " pdb=" CG MET D 531 " pdb=" SD MET D 531 " ideal model delta sigma weight residual 112.70 125.30 -12.60 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N GLU B 429 " pdb=" CA GLU B 429 " pdb=" C GLU B 429 " ideal model delta sigma weight residual 114.31 109.02 5.29 1.29e+00 6.01e-01 1.68e+01 ... (remaining 21210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7869 17.78 - 35.55: 1206 35.55 - 53.33: 411 53.33 - 71.11: 87 71.11 - 88.88: 26 Dihedral angle restraints: 9599 sinusoidal: 4018 harmonic: 5581 Sorted by residual: dihedral pdb=" CA ASP F 667 " pdb=" C ASP F 667 " pdb=" N VAL F 668 " pdb=" CA VAL F 668 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LEU B 525 " pdb=" C LEU B 525 " pdb=" N ASP B 526 " pdb=" CA ASP B 526 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LYS B 190 " pdb=" C LYS B 190 " pdb=" N ASP B 191 " pdb=" CA ASP B 191 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 9596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1724 0.040 - 0.080: 541 0.080 - 0.119: 90 0.119 - 0.159: 7 0.159 - 0.199: 3 Chirality restraints: 2365 Sorted by residual: chirality pdb=" CA ASP B 191 " pdb=" N ASP B 191 " pdb=" C ASP B 191 " pdb=" CB ASP B 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 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 8.70e-01 chirality pdb=" CB VAL F 459 " pdb=" CA VAL F 459 " pdb=" CG1 VAL F 459 " pdb=" CG2 VAL F 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2362 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 98 " -0.064 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO B 99 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 433 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO B 434 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 433 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 434 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 434 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 434 " -0.030 5.00e-02 4.00e+02 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 786 2.73 - 3.27: 15642 3.27 - 3.81: 25830 3.81 - 4.36: 30773 4.36 - 4.90: 52553 Nonbonded interactions: 125584 Sorted by model distance: nonbonded pdb=" OG1 THR D 504 " pdb=" OE1 GLU D 505 " model vdw 2.182 3.040 nonbonded pdb=" OE2 GLU A 706 " pdb=" N ASN A 713 " model vdw 2.207 3.120 nonbonded pdb=" N GLU E 448 " pdb=" OE1 GLU E 448 " model vdw 2.221 3.120 nonbonded pdb=" N GLU D 505 " pdb=" OE1 GLU D 505 " model vdw 2.231 3.120 nonbonded pdb=" O THR C 709 " pdb=" OG1 THR C 709 " model vdw 2.235 3.040 ... (remaining 125579 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: 3.970 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15712 Z= 0.162 Angle : 0.740 12.601 21215 Z= 0.445 Chirality : 0.038 0.199 2365 Planarity : 0.005 0.099 2761 Dihedral : 19.471 88.882 5985 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.90 % Favored : 95.25 % Rotamer: Outliers : 2.33 % Allowed : 36.28 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.20), residues: 1896 helix: 1.51 (0.15), residues: 1432 sheet: -3.69 (1.26), residues: 10 loop : -2.27 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 89 HIS 0.006 0.001 HIS F 463 PHE 0.018 0.001 PHE B 278 TYR 0.014 0.001 TYR C 686 ARG 0.013 0.001 ARG F 661 Details of bonding type rmsd hydrogen bonds : bond 0.19652 ( 1054) hydrogen bonds : angle 6.13446 ( 3120) covalent geometry : bond 0.00305 (15712) covalent geometry : angle 0.73981 (21215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 542 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 520 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 614 TYR cc_start: 0.8383 (t80) cc_final: 0.7999 (t80) REVERT: A 618 THR cc_start: 0.8465 (m) cc_final: 0.8047 (p) REVERT: A 637 SER cc_start: 0.8368 (p) cc_final: 0.8112 (m) REVERT: A 670 LEU cc_start: 0.8027 (mt) cc_final: 0.7668 (mp) REVERT: A 672 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7357 (mt-10) REVERT: A 680 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 58 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6138 (m-70) REVERT: B 64 GLU cc_start: 0.7966 (tp30) cc_final: 0.7565 (tp30) REVERT: B 183 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7567 (ttp) REVERT: B 223 MET cc_start: 0.8466 (tpp) cc_final: 0.8161 (mmm) REVERT: B 303 GLN cc_start: 0.7602 (tm-30) cc_final: 0.6818 (tm-30) REVERT: B 331 TYR cc_start: 0.7223 (m-80) cc_final: 0.6792 (m-80) REVERT: B 353 GLU cc_start: 0.7445 (pm20) cc_final: 0.7086 (pm20) REVERT: B 470 SER cc_start: 0.8621 (t) cc_final: 0.8291 (p) REVERT: B 527 ASP cc_start: 0.7359 (t70) cc_final: 0.7049 (t70) REVERT: B 545 GLN cc_start: 0.8364 (tp40) cc_final: 0.7984 (tp40) REVERT: B 658 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8043 (tp40) REVERT: B 676 SER cc_start: 0.8721 (t) cc_final: 0.8107 (p) REVERT: C 487 ASP cc_start: 0.7857 (m-30) cc_final: 0.7567 (m-30) REVERT: C 560 GLU cc_start: 0.7619 (tt0) cc_final: 0.7408 (tt0) REVERT: D 545 GLN cc_start: 0.8310 (tp40) cc_final: 0.8043 (tp40) REVERT: D 562 GLN cc_start: 0.8197 (mt0) cc_final: 0.7968 (mt0) REVERT: D 565 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: D 658 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: D 686 TYR cc_start: 0.8862 (t80) cc_final: 0.8649 (t80) REVERT: E 444 LYS cc_start: 0.3043 (OUTLIER) cc_final: -0.0134 (mttt) REVERT: E 487 ASP cc_start: 0.7404 (m-30) cc_final: 0.7084 (m-30) REVERT: E 524 GLN cc_start: 0.7949 (mt0) cc_final: 0.7746 (mt0) REVERT: E 537 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7755 (mp0) REVERT: E 545 GLN cc_start: 0.8195 (tp40) cc_final: 0.7957 (tp40) REVERT: E 580 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8055 (mtp180) REVERT: E 582 MET cc_start: 0.8482 (mtp) cc_final: 0.8146 (mtp) REVERT: E 611 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7736 (ttt90) REVERT: E 695 MET cc_start: 0.8500 (tpp) cc_final: 0.8200 (mmm) REVERT: E 700 ASP cc_start: 0.7904 (m-30) cc_final: 0.7700 (t0) REVERT: F 459 VAL cc_start: 0.8581 (p) cc_final: 0.8230 (t) REVERT: F 483 ASP cc_start: 0.7198 (m-30) cc_final: 0.6654 (m-30) REVERT: F 589 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.4966 (pp30) REVERT: F 613 ASP cc_start: 0.7948 (m-30) cc_final: 0.7584 (m-30) REVERT: F 658 GLN cc_start: 0.8526 (tp40) cc_final: 0.8251 (tp40) REVERT: F 699 THR cc_start: 0.8177 (m) cc_final: 0.7786 (p) outliers start: 40 outliers final: 20 residues processed: 562 average time/residue: 0.3179 time to fit residues: 249.0050 Evaluate side-chains 549 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 522 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 667 ASP Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 487 ASP Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 659 GLN B 57 HIS B 347 HIS B 359 HIS B 554 ASN C 647 GLN C 680 GLN E 590 GLN E 647 GLN F 477 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120686 restraints weight = 21571.327| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.64 r_work: 0.3436 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15712 Z= 0.188 Angle : 0.614 9.922 21215 Z= 0.317 Chirality : 0.039 0.163 2365 Planarity : 0.005 0.063 2761 Dihedral : 6.439 60.204 2154 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.69 % Favored : 95.46 % Rotamer: Outliers : 5.42 % Allowed : 30.17 % Favored : 64.41 % 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: 1.38 (0.20), residues: 1896 helix: 1.84 (0.14), residues: 1454 sheet: -3.59 (1.43), residues: 10 loop : -2.28 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 89 HIS 0.007 0.001 HIS B 57 PHE 0.022 0.002 PHE B 93 TYR 0.018 0.002 TYR C 686 ARG 0.009 0.001 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 1054) hydrogen bonds : angle 4.10534 ( 3120) covalent geometry : bond 0.00429 (15712) covalent geometry : angle 0.61389 (21215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 539 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 487 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: A 520 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 545 GLN cc_start: 0.8315 (tp40) cc_final: 0.8111 (tp40) REVERT: A 613 ASP cc_start: 0.7824 (m-30) cc_final: 0.7450 (m-30) REVERT: A 618 THR cc_start: 0.8540 (m) cc_final: 0.8016 (p) REVERT: A 637 SER cc_start: 0.8665 (p) cc_final: 0.8368 (m) REVERT: A 670 LEU cc_start: 0.8042 (mt) cc_final: 0.7681 (mp) REVERT: A 672 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 680 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 719 LEU cc_start: 0.8426 (mm) cc_final: 0.8197 (mt) REVERT: B 58 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6002 (m-70) REVERT: B 66 SER cc_start: 0.8900 (t) cc_final: 0.8575 (m) REVERT: B 72 ASP cc_start: 0.7927 (m-30) cc_final: 0.7623 (m-30) REVERT: B 160 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8578 (ttmt) REVERT: B 229 GLN cc_start: 0.7722 (pm20) cc_final: 0.7304 (pm20) REVERT: B 232 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6818 (tp40) REVERT: B 235 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8114 (pp) REVERT: B 258 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6558 (mt-10) REVERT: B 303 GLN cc_start: 0.7287 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 307 ASN cc_start: 0.7001 (m-40) cc_final: 0.6586 (m-40) REVERT: B 470 SER cc_start: 0.8696 (t) cc_final: 0.8389 (p) REVERT: B 506 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: B 527 ASP cc_start: 0.7115 (t70) cc_final: 0.6869 (t70) REVERT: B 545 GLN cc_start: 0.8335 (tp40) cc_final: 0.8107 (tp40) REVERT: B 611 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7787 (ttp-170) REVERT: B 612 ASP cc_start: 0.7726 (m-30) cc_final: 0.7441 (m-30) REVERT: B 616 ASN cc_start: 0.8271 (t0) cc_final: 0.7914 (t0) REVERT: B 676 SER cc_start: 0.8902 (t) cc_final: 0.8379 (p) REVERT: B 691 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: C 487 ASP cc_start: 0.7817 (m-30) cc_final: 0.7495 (m-30) REVERT: C 523 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8343 (mtp85) REVERT: C 529 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7609 (mmm160) REVERT: C 618 THR cc_start: 0.8556 (m) cc_final: 0.8084 (p) REVERT: C 685 GLU cc_start: 0.7407 (mp0) cc_final: 0.7095 (mp0) REVERT: D 442 PRO cc_start: 0.8530 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: D 493 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6848 (mtt180) REVERT: D 606 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: D 671 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8341 (mtmt) REVERT: D 686 TYR cc_start: 0.8785 (t80) cc_final: 0.8582 (t80) REVERT: E 444 LYS cc_start: 0.3274 (OUTLIER) cc_final: 0.0051 (mttt) REVERT: E 487 ASP cc_start: 0.7448 (m-30) cc_final: 0.7032 (m-30) REVERT: E 505 GLU cc_start: 0.7654 (mp0) cc_final: 0.7361 (mp0) REVERT: E 520 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: E 580 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8076 (mtp180) REVERT: E 582 MET cc_start: 0.8528 (mtp) cc_final: 0.8257 (mtp) REVERT: E 679 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7761 (mtp85) REVERT: E 680 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 685 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: F 483 ASP cc_start: 0.7370 (m-30) cc_final: 0.6850 (m-30) REVERT: F 495 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: F 617 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8367 (mm) REVERT: F 699 THR cc_start: 0.8252 (m) cc_final: 0.7907 (p) outliers start: 93 outliers final: 52 residues processed: 594 average time/residue: 0.3123 time to fit residues: 259.1391 Evaluate side-chains 591 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 525 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 680 GLN Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 606 GLU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 438 ILE 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 577 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 148 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 76 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 332 GLN B 347 HIS C 680 GLN E 647 GLN F 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119854 restraints weight = 21432.821| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.61 r_work: 0.3424 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15712 Z= 0.187 Angle : 0.589 10.153 21215 Z= 0.302 Chirality : 0.039 0.153 2365 Planarity : 0.005 0.065 2761 Dihedral : 4.756 53.663 2111 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.90 % Favored : 95.25 % Rotamer: Outliers : 5.71 % Allowed : 28.48 % Favored : 65.81 % 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: 1.55 (0.20), residues: 1896 helix: 1.96 (0.14), residues: 1458 sheet: -3.31 (1.57), residues: 10 loop : -2.27 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.005 0.001 HIS F 463 PHE 0.020 0.002 PHE B 311 TYR 0.016 0.001 TYR C 686 ARG 0.007 0.001 ARG E 611 Details of bonding type rmsd hydrogen bonds : bond 0.05483 ( 1054) hydrogen bonds : angle 3.86246 ( 3120) covalent geometry : bond 0.00433 (15712) covalent geometry : angle 0.58874 (21215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 523 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: A 520 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 593 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7406 (pp) REVERT: A 613 ASP cc_start: 0.7758 (m-30) cc_final: 0.7397 (m-30) REVERT: A 637 SER cc_start: 0.8744 (p) cc_final: 0.8398 (m) REVERT: A 670 LEU cc_start: 0.8082 (mt) cc_final: 0.7727 (mp) REVERT: A 672 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 680 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 58 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.5951 (m-70) REVERT: B 66 SER cc_start: 0.8828 (t) cc_final: 0.8534 (m) REVERT: B 72 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: B 106 LEU cc_start: 0.8388 (tp) cc_final: 0.8166 (tp) REVERT: B 160 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8579 (ttmt) REVERT: B 229 GLN cc_start: 0.7752 (pm20) cc_final: 0.7342 (pm20) REVERT: B 232 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6853 (tp40) REVERT: B 235 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8037 (pp) REVERT: B 294 GLN cc_start: 0.7511 (mt0) cc_final: 0.7218 (mt0) REVERT: B 303 GLN cc_start: 0.7255 (tm-30) cc_final: 0.6904 (tm-30) REVERT: B 470 SER cc_start: 0.8684 (t) cc_final: 0.8363 (p) REVERT: B 506 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: B 527 ASP cc_start: 0.7069 (t70) cc_final: 0.6834 (t70) REVERT: B 545 GLN cc_start: 0.8327 (tp40) cc_final: 0.8086 (tp40) REVERT: B 611 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7864 (ttp-170) REVERT: B 616 ASN cc_start: 0.8313 (t0) cc_final: 0.7925 (t0) REVERT: B 676 SER cc_start: 0.8799 (t) cc_final: 0.8351 (p) REVERT: C 487 ASP cc_start: 0.7863 (m-30) cc_final: 0.7552 (m-30) REVERT: C 500 MET cc_start: 0.8239 (mmm) cc_final: 0.7974 (mmm) REVERT: C 529 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7621 (mmm160) REVERT: C 561 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: C 618 THR cc_start: 0.8469 (m) cc_final: 0.7985 (p) REVERT: C 685 GLU cc_start: 0.7358 (mp0) cc_final: 0.7062 (mp0) REVERT: D 493 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6795 (mtt180) REVERT: D 554 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (m-40) REVERT: D 565 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: D 658 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: D 671 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8397 (mtmt) REVERT: D 675 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8329 (tt) REVERT: E 444 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.0174 (mttt) REVERT: E 487 ASP cc_start: 0.7461 (m-30) cc_final: 0.6955 (m-30) REVERT: E 505 GLU cc_start: 0.7691 (mp0) cc_final: 0.7397 (mp0) REVERT: E 580 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8057 (mtp180) REVERT: E 679 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7729 (mtp85) REVERT: E 680 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 685 GLU cc_start: 0.7498 (mp0) cc_final: 0.7193 (mp0) REVERT: E 693 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: F 436 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7220 (mp0) REVERT: F 483 ASP cc_start: 0.7489 (m-30) cc_final: 0.6931 (m-30) REVERT: F 495 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: F 617 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8356 (mm) REVERT: F 671 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (mttt) REVERT: F 676 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8629 (p) REVERT: F 695 MET cc_start: 0.8195 (mmm) cc_final: 0.7852 (tpp) REVERT: F 699 THR cc_start: 0.8317 (m) cc_final: 0.7973 (p) outliers start: 98 outliers final: 59 residues processed: 582 average time/residue: 0.3600 time to fit residues: 297.8362 Evaluate side-chains 599 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 520 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 487 ASP 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 577 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 183 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 66 optimal weight: 0.0980 chunk 79 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 ASN E 647 GLN F 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121904 restraints weight = 21465.500| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.62 r_work: 0.3453 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15712 Z= 0.124 Angle : 0.545 9.790 21215 Z= 0.279 Chirality : 0.037 0.151 2365 Planarity : 0.004 0.060 2761 Dihedral : 4.524 52.083 2109 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.79 % Allowed : 3.80 % Favored : 95.41 % Rotamer: Outliers : 5.53 % Allowed : 28.25 % 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: 1.98 (0.20), residues: 1896 helix: 2.27 (0.14), residues: 1457 sheet: -3.06 (1.65), residues: 10 loop : -2.15 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 276 HIS 0.004 0.001 HIS F 463 PHE 0.017 0.001 PHE E 450 TYR 0.013 0.001 TYR D 686 ARG 0.008 0.000 ARG D 568 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 1054) hydrogen bonds : angle 3.59366 ( 3120) covalent geometry : bond 0.00273 (15712) covalent geometry : angle 0.54464 (21215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 538 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: A 520 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 593 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7305 (pp) REVERT: A 613 ASP cc_start: 0.7880 (m-30) cc_final: 0.7416 (m-30) REVERT: A 637 SER cc_start: 0.8744 (p) cc_final: 0.8381 (m) REVERT: A 670 LEU cc_start: 0.8006 (mt) cc_final: 0.7643 (mp) REVERT: A 672 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 680 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 58 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5989 (m-70) REVERT: B 66 SER cc_start: 0.8782 (t) cc_final: 0.8568 (p) REVERT: B 206 ARG cc_start: 0.7215 (tpt-90) cc_final: 0.6809 (tpt170) REVERT: B 229 GLN cc_start: 0.7689 (pm20) cc_final: 0.7251 (pm20) REVERT: B 232 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6831 (tp40) REVERT: B 262 PHE cc_start: 0.7986 (p90) cc_final: 0.7356 (p90) REVERT: B 294 GLN cc_start: 0.7542 (mt0) cc_final: 0.7294 (mt0) REVERT: B 303 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6916 (tm-30) REVERT: B 470 SER cc_start: 0.8678 (t) cc_final: 0.8359 (p) REVERT: B 506 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: B 527 ASP cc_start: 0.7113 (t70) cc_final: 0.6894 (t70) REVERT: B 545 GLN cc_start: 0.8334 (tp40) cc_final: 0.8039 (tp40) REVERT: B 604 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 608 PHE cc_start: 0.8608 (m-80) cc_final: 0.8143 (m-80) REVERT: B 611 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7752 (ttp-170) REVERT: B 612 ASP cc_start: 0.7751 (m-30) cc_final: 0.7497 (m-30) REVERT: B 616 ASN cc_start: 0.8343 (t0) cc_final: 0.7953 (t0) REVERT: B 676 SER cc_start: 0.8762 (t) cc_final: 0.8316 (p) REVERT: C 487 ASP cc_start: 0.7894 (m-30) cc_final: 0.7558 (m-30) REVERT: C 500 MET cc_start: 0.8205 (mmm) cc_final: 0.7963 (mmm) REVERT: C 523 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8394 (mtm180) REVERT: C 561 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: C 585 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8061 (mt) REVERT: C 618 THR cc_start: 0.8440 (m) cc_final: 0.7923 (p) REVERT: C 675 LEU cc_start: 0.8316 (mm) cc_final: 0.8057 (mp) REVERT: C 680 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7877 (tm-30) REVERT: C 685 GLU cc_start: 0.7325 (mp0) cc_final: 0.7041 (mp0) REVERT: D 493 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6800 (mtt180) REVERT: D 565 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: D 658 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: D 671 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8385 (mtmt) REVERT: D 675 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8343 (tt) REVERT: E 444 LYS cc_start: 0.3302 (OUTLIER) cc_final: 0.0224 (mttt) REVERT: E 505 GLU cc_start: 0.7653 (mp0) cc_final: 0.7402 (mp0) REVERT: E 580 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8030 (mtp180) REVERT: E 679 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7656 (mtp85) REVERT: E 680 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7893 (tm-30) REVERT: E 685 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: F 459 VAL cc_start: 0.8578 (p) cc_final: 0.8226 (t) REVERT: F 483 ASP cc_start: 0.7436 (m-30) cc_final: 0.6912 (m-30) REVERT: F 495 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7551 (mmm-85) REVERT: F 617 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (mm) REVERT: F 676 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8619 (p) REVERT: F 695 MET cc_start: 0.8206 (mmm) cc_final: 0.7967 (tpp) REVERT: F 699 THR cc_start: 0.8323 (m) cc_final: 0.7946 (p) outliers start: 95 outliers final: 57 residues processed: 594 average time/residue: 0.3070 time to fit residues: 255.8403 Evaluate side-chains 593 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 519 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 487 ASP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE 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 37 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 161 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120342 restraints weight = 21697.710| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.62 r_work: 0.3428 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15712 Z= 0.164 Angle : 0.563 10.893 21215 Z= 0.287 Chirality : 0.038 0.159 2365 Planarity : 0.004 0.058 2761 Dihedral : 4.462 54.053 2107 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.79 % Allowed : 3.90 % Favored : 95.31 % Rotamer: Outliers : 5.88 % Allowed : 28.31 % Favored : 65.81 % 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: 1.96 (0.20), residues: 1896 helix: 2.25 (0.14), residues: 1460 sheet: -2.73 (1.75), residues: 10 loop : -2.16 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 276 HIS 0.004 0.001 HIS E 642 PHE 0.025 0.001 PHE B 311 TYR 0.014 0.001 TYR D 686 ARG 0.004 0.000 ARG E 611 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 1054) hydrogen bonds : angle 3.60300 ( 3120) covalent geometry : bond 0.00378 (15712) covalent geometry : angle 0.56271 (21215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 537 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 487 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: A 495 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: A 520 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 548 ASP cc_start: 0.8232 (t70) cc_final: 0.7896 (t70) REVERT: A 569 GLN cc_start: 0.8181 (mt0) cc_final: 0.7879 (mt0) REVERT: A 593 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7370 (pp) REVERT: A 613 ASP cc_start: 0.7839 (m-30) cc_final: 0.7402 (m-30) REVERT: A 670 LEU cc_start: 0.8084 (mt) cc_final: 0.7724 (mp) REVERT: A 672 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 680 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 58 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.5960 (m-70) REVERT: B 66 SER cc_start: 0.8776 (t) cc_final: 0.8576 (p) REVERT: B 74 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7570 (pp20) REVERT: B 223 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7933 (mmp) REVERT: B 229 GLN cc_start: 0.7703 (pm20) cc_final: 0.7264 (pm20) REVERT: B 303 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 470 SER cc_start: 0.8677 (t) cc_final: 0.8357 (p) REVERT: B 506 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: B 545 GLN cc_start: 0.8321 (tp40) cc_final: 0.8089 (tp40) REVERT: B 608 PHE cc_start: 0.8605 (m-80) cc_final: 0.8169 (m-80) REVERT: B 612 ASP cc_start: 0.7711 (m-30) cc_final: 0.7460 (m-30) REVERT: B 616 ASN cc_start: 0.8325 (t0) cc_final: 0.7927 (t0) REVERT: B 676 SER cc_start: 0.8768 (t) cc_final: 0.8334 (p) REVERT: C 448 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 487 ASP cc_start: 0.7921 (m-30) cc_final: 0.7598 (m-30) REVERT: C 500 MET cc_start: 0.8204 (mmm) cc_final: 0.7984 (mmm) REVERT: C 523 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8399 (mtm180) REVERT: C 561 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 618 THR cc_start: 0.8482 (m) cc_final: 0.7986 (p) REVERT: C 680 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7908 (tm-30) REVERT: C 685 GLU cc_start: 0.7430 (mp0) cc_final: 0.7112 (mp0) REVERT: D 493 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6823 (mtt180) REVERT: D 524 GLN cc_start: 0.8258 (mt0) cc_final: 0.7946 (mt0) REVERT: D 529 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6875 (mmm-85) REVERT: D 565 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: D 658 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 675 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8352 (tt) REVERT: D 695 MET cc_start: 0.7035 (tpt) cc_final: 0.6694 (tpt) REVERT: E 444 LYS cc_start: 0.3309 (OUTLIER) cc_final: 0.0270 (mttt) REVERT: E 505 GLU cc_start: 0.7674 (mp0) cc_final: 0.7420 (mp0) REVERT: E 679 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7673 (mtp85) REVERT: E 680 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7911 (tm-30) REVERT: E 685 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: F 436 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7021 (mp0) REVERT: F 459 VAL cc_start: 0.8604 (p) cc_final: 0.8239 (t) REVERT: F 483 ASP cc_start: 0.7530 (m-30) cc_final: 0.6975 (m-30) REVERT: F 495 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7544 (mmm-85) REVERT: F 617 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mm) REVERT: F 671 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8173 (mttp) REVERT: F 676 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8638 (p) REVERT: F 699 THR cc_start: 0.8318 (m) cc_final: 0.7953 (p) outliers start: 101 outliers final: 65 residues processed: 595 average time/residue: 0.3151 time to fit residues: 264.9558 Evaluate side-chains 611 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 529 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 596 GLN Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 487 ASP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 568 ARG Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 127 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 137 optimal weight: 0.0060 chunk 133 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 68 optimal weight: 0.0970 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121953 restraints weight = 21610.411| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.62 r_work: 0.3460 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15712 Z= 0.123 Angle : 0.552 10.907 21215 Z= 0.280 Chirality : 0.037 0.160 2365 Planarity : 0.004 0.058 2761 Dihedral : 4.364 52.624 2107 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.79 % Allowed : 3.43 % Favored : 95.78 % Rotamer: Outliers : 5.30 % Allowed : 28.77 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.20), residues: 1896 helix: 2.43 (0.14), residues: 1459 sheet: -2.35 (1.84), residues: 10 loop : -2.04 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 276 HIS 0.004 0.001 HIS F 463 PHE 0.023 0.001 PHE B 262 TYR 0.013 0.001 TYR D 686 ARG 0.003 0.000 ARG C 447 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 1054) hydrogen bonds : angle 3.48106 ( 3120) covalent geometry : bond 0.00271 (15712) covalent geometry : angle 0.55246 (21215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 539 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 487 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: A 520 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 569 GLN cc_start: 0.8180 (mt0) cc_final: 0.7889 (mt0) REVERT: A 613 ASP cc_start: 0.7834 (m-30) cc_final: 0.7411 (m-30) REVERT: A 670 LEU cc_start: 0.8030 (mt) cc_final: 0.7691 (mp) REVERT: A 672 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 680 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 706 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 58 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.5964 (m-70) REVERT: B 66 SER cc_start: 0.8781 (t) cc_final: 0.8523 (p) REVERT: B 74 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7535 (pp20) REVERT: B 229 GLN cc_start: 0.7701 (pm20) cc_final: 0.7266 (pm20) REVERT: B 246 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 251 ASP cc_start: 0.8313 (t0) cc_final: 0.8006 (t0) REVERT: B 262 PHE cc_start: 0.7676 (p90) cc_final: 0.6397 (p90) REVERT: B 470 SER cc_start: 0.8665 (t) cc_final: 0.8358 (p) REVERT: B 506 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 527 ASP cc_start: 0.7060 (t70) cc_final: 0.6849 (t70) REVERT: B 545 GLN cc_start: 0.8302 (tp40) cc_final: 0.8010 (tp40) REVERT: B 608 PHE cc_start: 0.8614 (m-80) cc_final: 0.8097 (m-80) REVERT: B 611 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7607 (ttp-170) REVERT: B 612 ASP cc_start: 0.7688 (m-30) cc_final: 0.7405 (m-30) REVERT: B 616 ASN cc_start: 0.8303 (t0) cc_final: 0.7904 (t0) REVERT: B 676 SER cc_start: 0.8754 (t) cc_final: 0.8319 (p) REVERT: C 448 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 487 ASP cc_start: 0.7892 (m-30) cc_final: 0.7585 (m-30) REVERT: C 523 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8390 (mtm180) REVERT: C 561 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: C 675 LEU cc_start: 0.8297 (mm) cc_final: 0.8019 (mt) REVERT: C 680 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 685 GLU cc_start: 0.7367 (mp0) cc_final: 0.7059 (mp0) REVERT: D 493 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6804 (mtt180) REVERT: D 524 GLN cc_start: 0.8244 (mt0) cc_final: 0.7932 (mt0) REVERT: D 529 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6887 (mmm-85) REVERT: D 565 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: D 658 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: D 675 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8359 (tt) REVERT: D 695 MET cc_start: 0.7030 (tpt) cc_final: 0.6689 (tpt) REVERT: E 505 GLU cc_start: 0.7649 (mp0) cc_final: 0.7393 (mp0) REVERT: E 611 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8044 (ttt90) REVERT: E 680 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7925 (tm-30) REVERT: E 685 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: F 432 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7745 (mt) REVERT: F 436 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7019 (mp0) REVERT: F 459 VAL cc_start: 0.8588 (p) cc_final: 0.8226 (t) REVERT: F 483 ASP cc_start: 0.7489 (m-30) cc_final: 0.6946 (m-30) REVERT: F 495 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7501 (mmm-85) REVERT: F 617 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (mm) REVERT: F 676 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (p) REVERT: F 699 THR cc_start: 0.8356 (m) cc_final: 0.7974 (p) outliers start: 91 outliers final: 63 residues processed: 586 average time/residue: 0.3264 time to fit residues: 268.6491 Evaluate side-chains 601 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 524 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 596 GLN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 640 LEU Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 56 HIS B 347 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN 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 = 0.3733 r_free = 0.3733 target = 0.132883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118660 restraints weight = 21686.942| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.62 r_work: 0.3412 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15712 Z= 0.227 Angle : 0.613 11.720 21215 Z= 0.313 Chirality : 0.041 0.151 2365 Planarity : 0.005 0.052 2761 Dihedral : 4.500 55.942 2103 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.69 % Allowed : 3.96 % Favored : 95.36 % Rotamer: Outliers : 6.17 % Allowed : 27.90 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.20), residues: 1896 helix: 2.15 (0.14), residues: 1458 sheet: -2.61 (1.80), residues: 10 loop : -2.15 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 276 HIS 0.005 0.001 HIS E 642 PHE 0.026 0.002 PHE B 262 TYR 0.018 0.002 TYR D 686 ARG 0.005 0.001 ARG E 523 Details of bonding type rmsd hydrogen bonds : bond 0.05639 ( 1054) hydrogen bonds : angle 3.72381 ( 3120) covalent geometry : bond 0.00534 (15712) covalent geometry : angle 0.61288 (21215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 537 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7296 (mp) REVERT: A 487 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: A 495 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7137 (mtm180) REVERT: A 520 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 548 ASP cc_start: 0.8248 (t70) cc_final: 0.7899 (t70) REVERT: A 613 ASP cc_start: 0.7873 (m-30) cc_final: 0.7634 (m-30) REVERT: A 670 LEU cc_start: 0.8122 (mt) cc_final: 0.7764 (mp) REVERT: A 672 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 680 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 58 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.5925 (m-70) REVERT: B 66 SER cc_start: 0.8807 (t) cc_final: 0.8527 (p) REVERT: B 106 LEU cc_start: 0.8360 (tp) cc_final: 0.8089 (tp) REVERT: B 174 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7579 (tp30) REVERT: B 229 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B 232 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6719 (tp40) REVERT: B 246 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 291 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6322 (mmm160) REVERT: B 470 SER cc_start: 0.8700 (t) cc_final: 0.8362 (p) REVERT: B 506 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: B 545 GLN cc_start: 0.8347 (tp40) cc_final: 0.8106 (tp40) REVERT: B 608 PHE cc_start: 0.8618 (m-80) cc_final: 0.8203 (m-80) REVERT: B 611 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7715 (ttp-170) REVERT: B 612 ASP cc_start: 0.7740 (m-30) cc_final: 0.7522 (m-30) REVERT: B 616 ASN cc_start: 0.8317 (t0) cc_final: 0.7904 (t0) REVERT: B 676 SER cc_start: 0.8786 (t) cc_final: 0.8357 (p) REVERT: C 487 ASP cc_start: 0.7926 (m-30) cc_final: 0.7637 (m-30) REVERT: C 523 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8396 (mtm180) REVERT: C 561 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: C 618 THR cc_start: 0.8461 (m) cc_final: 0.7973 (p) REVERT: C 675 LEU cc_start: 0.8337 (mm) cc_final: 0.8076 (mt) REVERT: C 680 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7852 (tm-30) REVERT: C 685 GLU cc_start: 0.7542 (mp0) cc_final: 0.7277 (mp0) REVERT: D 493 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6765 (mtt180) REVERT: D 529 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.6945 (mmm-85) REVERT: D 565 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: D 658 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: D 675 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8349 (tt) REVERT: D 695 MET cc_start: 0.7031 (tpt) cc_final: 0.6709 (tpt) REVERT: E 487 ASP cc_start: 0.7504 (m-30) cc_final: 0.7038 (m-30) REVERT: E 505 GLU cc_start: 0.7749 (mp0) cc_final: 0.7479 (mp0) REVERT: E 679 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7701 (mtp85) REVERT: E 680 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 685 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: F 432 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.7749 (mp) REVERT: F 436 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7228 (mp0) REVERT: F 459 VAL cc_start: 0.8632 (p) cc_final: 0.8281 (t) REVERT: F 483 ASP cc_start: 0.7513 (m-30) cc_final: 0.6962 (m-30) REVERT: F 495 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: F 617 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8298 (mm) REVERT: F 671 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8228 (mttp) REVERT: F 676 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (p) REVERT: F 699 THR cc_start: 0.8347 (m) cc_final: 0.8009 (p) outliers start: 106 outliers final: 69 residues processed: 593 average time/residue: 0.3354 time to fit residues: 282.3748 Evaluate side-chains 622 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 533 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 565 ASP Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 568 ARG Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 160 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 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 56 HIS B 332 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120088 restraints weight = 21470.298| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.62 r_work: 0.3433 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15712 Z= 0.164 Angle : 0.586 11.287 21215 Z= 0.301 Chirality : 0.039 0.149 2365 Planarity : 0.004 0.056 2761 Dihedral : 4.421 56.656 2103 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.69 % Allowed : 3.38 % Favored : 95.94 % Rotamer: Outliers : 5.53 % Allowed : 28.48 % Favored : 65.99 % 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: 1.99 (0.20), residues: 1896 helix: 2.29 (0.14), residues: 1455 sheet: -3.00 (1.46), residues: 10 loop : -2.17 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 276 HIS 0.008 0.001 HIS B 56 PHE 0.051 0.002 PHE B 262 TYR 0.019 0.001 TYR E 614 ARG 0.006 0.000 ARG D 568 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 1054) hydrogen bonds : angle 3.60751 ( 3120) covalent geometry : bond 0.00382 (15712) covalent geometry : angle 0.58560 (21215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 542 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7266 (mp) REVERT: A 436 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7067 (mp0) REVERT: A 487 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6681 (m-30) REVERT: A 520 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 548 ASP cc_start: 0.8221 (t70) cc_final: 0.7909 (t70) REVERT: A 569 GLN cc_start: 0.8189 (mt0) cc_final: 0.7881 (mt0) REVERT: A 613 ASP cc_start: 0.7857 (m-30) cc_final: 0.7560 (m-30) REVERT: A 670 LEU cc_start: 0.8063 (mt) cc_final: 0.7717 (mp) REVERT: A 672 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 680 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 55 ARG cc_start: 0.6331 (tpp-160) cc_final: 0.5893 (ttm170) REVERT: B 58 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.5812 (m-70) REVERT: B 66 SER cc_start: 0.8784 (t) cc_final: 0.8504 (p) REVERT: B 174 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7541 (tp30) REVERT: B 223 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7934 (mmp) REVERT: B 229 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: B 271 MET cc_start: 0.4445 (mmt) cc_final: 0.4056 (mmp) REVERT: B 470 SER cc_start: 0.8679 (t) cc_final: 0.8350 (p) REVERT: B 506 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: B 545 GLN cc_start: 0.8320 (tp40) cc_final: 0.8088 (tp40) REVERT: B 608 PHE cc_start: 0.8617 (m-80) cc_final: 0.8184 (m-80) REVERT: B 611 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7726 (ttp-170) REVERT: B 612 ASP cc_start: 0.7743 (m-30) cc_final: 0.7512 (m-30) REVERT: B 616 ASN cc_start: 0.8305 (t0) cc_final: 0.7880 (t0) REVERT: B 676 SER cc_start: 0.8774 (t) cc_final: 0.8327 (p) REVERT: C 487 ASP cc_start: 0.7892 (m-30) cc_final: 0.7628 (m-30) REVERT: C 523 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8401 (mtm180) REVERT: C 561 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: C 618 THR cc_start: 0.8442 (m) cc_final: 0.7936 (p) REVERT: C 675 LEU cc_start: 0.8320 (mm) cc_final: 0.8068 (mp) REVERT: C 680 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 685 GLU cc_start: 0.7442 (mp0) cc_final: 0.7119 (mp0) REVERT: D 493 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6831 (mtt180) REVERT: D 529 ARG cc_start: 0.7294 (mmm-85) cc_final: 0.6846 (mmm-85) REVERT: D 579 THR cc_start: 0.8584 (m) cc_final: 0.8334 (p) REVERT: D 658 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: D 675 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 695 MET cc_start: 0.7053 (tpt) cc_final: 0.6719 (tpt) REVERT: E 444 LYS cc_start: 0.3301 (OUTLIER) cc_final: 0.0359 (mttt) REVERT: E 487 ASP cc_start: 0.7477 (m-30) cc_final: 0.7004 (m-30) REVERT: E 505 GLU cc_start: 0.7719 (mp0) cc_final: 0.7475 (mp0) REVERT: E 611 ARG cc_start: 0.8274 (ttp80) cc_final: 0.8067 (ttt90) REVERT: E 680 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 685 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: F 432 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7792 (mt) REVERT: F 436 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7083 (mp0) REVERT: F 459 VAL cc_start: 0.8618 (p) cc_final: 0.8262 (t) REVERT: F 483 ASP cc_start: 0.7520 (m-30) cc_final: 0.6972 (m-30) REVERT: F 495 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: F 617 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (mm) REVERT: F 671 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8222 (mttp) REVERT: F 676 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8653 (p) REVERT: F 699 THR cc_start: 0.8349 (m) cc_final: 0.7982 (p) outliers start: 95 outliers final: 66 residues processed: 593 average time/residue: 0.3145 time to fit residues: 261.4873 Evaluate side-chains 619 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 536 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 568 ARG Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 640 LEU Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 164 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 93 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 87 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 56 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121769 restraints weight = 21424.629| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.61 r_work: 0.3459 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15712 Z= 0.126 Angle : 0.584 11.536 21215 Z= 0.298 Chirality : 0.037 0.148 2365 Planarity : 0.004 0.057 2761 Dihedral : 4.323 57.293 2103 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.43 % Favored : 95.94 % Rotamer: Outliers : 4.37 % Allowed : 29.88 % Favored : 65.75 % 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: 2.23 (0.20), residues: 1896 helix: 2.46 (0.14), residues: 1460 sheet: -2.53 (1.59), residues: 10 loop : -2.11 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 276 HIS 0.007 0.001 HIS B 56 PHE 0.052 0.001 PHE B 262 TYR 0.017 0.001 TYR E 614 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 1054) hydrogen bonds : angle 3.48183 ( 3120) covalent geometry : bond 0.00281 (15712) covalent geometry : angle 0.58387 (21215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 545 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 436 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7070 (mp0) REVERT: A 487 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: A 520 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 569 GLN cc_start: 0.8168 (mt0) cc_final: 0.7883 (mt0) REVERT: A 613 ASP cc_start: 0.7853 (m-30) cc_final: 0.7493 (m-30) REVERT: A 670 LEU cc_start: 0.8017 (mt) cc_final: 0.7679 (mp) REVERT: A 672 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 680 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 55 ARG cc_start: 0.6302 (tpp-160) cc_final: 0.5895 (ttm170) REVERT: B 58 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.5604 (m-70) REVERT: B 66 SER cc_start: 0.8792 (t) cc_final: 0.8528 (p) REVERT: B 174 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7549 (tp30) REVERT: B 223 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7895 (mmp) REVERT: B 229 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: B 246 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 271 MET cc_start: 0.4141 (mmt) cc_final: 0.3723 (mmp) REVERT: B 331 TYR cc_start: 0.7085 (m-80) cc_final: 0.6712 (m-80) REVERT: B 470 SER cc_start: 0.8667 (t) cc_final: 0.8363 (p) REVERT: B 506 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 519 MET cc_start: 0.8349 (tpp) cc_final: 0.7979 (tpt) REVERT: B 545 GLN cc_start: 0.8300 (tp40) cc_final: 0.8004 (tp40) REVERT: B 608 PHE cc_start: 0.8630 (m-80) cc_final: 0.8141 (m-80) REVERT: B 611 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7750 (ttp-170) REVERT: B 612 ASP cc_start: 0.7725 (m-30) cc_final: 0.7488 (m-30) REVERT: B 616 ASN cc_start: 0.8303 (t0) cc_final: 0.7879 (t0) REVERT: B 676 SER cc_start: 0.8762 (t) cc_final: 0.8315 (p) REVERT: C 487 ASP cc_start: 0.7838 (m-30) cc_final: 0.7587 (m-30) REVERT: C 675 LEU cc_start: 0.8317 (mm) cc_final: 0.8053 (mp) REVERT: C 680 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7855 (tm-30) REVERT: C 685 GLU cc_start: 0.7375 (mp0) cc_final: 0.7055 (mp0) REVERT: D 493 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6840 (mtt180) REVERT: D 529 ARG cc_start: 0.7225 (mmm-85) cc_final: 0.6858 (mmm-85) REVERT: D 579 THR cc_start: 0.8557 (m) cc_final: 0.8346 (p) REVERT: D 658 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: D 695 MET cc_start: 0.7027 (tpt) cc_final: 0.6698 (tpt) REVERT: E 487 ASP cc_start: 0.7452 (m-30) cc_final: 0.6970 (m-30) REVERT: E 505 GLU cc_start: 0.7673 (mp0) cc_final: 0.7452 (mp0) REVERT: E 523 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8165 (mtm180) REVERT: E 524 GLN cc_start: 0.7727 (mt0) cc_final: 0.7504 (mt0) REVERT: E 577 LEU cc_start: 0.8295 (tt) cc_final: 0.8014 (tp) REVERT: E 680 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7893 (tm-30) REVERT: F 436 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7220 (mp0) REVERT: F 459 VAL cc_start: 0.8604 (p) cc_final: 0.8234 (t) REVERT: F 483 ASP cc_start: 0.7497 (m-30) cc_final: 0.6937 (m-30) REVERT: F 495 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7513 (mmm-85) REVERT: F 617 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (mm) REVERT: F 676 SER cc_start: 0.8884 (t) cc_final: 0.8643 (p) REVERT: F 699 THR cc_start: 0.8338 (m) cc_final: 0.7977 (p) outliers start: 75 outliers final: 57 residues processed: 585 average time/residue: 0.3389 time to fit residues: 279.0897 Evaluate side-chains 600 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 532 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 659 GLN B 56 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119822 restraints weight = 21712.527| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.63 r_work: 0.3429 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15712 Z= 0.183 Angle : 0.618 12.088 21215 Z= 0.317 Chirality : 0.040 0.165 2365 Planarity : 0.005 0.054 2761 Dihedral : 4.384 59.610 2102 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.64 % Favored : 95.73 % Rotamer: Outliers : 4.43 % Allowed : 29.64 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.20), residues: 1896 helix: 2.29 (0.14), residues: 1461 sheet: -2.82 (1.61), residues: 10 loop : -2.16 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 276 HIS 0.007 0.001 HIS B 56 PHE 0.051 0.002 PHE B 262 TYR 0.015 0.002 TYR D 686 ARG 0.007 0.001 ARG C 523 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1054) hydrogen bonds : angle 3.58592 ( 3120) covalent geometry : bond 0.00431 (15712) covalent geometry : angle 0.61807 (21215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 538 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7120 (mp0) REVERT: A 487 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: A 520 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 548 ASP cc_start: 0.8227 (t70) cc_final: 0.7911 (t70) REVERT: A 613 ASP cc_start: 0.7874 (m-30) cc_final: 0.7580 (m-30) REVERT: A 670 LEU cc_start: 0.8060 (mt) cc_final: 0.7737 (mp) REVERT: A 672 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 680 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 55 ARG cc_start: 0.6354 (tpp-160) cc_final: 0.5969 (ttm170) REVERT: B 58 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5509 (m-70) REVERT: B 66 SER cc_start: 0.8806 (t) cc_final: 0.8535 (p) REVERT: B 174 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7617 (tp30) REVERT: B 229 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: B 246 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 271 MET cc_start: 0.3921 (mmt) cc_final: 0.3546 (mmt) REVERT: B 470 SER cc_start: 0.8680 (t) cc_final: 0.8362 (p) REVERT: B 506 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: B 519 MET cc_start: 0.8364 (tpp) cc_final: 0.8153 (tpt) REVERT: B 545 GLN cc_start: 0.8332 (tp40) cc_final: 0.8106 (tp40) REVERT: B 608 PHE cc_start: 0.8624 (m-80) cc_final: 0.8192 (m-80) REVERT: B 611 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7768 (ttp-170) REVERT: B 612 ASP cc_start: 0.7730 (m-30) cc_final: 0.7510 (m-30) REVERT: B 616 ASN cc_start: 0.8357 (t0) cc_final: 0.7923 (t0) REVERT: B 676 SER cc_start: 0.8765 (t) cc_final: 0.8311 (p) REVERT: C 487 ASP cc_start: 0.7874 (m-30) cc_final: 0.7613 (m-30) REVERT: C 675 LEU cc_start: 0.8340 (mm) cc_final: 0.8084 (mp) REVERT: C 680 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7855 (tm-30) REVERT: C 685 GLU cc_start: 0.7467 (mp0) cc_final: 0.7209 (mp0) REVERT: D 493 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6831 (mtt180) REVERT: D 529 ARG cc_start: 0.7290 (mmm-85) cc_final: 0.6827 (mmm-85) REVERT: D 579 THR cc_start: 0.8592 (m) cc_final: 0.8339 (p) REVERT: D 658 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: D 695 MET cc_start: 0.7036 (tpt) cc_final: 0.6708 (tpt) REVERT: E 487 ASP cc_start: 0.7461 (m-30) cc_final: 0.6986 (m-30) REVERT: E 505 GLU cc_start: 0.7699 (mp0) cc_final: 0.7467 (mp0) REVERT: E 680 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7895 (tm-30) REVERT: F 436 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7254 (mp0) REVERT: F 459 VAL cc_start: 0.8639 (p) cc_final: 0.8267 (t) REVERT: F 483 ASP cc_start: 0.7498 (m-30) cc_final: 0.6946 (m-30) REVERT: F 495 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7536 (mmm-85) REVERT: F 529 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6883 (mmm160) REVERT: F 617 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8304 (mm) REVERT: F 671 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8254 (mttp) REVERT: F 676 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8693 (p) REVERT: F 699 THR cc_start: 0.8328 (m) cc_final: 0.7977 (p) outliers start: 76 outliers final: 60 residues processed: 585 average time/residue: 0.3156 time to fit residues: 260.9213 Evaluate side-chains 610 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 671 LYS Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 438 ILE 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 527 ASP Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 640 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 493 ARG Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain E residue 428 ASP Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 571 THR Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 GLU Chi-restraints excluded: chain F residue 637 SER Chi-restraints excluded: chain F residue 640 LEU Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain F residue 676 SER Chi-restraints excluded: chain F residue 684 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 GLN F 477 ASN F 512 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120664 restraints weight = 21566.058| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.62 r_work: 0.3442 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15712 Z= 0.151 Angle : 0.602 12.061 21215 Z= 0.308 Chirality : 0.039 0.161 2365 Planarity : 0.005 0.054 2761 Dihedral : 4.350 59.946 2102 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.43 % Favored : 95.94 % Rotamer: Outliers : 4.54 % Allowed : 29.18 % Favored : 66.28 % 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: 2.14 (0.20), residues: 1896 helix: 2.40 (0.14), residues: 1456 sheet: -2.77 (1.59), residues: 10 loop : -2.12 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 276 HIS 0.005 0.001 HIS B 56 PHE 0.050 0.001 PHE B 262 TYR 0.014 0.001 TYR D 686 ARG 0.007 0.000 ARG C 523 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1054) hydrogen bonds : angle 3.53907 ( 3120) covalent geometry : bond 0.00350 (15712) covalent geometry : angle 0.60178 (21215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9623.55 seconds wall clock time: 166 minutes 58.29 seconds (10018.29 seconds total)