Starting phenix.real_space_refine on Sat Feb 17 15:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t8b_10399/02_2024/6t8b_10399_updated.pdb" } resolution = 3.65 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 4 5.21 5 S 93 5.16 5 C 11959 2.51 5 N 3294 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19077 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3020 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3021 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "E" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2991 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain breaks: 1 Chain: "F" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3028 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 1 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.48, per 1000 atoms: 0.55 Number of scatterers: 19077 At special positions: 0 Unit cell: (139.384, 99.56, 135.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 55 15.00 Mg 4 11.99 O 3672 8.00 N 3294 7.00 C 11959 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 - 3.50 Amino acid : False - 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: 7.43 Conformation dependent library (CDL) restraints added in 3.7 seconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 21 sheets defined 34.9% alpha, 12.5% beta 20 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.935A pdb=" N PHE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 removed outlier: 5.718A pdb=" N LYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 427 No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 472 through 486 removed outlier: 3.733A pdb=" N ASN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 543 Processing helix chain 'A' and resid 550 through 562 Processing helix chain 'A' and resid 600 through 603 No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 606 through 618 removed outlier: 4.351A pdb=" N GLU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.997A pdb=" N ASN A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.976A pdb=" N ILE A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 378 through 391 removed outlier: 4.936A pdb=" N ASN B 383 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 386 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 388 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 391 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 427 No H-bonds generated for 'chain 'B' and resid 424 through 427' Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 524 through 545 removed outlier: 4.061A pdb=" N MET B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 597 through 603 Processing helix chain 'B' and resid 605 through 617 removed outlier: 3.504A pdb=" N VAL B 608 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 609 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU B 610 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 663 No H-bonds generated for 'chain 'B' and resid 660 through 663' Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.780A pdb=" N LEU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 333 through 350 removed outlier: 3.583A pdb=" N MET C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 391 removed outlier: 4.072A pdb=" N LEU C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.722A pdb=" N LEU C 427 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 477 through 484 Processing helix chain 'C' and resid 521 through 543 Processing helix chain 'C' and resid 550 through 562 Processing helix chain 'C' and resid 597 through 618 removed outlier: 7.522A pdb=" N LYS C 606 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 607 " --> pdb=" O ILE C 603 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU C 610 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C 611 " --> pdb=" O LYS C 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 644 Processing helix chain 'C' and resid 658 through 663 Processing helix chain 'C' and resid 698 through 709 removed outlier: 4.107A pdb=" N VAL C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.707A pdb=" N GLU D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 392 removed outlier: 4.911A pdb=" N LYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 Processing helix chain 'D' and resid 430 through 433 No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 522 through 545 removed outlier: 4.162A pdb=" N ASN D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 542 " --> pdb=" O ARG D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 Processing helix chain 'D' and resid 597 through 600 No H-bonds generated for 'chain 'D' and resid 597 through 600' Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.881A pdb=" N ALA D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 658 through 663 Processing helix chain 'D' and resid 698 through 711 removed outlier: 3.614A pdb=" N HIS D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'E' and resid 333 through 349 Processing helix chain 'E' and resid 378 through 391 removed outlier: 5.322A pdb=" N LYS E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 524 through 545 removed outlier: 3.675A pdb=" N ARG E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 543 " --> pdb=" O TYR E 539 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET E 545 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 559 removed outlier: 3.780A pdb=" N LYS E 556 " --> pdb=" O GLY E 552 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 557 " --> pdb=" O PHE E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 604 Processing helix chain 'E' and resid 612 through 621 removed outlier: 4.099A pdb=" N GLN E 617 " --> pdb=" O ALA E 613 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS E 618 " --> pdb=" O ARG E 614 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG E 620 " --> pdb=" O ALA E 616 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA E 621 " --> pdb=" O GLN E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 643 No H-bonds generated for 'chain 'E' and resid 640 through 643' Processing helix chain 'E' and resid 657 through 663 removed outlier: 3.831A pdb=" N THR E 662 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 711 Processing helix chain 'E' and resid 718 through 720 No H-bonds generated for 'chain 'E' and resid 718 through 720' Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 333 through 350 removed outlier: 4.077A pdb=" N PHE F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 removed outlier: 4.748A pdb=" N LEU F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 423 through 427 Processing helix chain 'F' and resid 430 through 433 No H-bonds generated for 'chain 'F' and resid 430 through 433' Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 505 through 507 No H-bonds generated for 'chain 'F' and resid 505 through 507' Processing helix chain 'F' and resid 521 through 545 removed outlier: 4.084A pdb=" N ALA F 525 " --> pdb=" O MET F 521 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN F 526 " --> pdb=" O LYS F 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET F 545 " --> pdb=" O LEU F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 Processing helix chain 'F' and resid 597 through 617 removed outlier: 3.522A pdb=" N ILE F 603 " --> pdb=" O ASP F 599 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS F 606 " --> pdb=" O MET F 602 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS F 607 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL F 608 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU F 609 " --> pdb=" O GLY F 605 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU F 610 " --> pdb=" O LYS F 606 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU F 611 " --> pdb=" O LYS F 607 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 645 removed outlier: 4.025A pdb=" N ASN F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 664 removed outlier: 3.979A pdb=" N ILE F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 709 removed outlier: 3.979A pdb=" N ALA F 707 " --> pdb=" O ARG F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 720 No H-bonds generated for 'chain 'F' and resid 718 through 720' Processing sheet with id= A, first strand: chain 'A' and resid 397 through 399 removed outlier: 3.541A pdb=" N ARG A 398 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 358 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN A 371 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL A 356 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 651 removed outlier: 3.635A pdb=" N ARG A 649 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE A 452 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 495 through 498 removed outlier: 6.220A pdb=" N HIS A 625 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 594 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 627 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.774A pdb=" N ARG B 398 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN B 371 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL B 356 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 689 through 691 removed outlier: 3.809A pdb=" N ALA B 651 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 648 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N LEU B 462 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 626 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 464 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU B 628 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 590 " --> pdb=" O HIS B 625 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE B 627 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 592 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 629 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL B 594 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 440 through 445 removed outlier: 6.907A pdb=" N ILE B 452 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 412 through 414 removed outlier: 3.761A pdb=" N SER C 358 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN C 371 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL C 356 " --> pdb=" O GLN C 371 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 691 through 693 removed outlier: 7.069A pdb=" N ILE C 452 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 648 through 652 removed outlier: 6.644A pdb=" N ILE C 590 " --> pdb=" O HIS C 625 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE C 627 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 592 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA C 629 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 594 " --> pdb=" O ALA C 629 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 495 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP C 595 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 497 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 359 through 361 Processing sheet with id= K, first strand: chain 'D' and resid 461 through 463 removed outlier: 8.955A pdb=" N LEU D 462 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 626 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 590 " --> pdb=" O HIS D 625 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 627 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL D 592 " --> pdb=" O ILE D 627 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 649 through 652 removed outlier: 3.746A pdb=" N ALA D 651 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 440 through 445 removed outlier: 3.697A pdb=" N ILE D 452 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 398 through 400 removed outlier: 3.791A pdb=" N SER E 358 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN E 371 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL E 356 " --> pdb=" O GLN E 371 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 440 through 442 removed outlier: 3.618A pdb=" N THR E 454 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 494 through 498 removed outlier: 6.775A pdb=" N VAL E 591 " --> pdb=" O ILE E 495 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE E 497 " --> pdb=" O VAL E 591 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL E 593 " --> pdb=" O ILE E 497 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 677 through 680 Processing sheet with id= R, first strand: chain 'F' and resid 398 through 400 removed outlier: 3.512A pdb=" N ARG F 398 " --> pdb=" O GLU F 412 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN F 371 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL F 356 " --> pdb=" O GLN F 371 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 493 through 498 removed outlier: 6.291A pdb=" N HIS F 625 " --> pdb=" O VAL F 592 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL F 594 " --> pdb=" O HIS F 625 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE F 627 " --> pdb=" O VAL F 594 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 677 through 680 Processing sheet with id= U, first strand: chain 'F' and resid 440 through 445 removed outlier: 6.913A pdb=" N ILE F 452 " --> pdb=" O LEU F 443 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 8.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6315 1.36 - 1.51: 5241 1.51 - 1.66: 7759 1.66 - 1.80: 153 1.80 - 1.95: 24 Bond restraints: 19492 Sorted by residual: bond pdb=" C VAL F 608 " pdb=" N GLU F 609 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.37e-02 5.33e+03 3.48e+00 bond pdb=" C MET F 459 " pdb=" N PRO F 460 " ideal model delta sigma weight residual 1.338 1.370 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C MET D 459 " pdb=" N PRO D 460 " ideal model delta sigma weight residual 1.338 1.367 -0.029 1.90e-02 2.77e+03 2.25e+00 bond pdb=" C MET C 459 " pdb=" N PRO C 460 " ideal model delta sigma weight residual 1.338 1.366 -0.028 1.90e-02 2.77e+03 2.18e+00 bond pdb=" C LEU F 463 " pdb=" N VAL F 464 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.29e-02 6.01e+03 1.36e+00 ... (remaining 19487 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.21: 1040 106.21 - 113.73: 11539 113.73 - 121.26: 9050 121.26 - 128.78: 4879 128.78 - 136.30: 137 Bond angle restraints: 26645 Sorted by residual: angle pdb=" N GLN D 617 " pdb=" CA GLN D 617 " pdb=" C GLN D 617 " ideal model delta sigma weight residual 114.75 103.55 11.20 1.26e+00 6.30e-01 7.90e+01 angle pdb=" CA GLN D 617 " pdb=" C GLN D 617 " pdb=" N LYS D 618 " ideal model delta sigma weight residual 119.80 113.48 6.32 1.34e+00 5.57e-01 2.23e+01 angle pdb=" N VAL D 364 " pdb=" CA VAL D 364 " pdb=" C VAL D 364 " ideal model delta sigma weight residual 113.71 110.08 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" C GLU C 596 " pdb=" N PHE C 597 " pdb=" CA PHE C 597 " ideal model delta sigma weight residual 120.28 125.64 -5.36 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C MET A 459 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 120.60 112.99 7.61 2.20e+00 2.07e-01 1.20e+01 ... (remaining 26640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 11721 31.74 - 63.48: 262 63.48 - 95.22: 5 95.22 - 126.95: 4 126.95 - 158.69: 4 Dihedral angle restraints: 11996 sinusoidal: 5186 harmonic: 6810 Sorted by residual: dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 98.69 -158.69 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 89.24 -149.24 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 85.64 -145.64 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 11993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2022 0.036 - 0.072: 781 0.072 - 0.108: 270 0.108 - 0.144: 103 0.144 - 0.180: 9 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA MET F 459 " pdb=" N MET F 459 " pdb=" C MET F 459 " pdb=" CB MET F 459 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ILE F 495 " pdb=" N ILE F 495 " pdb=" C ILE F 495 " pdb=" CB ILE F 495 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA VAL C 474 " pdb=" N VAL C 474 " pdb=" C VAL C 474 " pdb=" CB VAL C 474 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 3182 not shown) Planarity restraints: 3236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 459 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO C 460 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 459 " 0.040 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO F 460 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO F 460 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 460 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 459 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 460 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.027 5.00e-02 4.00e+02 ... (remaining 3233 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 140 2.53 - 3.12: 15236 3.12 - 3.72: 28990 3.72 - 4.31: 42177 4.31 - 4.90: 68408 Nonbonded interactions: 154951 Sorted by model distance: nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 1.942 2.170 nonbonded pdb=" OG SER B 473 " pdb="MG MG B 802 " model vdw 1.961 2.170 nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 1.965 2.170 nonbonded pdb=" O3B ADP F 801 " pdb="MG MG F 802 " model vdw 1.987 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.012 2.170 ... (remaining 154946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 315 through 570 or resid 586 through 720)) selection = (chain 'B' and (resid 315 through 570 or resid 586 through 720)) selection = (chain 'C' and (resid 315 through 570 or resid 586 through 720)) selection = (chain 'D' and resid 315 through 720) selection = (chain 'E' and resid 315 through 720) selection = (chain 'F' and (resid 315 through 570 or resid 586 through 720)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 3.930 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 54.570 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19492 Z= 0.252 Angle : 0.721 11.199 26645 Z= 0.403 Chirality : 0.046 0.180 3185 Planarity : 0.006 0.066 3236 Dihedral : 12.526 158.693 7580 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -4.40 (0.14), residues: 2346 helix: -2.26 (0.14), residues: 903 sheet: -3.49 (0.21), residues: 392 loop : -3.22 (0.16), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 530 HIS 0.004 0.001 HIS B 702 PHE 0.022 0.002 PHE F 423 TYR 0.022 0.002 TYR A 507 ARG 0.007 0.001 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLN cc_start: 0.8684 (tp40) cc_final: 0.8461 (tp40) REVERT: A 450 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7795 (mtm-85) REVERT: A 501 MET cc_start: 0.8580 (mpp) cc_final: 0.8220 (mpp) REVERT: A 681 LEU cc_start: 0.9283 (tp) cc_final: 0.9072 (tt) REVERT: B 446 ASP cc_start: 0.7638 (p0) cc_final: 0.7396 (p0) REVERT: B 517 VAL cc_start: 0.9322 (t) cc_final: 0.9057 (t) REVERT: B 549 ASN cc_start: 0.9111 (p0) cc_final: 0.8825 (p0) REVERT: B 590 ILE cc_start: 0.9326 (mm) cc_final: 0.9079 (mt) REVERT: C 327 LYS cc_start: 0.7630 (pmmt) cc_final: 0.6611 (pmmt) REVERT: C 339 MET cc_start: 0.7627 (ttm) cc_final: 0.7066 (ttm) REVERT: C 455 ASP cc_start: 0.8400 (t0) cc_final: 0.8196 (t0) REVERT: C 506 ILE cc_start: 0.9440 (tp) cc_final: 0.8917 (tp) REVERT: C 631 GLN cc_start: 0.7755 (mt0) cc_final: 0.7495 (mt0) REVERT: D 331 TYR cc_start: 0.6242 (m-10) cc_final: 0.5825 (m-80) REVERT: D 443 LEU cc_start: 0.7605 (mt) cc_final: 0.7344 (mt) REVERT: D 489 PRO cc_start: 0.6375 (Cg_exo) cc_final: 0.5939 (Cg_endo) REVERT: D 607 LYS cc_start: 0.7752 (mttm) cc_final: 0.7470 (mppt) REVERT: D 675 HIS cc_start: 0.8525 (m-70) cc_final: 0.8207 (m-70) REVERT: D 716 TYR cc_start: 0.7850 (m-10) cc_final: 0.7279 (m-80) REVERT: E 500 LYS cc_start: 0.7906 (mttm) cc_final: 0.7417 (mttm) REVERT: E 529 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7267 (ptt90) REVERT: E 556 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7654 (mtmt) REVERT: E 599 ASP cc_start: 0.6345 (m-30) cc_final: 0.6086 (m-30) REVERT: E 600 MET cc_start: 0.7097 (ttp) cc_final: 0.6664 (tpt) REVERT: E 601 MET cc_start: 0.6313 (mmm) cc_final: 0.5682 (tmm) REVERT: E 666 GLN cc_start: 0.7714 (mt0) cc_final: 0.7020 (mt0) REVERT: E 695 PHE cc_start: 0.8144 (t80) cc_final: 0.7807 (t80) REVERT: F 345 ILE cc_start: 0.8939 (mm) cc_final: 0.8654 (mt) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.3645 time to fit residues: 330.8385 Evaluate side-chains 364 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 328 GLN B 383 ASN B 435 HIS B 617 GLN B 671 GLN C 371 GLN C 645 ASN C 692 HIS C 702 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 477 ASN D 526 ASN ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 GLN F 328 GLN F 383 ASN F 445 HIS F 617 GLN F 653 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 19492 Z= 0.279 Angle : 0.683 7.984 26645 Z= 0.341 Chirality : 0.047 0.298 3185 Planarity : 0.005 0.051 3236 Dihedral : 15.828 168.093 3099 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.50 % Allowed : 9.93 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.21 (0.16), residues: 2346 helix: -1.14 (0.17), residues: 912 sheet: -2.90 (0.23), residues: 392 loop : -2.65 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 530 HIS 0.006 0.001 HIS C 702 PHE 0.016 0.002 PHE D 597 TYR 0.017 0.002 TYR D 680 ARG 0.007 0.001 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 359 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 450 ARG cc_start: 0.8186 (ptp-170) cc_final: 0.7879 (mtm-85) REVERT: A 501 MET cc_start: 0.8726 (mpp) cc_final: 0.8424 (mpp) REVERT: A 659 ASP cc_start: 0.8196 (m-30) cc_final: 0.7570 (m-30) REVERT: A 662 THR cc_start: 0.9367 (m) cc_final: 0.9137 (p) REVERT: A 681 LEU cc_start: 0.9331 (tp) cc_final: 0.9115 (tt) REVERT: B 503 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6626 (mm-30) REVERT: B 590 ILE cc_start: 0.9401 (mm) cc_final: 0.9129 (mt) REVERT: C 631 GLN cc_start: 0.7776 (mt0) cc_final: 0.7440 (mt0) REVERT: C 661 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8411 (mtt-85) REVERT: D 443 LEU cc_start: 0.8141 (mt) cc_final: 0.7862 (mt) REVERT: D 607 LYS cc_start: 0.7774 (mttm) cc_final: 0.7428 (mppt) REVERT: D 716 TYR cc_start: 0.7880 (m-10) cc_final: 0.7198 (m-80) REVERT: E 331 TYR cc_start: 0.6347 (p90) cc_final: 0.6099 (p90) REVERT: E 529 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7293 (ptt90) REVERT: E 556 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7620 (mtmt) REVERT: E 600 MET cc_start: 0.7356 (ttp) cc_final: 0.6689 (tpt) REVERT: E 601 MET cc_start: 0.6177 (mmm) cc_final: 0.5736 (tmm) REVERT: E 666 GLN cc_start: 0.7748 (mt0) cc_final: 0.7434 (mt0) REVERT: E 695 PHE cc_start: 0.8281 (t80) cc_final: 0.7947 (t80) REVERT: F 617 GLN cc_start: 0.8523 (mt0) cc_final: 0.8293 (mt0) outliers start: 50 outliers final: 31 residues processed: 393 average time/residue: 0.3131 time to fit residues: 186.6237 Evaluate side-chains 332 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 301 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 233 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 328 GLN B 617 GLN C 371 GLN C 419 GLN C 617 GLN C 645 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 554 ASN E 477 ASN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN F 328 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19492 Z= 0.257 Angle : 0.647 10.508 26645 Z= 0.319 Chirality : 0.046 0.202 3185 Planarity : 0.005 0.047 3236 Dihedral : 15.679 179.342 3099 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.44 % Allowed : 10.88 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.63 (0.16), residues: 2346 helix: -0.68 (0.17), residues: 921 sheet: -2.44 (0.25), residues: 374 loop : -2.41 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 530 HIS 0.008 0.001 HIS C 702 PHE 0.014 0.002 PHE D 597 TYR 0.015 0.002 TYR B 539 ARG 0.009 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 337 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.7044 (tptt) cc_final: 0.6791 (tptt) REVERT: A 353 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 450 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7816 (mtm-85) REVERT: A 501 MET cc_start: 0.8893 (mpp) cc_final: 0.8540 (mpp) REVERT: A 659 ASP cc_start: 0.8204 (m-30) cc_final: 0.7605 (m-30) REVERT: A 662 THR cc_start: 0.9370 (m) cc_final: 0.9131 (p) REVERT: B 370 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9095 (pt) REVERT: B 503 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6724 (mm-30) REVERT: C 339 MET cc_start: 0.7516 (ttm) cc_final: 0.6923 (ttm) REVERT: C 661 ARG cc_start: 0.8876 (ttm-80) cc_final: 0.8379 (mtt-85) REVERT: D 607 LYS cc_start: 0.7669 (mttm) cc_final: 0.7318 (mppt) REVERT: D 708 TRP cc_start: 0.8166 (m100) cc_final: 0.7951 (m100) REVERT: D 716 TYR cc_start: 0.7707 (m-10) cc_final: 0.7040 (m-80) REVERT: E 317 PRO cc_start: 0.6585 (Cg_endo) cc_final: 0.6244 (Cg_exo) REVERT: E 331 TYR cc_start: 0.6014 (p90) cc_final: 0.5810 (p90) REVERT: E 529 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7280 (ptt90) REVERT: E 556 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7588 (mtmt) REVERT: E 600 MET cc_start: 0.7371 (ttp) cc_final: 0.6577 (tpt) REVERT: E 601 MET cc_start: 0.6103 (mmm) cc_final: 0.5696 (tmm) REVERT: E 695 PHE cc_start: 0.8310 (t80) cc_final: 0.7991 (t80) outliers start: 69 outliers final: 39 residues processed: 381 average time/residue: 0.3047 time to fit residues: 177.7805 Evaluate side-chains 339 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 299 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 665 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 145 optimal weight: 0.0870 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN C 419 GLN C 617 GLN C 645 ASN C 702 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 477 ASN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19492 Z= 0.268 Angle : 0.641 8.867 26645 Z= 0.315 Chirality : 0.046 0.197 3185 Planarity : 0.005 0.043 3236 Dihedral : 15.422 175.138 3099 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.34 % Allowed : 12.18 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.34 (0.17), residues: 2346 helix: -0.57 (0.17), residues: 929 sheet: -2.18 (0.25), residues: 375 loop : -2.17 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 530 HIS 0.004 0.001 HIS C 702 PHE 0.022 0.002 PHE A 597 TYR 0.015 0.001 TYR A 432 ARG 0.009 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 317 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.7039 (tptt) cc_final: 0.6799 (tptt) REVERT: A 353 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 450 ARG cc_start: 0.8223 (ptp-170) cc_final: 0.7817 (mtm-85) REVERT: A 501 MET cc_start: 0.8888 (mpp) cc_final: 0.8616 (mpp) REVERT: A 597 PHE cc_start: 0.8631 (t80) cc_final: 0.8050 (t80) REVERT: A 600 MET cc_start: 0.8025 (ttp) cc_final: 0.7792 (ttp) REVERT: A 659 ASP cc_start: 0.8182 (m-30) cc_final: 0.7593 (m-30) REVERT: A 662 THR cc_start: 0.9377 (m) cc_final: 0.9114 (p) REVERT: A 665 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: B 370 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9059 (pt) REVERT: B 503 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6686 (mm-30) REVERT: B 600 MET cc_start: 0.8734 (ttp) cc_final: 0.8179 (ttt) REVERT: C 599 ASP cc_start: 0.7760 (m-30) cc_final: 0.7525 (m-30) REVERT: C 661 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8328 (mtt-85) REVERT: D 521 MET cc_start: 0.6935 (tpt) cc_final: 0.6532 (tpp) REVERT: D 542 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7619 (mtm) REVERT: D 549 ASN cc_start: 0.8116 (p0) cc_final: 0.7337 (m-40) REVERT: D 607 LYS cc_start: 0.7643 (mttm) cc_final: 0.7259 (mppt) REVERT: D 617 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 716 TYR cc_start: 0.7638 (m-10) cc_final: 0.7031 (m-80) REVERT: E 317 PRO cc_start: 0.6469 (Cg_endo) cc_final: 0.6164 (Cg_exo) REVERT: E 331 TYR cc_start: 0.6085 (p90) cc_final: 0.5856 (p90) REVERT: E 529 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7284 (ptt90) REVERT: E 601 MET cc_start: 0.6146 (mmm) cc_final: 0.5646 (tmm) REVERT: E 695 PHE cc_start: 0.8331 (t80) cc_final: 0.7863 (t80) REVERT: F 602 MET cc_start: 0.7870 (tpp) cc_final: 0.7554 (mtp) REVERT: F 630 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8302 (p) outliers start: 67 outliers final: 44 residues processed: 362 average time/residue: 0.2979 time to fit residues: 166.2619 Evaluate side-chains 336 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 288 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 617 GLN C 645 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 554 ASN E 477 ASN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19492 Z= 0.256 Angle : 0.629 7.649 26645 Z= 0.309 Chirality : 0.045 0.204 3185 Planarity : 0.005 0.046 3236 Dihedral : 15.213 168.091 3099 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.24 % Allowed : 13.07 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.13 (0.17), residues: 2346 helix: -0.42 (0.18), residues: 935 sheet: -1.99 (0.26), residues: 367 loop : -2.07 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 530 HIS 0.009 0.001 HIS C 702 PHE 0.014 0.001 PHE D 597 TYR 0.014 0.001 TYR A 432 ARG 0.009 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 308 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.7020 (tptt) cc_final: 0.6795 (tptt) REVERT: A 353 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 450 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.7810 (mtm-85) REVERT: A 501 MET cc_start: 0.8928 (mpp) cc_final: 0.8669 (mpp) REVERT: A 617 GLN cc_start: 0.8509 (mt0) cc_final: 0.8254 (mt0) REVERT: A 659 ASP cc_start: 0.8182 (m-30) cc_final: 0.7578 (m-30) REVERT: A 662 THR cc_start: 0.9402 (m) cc_final: 0.9136 (p) REVERT: A 665 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: B 370 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9119 (pt) REVERT: B 503 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6690 (mm-30) REVERT: B 523 GLU cc_start: 0.7899 (mp0) cc_final: 0.7573 (mp0) REVERT: C 653 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 715 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7662 (p0) REVERT: D 371 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8425 (tm-30) REVERT: D 542 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7542 (mtm) REVERT: D 607 LYS cc_start: 0.7602 (mttm) cc_final: 0.7271 (mppt) REVERT: D 617 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 716 TYR cc_start: 0.7575 (m-10) cc_final: 0.6824 (m-10) REVERT: E 331 TYR cc_start: 0.6009 (p90) cc_final: 0.5758 (p90) REVERT: E 529 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7289 (ptt90) REVERT: E 599 ASP cc_start: 0.5808 (m-30) cc_final: 0.5447 (m-30) REVERT: E 601 MET cc_start: 0.6096 (mmm) cc_final: 0.5597 (tmm) REVERT: E 666 GLN cc_start: 0.7822 (mt0) cc_final: 0.7297 (mt0) REVERT: E 695 PHE cc_start: 0.8357 (t80) cc_final: 0.7871 (t80) outliers start: 65 outliers final: 40 residues processed: 353 average time/residue: 0.2901 time to fit residues: 158.3764 Evaluate side-chains 328 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 645 ASN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 371 GLN E 477 ASN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19492 Z= 0.239 Angle : 0.620 7.290 26645 Z= 0.304 Chirality : 0.045 0.207 3185 Planarity : 0.005 0.051 3236 Dihedral : 15.055 162.575 3099 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.44 % Allowed : 13.97 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.93 (0.17), residues: 2346 helix: -0.27 (0.18), residues: 929 sheet: -1.93 (0.26), residues: 364 loop : -1.91 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 530 HIS 0.003 0.001 HIS B 625 PHE 0.014 0.001 PHE C 597 TYR 0.014 0.001 TYR A 432 ARG 0.012 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 297 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.7029 (tptt) cc_final: 0.6819 (tptt) REVERT: A 353 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 450 ARG cc_start: 0.8251 (ptp-170) cc_final: 0.7814 (mtm-85) REVERT: A 501 MET cc_start: 0.8913 (mpp) cc_final: 0.8650 (mpp) REVERT: A 659 ASP cc_start: 0.8161 (m-30) cc_final: 0.7531 (m-30) REVERT: A 662 THR cc_start: 0.9409 (m) cc_final: 0.9123 (p) REVERT: A 665 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 370 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9105 (pt) REVERT: B 503 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6709 (mm-30) REVERT: B 600 MET cc_start: 0.8754 (ttp) cc_final: 0.8076 (ttt) REVERT: C 653 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8585 (tm-30) REVERT: D 339 MET cc_start: 0.7688 (tpp) cc_final: 0.7290 (tpp) REVERT: D 371 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 542 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7335 (mtm) REVERT: D 549 ASN cc_start: 0.8108 (p0) cc_final: 0.7163 (m-40) REVERT: D 607 LYS cc_start: 0.7698 (mttm) cc_final: 0.7343 (mmtm) REVERT: D 617 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 716 TYR cc_start: 0.7541 (m-10) cc_final: 0.6933 (m-80) REVERT: E 331 TYR cc_start: 0.5978 (p90) cc_final: 0.5731 (p90) REVERT: E 529 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7291 (ptt90) REVERT: E 599 ASP cc_start: 0.5829 (m-30) cc_final: 0.5475 (m-30) REVERT: E 601 MET cc_start: 0.6085 (mmm) cc_final: 0.5587 (tmm) REVERT: E 666 GLN cc_start: 0.7642 (mt0) cc_final: 0.7357 (mt0) REVERT: E 695 PHE cc_start: 0.8350 (t80) cc_final: 0.7845 (t80) REVERT: F 602 MET cc_start: 0.8033 (tpp) cc_final: 0.7716 (tpp) outliers start: 69 outliers final: 47 residues processed: 344 average time/residue: 0.2899 time to fit residues: 155.3995 Evaluate side-chains 341 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 501 MET Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 0.0470 chunk 193 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 229 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS B 328 GLN B 617 GLN C 645 ASN C 653 GLN ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN E 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19492 Z= 0.182 Angle : 0.599 7.355 26645 Z= 0.291 Chirality : 0.044 0.180 3185 Planarity : 0.004 0.049 3236 Dihedral : 14.828 157.450 3099 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.04 % Allowed : 14.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.69 (0.17), residues: 2346 helix: -0.07 (0.18), residues: 923 sheet: -1.91 (0.26), residues: 360 loop : -1.73 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 530 HIS 0.003 0.001 HIS D 512 PHE 0.014 0.001 PHE C 597 TYR 0.014 0.001 TYR A 432 ARG 0.012 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 322 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7795 (mtm-85) REVERT: A 501 MET cc_start: 0.8882 (mpp) cc_final: 0.8597 (mpp) REVERT: B 370 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9071 (pt) REVERT: B 503 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6832 (mm-30) REVERT: B 523 GLU cc_start: 0.7831 (mp0) cc_final: 0.7612 (mp0) REVERT: D 339 MET cc_start: 0.7676 (tpp) cc_final: 0.7312 (tpp) REVERT: D 371 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 542 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7279 (mtm) REVERT: D 549 ASN cc_start: 0.8137 (p0) cc_final: 0.7138 (m-40) REVERT: D 567 LEU cc_start: 0.7589 (mp) cc_final: 0.7170 (tp) REVERT: D 607 LYS cc_start: 0.7710 (mttm) cc_final: 0.7167 (mmtm) REVERT: D 617 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7418 (tm-30) REVERT: D 690 ARG cc_start: 0.8215 (ttt180) cc_final: 0.7989 (ttt180) REVERT: E 477 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7259 (t0) REVERT: E 529 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7302 (ptt90) REVERT: E 601 MET cc_start: 0.6020 (mmm) cc_final: 0.5606 (tmm) REVERT: E 666 GLN cc_start: 0.7675 (mt0) cc_final: 0.7313 (mt0) REVERT: E 695 PHE cc_start: 0.8307 (t80) cc_final: 0.7886 (t80) REVERT: F 602 MET cc_start: 0.7838 (tpp) cc_final: 0.7557 (tpp) outliers start: 61 outliers final: 41 residues processed: 362 average time/residue: 0.3093 time to fit residues: 170.8740 Evaluate side-chains 337 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 293 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 510 ILE Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 649 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 328 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN C 702 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 477 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19492 Z= 0.240 Angle : 0.634 9.636 26645 Z= 0.307 Chirality : 0.045 0.207 3185 Planarity : 0.005 0.056 3236 Dihedral : 14.755 152.020 3099 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.14 % Allowed : 15.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.57 (0.17), residues: 2346 helix: -0.04 (0.18), residues: 934 sheet: -1.81 (0.26), residues: 359 loop : -1.62 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 530 HIS 0.004 0.001 HIS C 702 PHE 0.031 0.001 PHE C 597 TYR 0.020 0.001 TYR A 331 ARG 0.012 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 300 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5848 (tptt) REVERT: A 450 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7815 (mtm-85) REVERT: A 501 MET cc_start: 0.8879 (mpp) cc_final: 0.8624 (mpp) REVERT: B 370 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9086 (pt) REVERT: B 503 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 523 GLU cc_start: 0.7883 (mp0) cc_final: 0.7610 (mp0) REVERT: B 548 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: B 600 MET cc_start: 0.8793 (ttp) cc_final: 0.8530 (ttp) REVERT: D 339 MET cc_start: 0.7681 (tpp) cc_final: 0.7313 (tpp) REVERT: D 371 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8401 (tm-30) REVERT: D 542 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7268 (mtm) REVERT: D 549 ASN cc_start: 0.8175 (p0) cc_final: 0.7207 (m-40) REVERT: D 567 LEU cc_start: 0.7607 (mp) cc_final: 0.7228 (tp) REVERT: D 607 LYS cc_start: 0.7696 (mttm) cc_final: 0.7186 (mmtm) REVERT: D 617 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7507 (tm-30) REVERT: D 690 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7944 (ttt180) REVERT: E 477 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7319 (t0) REVERT: E 529 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7318 (ptt90) REVERT: E 599 ASP cc_start: 0.6014 (m-30) cc_final: 0.5688 (m-30) REVERT: E 601 MET cc_start: 0.6065 (mmm) cc_final: 0.5632 (tmm) REVERT: E 666 GLN cc_start: 0.7698 (mt0) cc_final: 0.7404 (mt0) REVERT: E 695 PHE cc_start: 0.8339 (t80) cc_final: 0.7888 (t80) REVERT: F 602 MET cc_start: 0.7828 (tpp) cc_final: 0.7540 (tpp) outliers start: 63 outliers final: 47 residues processed: 337 average time/residue: 0.2992 time to fit residues: 154.3387 Evaluate side-chains 343 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 415 ASN Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 ASN Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 193 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19492 Z= 0.189 Angle : 0.630 11.665 26645 Z= 0.304 Chirality : 0.045 0.205 3185 Planarity : 0.005 0.058 3236 Dihedral : 14.642 144.140 3099 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.59 % Allowed : 16.22 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.43 (0.18), residues: 2346 helix: 0.05 (0.18), residues: 931 sheet: -1.68 (0.26), residues: 359 loop : -1.54 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 530 HIS 0.014 0.001 HIS C 702 PHE 0.014 0.001 PHE D 597 TYR 0.027 0.001 TYR F 432 ARG 0.013 0.000 ARG F 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 312 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5637 (tptt) REVERT: A 450 ARG cc_start: 0.8203 (ptp-170) cc_final: 0.7794 (mtm-85) REVERT: A 501 MET cc_start: 0.8841 (mpp) cc_final: 0.8620 (mpp) REVERT: B 331 TYR cc_start: 0.7337 (m-10) cc_final: 0.7132 (m-10) REVERT: B 370 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9065 (pt) REVERT: B 503 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6864 (mm-30) REVERT: B 523 GLU cc_start: 0.7868 (mp0) cc_final: 0.7518 (mp0) REVERT: B 600 MET cc_start: 0.8645 (ttp) cc_final: 0.8400 (ttp) REVERT: D 339 MET cc_start: 0.7673 (tpp) cc_final: 0.7334 (tpp) REVERT: D 371 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 542 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7286 (mtm) REVERT: D 549 ASN cc_start: 0.8158 (p0) cc_final: 0.7238 (m-40) REVERT: D 567 LEU cc_start: 0.7618 (mp) cc_final: 0.7231 (tp) REVERT: D 607 LYS cc_start: 0.7709 (mttm) cc_final: 0.7141 (mmtm) REVERT: D 617 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 690 ARG cc_start: 0.8148 (ttt180) cc_final: 0.7912 (ttt180) REVERT: E 477 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7407 (t0) REVERT: E 529 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7299 (ptt90) REVERT: E 601 MET cc_start: 0.6185 (mmm) cc_final: 0.5602 (tmm) REVERT: E 666 GLN cc_start: 0.7820 (mt0) cc_final: 0.7545 (mt0) REVERT: E 695 PHE cc_start: 0.8324 (t80) cc_final: 0.7883 (t80) REVERT: F 602 MET cc_start: 0.7867 (tpp) cc_final: 0.7587 (tpp) outliers start: 52 outliers final: 43 residues processed: 344 average time/residue: 0.3033 time to fit residues: 160.1180 Evaluate side-chains 328 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 281 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN C 477 ASN C 702 HIS ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19492 Z= 0.299 Angle : 0.669 9.962 26645 Z= 0.325 Chirality : 0.046 0.170 3185 Planarity : 0.005 0.064 3236 Dihedral : 14.648 142.583 3099 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.54 % Allowed : 16.52 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.47 (0.17), residues: 2346 helix: -0.02 (0.18), residues: 943 sheet: -1.67 (0.27), residues: 355 loop : -1.53 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 530 HIS 0.019 0.001 HIS C 702 PHE 0.024 0.002 PHE D 423 TYR 0.026 0.002 TYR F 432 ARG 0.013 0.001 ARG F 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 290 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5691 (tptt) REVERT: A 450 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7825 (mtm-85) REVERT: A 501 MET cc_start: 0.8827 (mpp) cc_final: 0.8568 (mpp) REVERT: B 370 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9071 (pt) REVERT: B 503 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 600 MET cc_start: 0.8686 (ttp) cc_final: 0.8417 (ttp) REVERT: C 550 LEU cc_start: 0.8924 (tt) cc_final: 0.8710 (tp) REVERT: D 371 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 542 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7257 (mtm) REVERT: D 549 ASN cc_start: 0.8112 (p0) cc_final: 0.7244 (m-40) REVERT: D 567 LEU cc_start: 0.7645 (mp) cc_final: 0.7252 (tp) REVERT: D 607 LYS cc_start: 0.7723 (mttm) cc_final: 0.7296 (mppt) REVERT: D 617 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7481 (tm-30) REVERT: E 477 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7553 (t0) REVERT: E 529 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7345 (ptt90) REVERT: E 599 ASP cc_start: 0.5999 (m-30) cc_final: 0.5674 (m-30) REVERT: E 601 MET cc_start: 0.6219 (mmm) cc_final: 0.5554 (tmm) REVERT: E 695 PHE cc_start: 0.8415 (t80) cc_final: 0.7843 (t80) REVERT: E 720 ILE cc_start: 0.6869 (mp) cc_final: 0.6437 (mp) outliers start: 51 outliers final: 42 residues processed: 322 average time/residue: 0.2851 time to fit residues: 142.7322 Evaluate side-chains 326 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 539 TYR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 702 HIS Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain E residue 429 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 539 TYR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 600 MET Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 526 ASN Chi-restraints excluded: chain F residue 630 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 189 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102990 restraints weight = 29369.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104387 restraints weight = 20891.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105202 restraints weight = 16839.525| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19492 Z= 0.237 Angle : 0.646 10.024 26645 Z= 0.315 Chirality : 0.045 0.169 3185 Planarity : 0.005 0.061 3236 Dihedral : 14.588 139.203 3099 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.50 % Allowed : 16.92 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.39 (0.18), residues: 2346 helix: 0.04 (0.18), residues: 933 sheet: -1.63 (0.27), residues: 355 loop : -1.46 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 530 HIS 0.004 0.001 HIS A 360 PHE 0.021 0.001 PHE D 423 TYR 0.026 0.001 TYR F 432 ARG 0.013 0.000 ARG F 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.85 seconds wall clock time: 74 minutes 58.26 seconds (4498.26 seconds total)