Starting phenix.real_space_refine on Mon Jul 22 01:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s94_40236/07_2024/8s94_40236_neut.cif" } resolution = 3.94 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= -0.001 sd= 0.038 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 12 5.49 5 Mg 6 5.21 5 S 81 5.16 5 C 10230 2.51 5 N 2841 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 588": "OD1" <-> "OD2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ASP 455": "OD1" <-> "OD2" Residue "C ASP 521": "OD1" <-> "OD2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 407": "OD1" <-> "OD2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F ASP 557": "OD1" <-> "OD2" Residue "F GLU 637": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B ASP 588": "OD1" <-> "OD2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E ASP 540": "OD1" <-> "OD2" Residue "E ASP 557": "OD1" <-> "OD2" Residue "E PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 622": "OE1" <-> "OE2" Residue "E GLU 637": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16305 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "D" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "F" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "E" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Chain: "A" 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} Chain: "D" 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} Chain: "C" 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} 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} Chain: "B" 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} Chain: "E" 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: 8.72, per 1000 atoms: 0.53 Number of scatterers: 16305 At special positions: 0 Unit cell: (150.96, 149.85, 69.93, 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 81 16.00 P 12 15.00 Mg 6 11.99 O 3135 8.00 N 2841 7.00 C 10230 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: 5.69 Conformation dependent library (CDL) restraints added in 2.7 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 48.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.854A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.566A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.574A pdb=" N GLU A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.818A pdb=" N LEU A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 3.815A pdb=" N ARG A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.794A pdb=" N LYS A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 701 removed outlier: 4.123A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.572A pdb=" N GLU A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.026A pdb=" N GLU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 4.104A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.720A pdb=" N TYR D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 removed outlier: 4.516A pdb=" N GLY D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.873A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 330 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.809A pdb=" N LYS D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.787A pdb=" N LEU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 4.048A pdb=" N ASP D 407 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.735A pdb=" N GLU D 432 " --> pdb=" O HIS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 468 through 473 removed outlier: 3.602A pdb=" N ASN D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 539 through 554 removed outlier: 3.868A pdb=" N ASN D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN D 544 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 569 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 589 through 604 removed outlier: 3.888A pdb=" N SER D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 removed outlier: 3.931A pdb=" N GLN D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 639 " --> pdb=" O ILE D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.813A pdb=" N LEU D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 646 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.508A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.668A pdb=" N LYS C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.602A pdb=" N ALA C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 537 removed outlier: 3.577A pdb=" N GLN C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.604A pdb=" N GLU C 607 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 613 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 674 removed outlier: 3.702A pdb=" N LYS C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 669 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 671 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 672 " --> pdb=" O LYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 701 removed outlier: 4.030A pdb=" N ARG C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.662A pdb=" N GLU C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.309A pdb=" N SER C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.620A pdb=" N TYR F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 309 removed outlier: 3.958A pdb=" N ARG F 303 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 removed outlier: 4.211A pdb=" N ALA F 325 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.729A pdb=" N PHE F 361 " --> pdb=" O GLY F 357 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR F 369 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.698A pdb=" N LEU F 385 " --> pdb=" O THR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.738A pdb=" N ASP F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 427 through 433 removed outlier: 3.534A pdb=" N GLU F 432 " --> pdb=" O HIS F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 468 through 473 removed outlier: 3.584A pdb=" N ASN F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.829A pdb=" N SER F 481 " --> pdb=" O PRO F 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG F 482 " --> pdb=" O LEU F 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 478 through 482' Processing helix chain 'F' and resid 496 through 508 removed outlier: 3.509A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 531 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.878A pdb=" N ASN F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 569 Processing helix chain 'F' and resid 571 through 577 removed outlier: 3.682A pdb=" N ALA F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 604 removed outlier: 3.506A pdb=" N MET F 604 " --> pdb=" O MET F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 639 removed outlier: 4.099A pdb=" N GLN F 627 " --> pdb=" O ASN F 623 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 637 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS F 638 " --> pdb=" O LEU F 634 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 removed outlier: 3.714A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU F 647 " --> pdb=" O SER F 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.636A pdb=" N LYS B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.586A pdb=" N GLU B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 613 removed outlier: 3.528A pdb=" N GLU B 607 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 613 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.730A pdb=" N LYS B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 671 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 4.048A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.607A pdb=" N GLU B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 748 through 753 removed outlier: 4.077A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.717A pdb=" N TYR E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.480A pdb=" N GLY E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 330 removed outlier: 3.564A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY E 330 " --> pdb=" O MET E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.764A pdb=" N LYS E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.653A pdb=" N LEU E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.814A pdb=" N ASP E 407 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 426 Processing helix chain 'E' and resid 427 through 433 removed outlier: 3.799A pdb=" N GLU E 432 " --> pdb=" O HIS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 468 through 473 removed outlier: 3.515A pdb=" N ASN E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 520 through 531 Processing helix chain 'E' and resid 539 through 554 removed outlier: 3.872A pdb=" N ASN E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 569 Processing helix chain 'E' and resid 575 through 583 removed outlier: 3.507A pdb=" N ALA E 580 " --> pdb=" O ALA E 576 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 581 " --> pdb=" O GLU E 577 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET E 583 " --> pdb=" O HIS E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 604 removed outlier: 3.821A pdb=" N SER E 598 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 599 " --> pdb=" O THR E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 639 removed outlier: 3.905A pdb=" N GLN E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.727A pdb=" N LEU E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E 646 " --> pdb=" O GLN E 642 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 647 " --> pdb=" O SER E 643 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.691A pdb=" N GLY A 454 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA3, first strand: chain 'D' and resid 334 through 335 removed outlier: 4.493A pdb=" N ARG D 334 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.909A pdb=" N VAL D 373 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS D 412 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 375 " --> pdb=" O CYS D 412 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D 414 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 452 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 454 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 456 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 348 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR D 457 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 350 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU D 349 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU D 489 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 351 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 435 through 438 removed outlier: 3.758A pdb=" N LEU D 447 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 438 " --> pdb=" O CYS D 445 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 477 through 478 removed outlier: 7.203A pdb=" N VAL C 477 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 559 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 454 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'F' and resid 334 through 335 removed outlier: 4.537A pdb=" N ARG F 334 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 342 " --> pdb=" O ARG F 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 409 through 414 removed outlier: 3.813A pdb=" N THR F 452 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 454 " --> pdb=" O CYS F 411 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 456 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY F 352 " --> pdb=" O THR F 457 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 349 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU F 489 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL F 351 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 435 through 438 removed outlier: 3.806A pdb=" N LEU F 447 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 438 " --> pdb=" O CYS F 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.522A pdb=" N ALA B 559 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 454 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB4, first strand: chain 'E' and resid 372 through 374 removed outlier: 3.777A pdb=" N VAL E 373 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS E 412 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 452 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 454 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 456 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY E 352 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 349 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU E 489 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 351 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 435 through 438 removed outlier: 3.803A pdb=" N LEU E 447 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 438 " --> pdb=" O CYS E 445 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5439 1.34 - 1.46: 3343 1.46 - 1.58: 7625 1.58 - 1.70: 18 1.70 - 1.82: 126 Bond restraints: 16551 Sorted by residual: bond pdb=" CB LYS A 578 " pdb=" CG LYS A 578 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS F 460 " pdb=" CG LYS F 460 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CB GLN B 394 " pdb=" CG GLN B 394 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" CG LYS F 460 " pdb=" CD LYS F 460 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CA LEU E 480 " pdb=" CB LEU E 480 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.31e-02 5.83e+03 1.30e+00 ... (remaining 16546 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.73: 440 106.73 - 113.99: 9643 113.99 - 121.24: 7908 121.24 - 128.50: 4338 128.50 - 135.75: 78 Bond angle restraints: 22407 Sorted by residual: angle pdb=" N VAL F 541 " pdb=" CA VAL F 541 " pdb=" C VAL F 541 " ideal model delta sigma weight residual 112.98 106.45 6.53 1.25e+00 6.40e-01 2.73e+01 angle pdb=" N VAL E 541 " pdb=" CA VAL E 541 " pdb=" C VAL E 541 " ideal model delta sigma weight residual 112.98 106.60 6.38 1.25e+00 6.40e-01 2.61e+01 angle pdb=" N VAL D 541 " pdb=" CA VAL D 541 " pdb=" C VAL D 541 " ideal model delta sigma weight residual 112.98 106.86 6.12 1.25e+00 6.40e-01 2.40e+01 angle pdb=" N SER E 481 " pdb=" CA SER E 481 " pdb=" C SER E 481 " ideal model delta sigma weight residual 114.62 109.34 5.28 1.14e+00 7.69e-01 2.14e+01 angle pdb=" CB LYS F 460 " pdb=" CG LYS F 460 " pdb=" CD LYS F 460 " ideal model delta sigma weight residual 111.30 120.81 -9.51 2.30e+00 1.89e-01 1.71e+01 ... (remaining 22402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8714 17.90 - 35.80: 1077 35.80 - 53.71: 244 53.71 - 71.61: 41 71.61 - 89.51: 28 Dihedral angle restraints: 10104 sinusoidal: 4101 harmonic: 6003 Sorted by residual: dihedral pdb=" CA LEU D 639 " pdb=" C LEU D 639 " pdb=" N GLU D 640 " pdb=" CA GLU D 640 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU F 639 " pdb=" C LEU F 639 " pdb=" N GLU F 640 " pdb=" CA GLU F 640 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU E 518 " pdb=" C LEU E 518 " pdb=" N TRP E 519 " pdb=" CA TRP E 519 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1985 0.044 - 0.087: 495 0.087 - 0.131: 115 0.131 - 0.175: 15 0.175 - 0.218: 3 Chirality restraints: 2613 Sorted by residual: chirality pdb=" CB ILE C 658 " pdb=" CA ILE C 658 " pdb=" CG1 ILE C 658 " pdb=" CG2 ILE C 658 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE B 658 " pdb=" CA ILE B 658 " pdb=" CG1 ILE B 658 " pdb=" CG2 ILE B 658 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU D 639 " pdb=" CB LEU D 639 " pdb=" CD1 LEU D 639 " pdb=" CD2 LEU D 639 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 2610 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 408 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C ASN C 408 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN C 408 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 409 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 564 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C THR D 564 " -0.030 2.00e-02 2.50e+03 pdb=" O THR D 564 " 0.011 2.00e-02 2.50e+03 pdb=" N THR D 565 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 369 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO E 370 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 370 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 370 " -0.024 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 992 2.73 - 3.28: 16003 3.28 - 3.82: 23406 3.82 - 4.36: 26332 4.36 - 4.90: 47483 Nonbonded interactions: 114216 Sorted by model distance: nonbonded pdb=" OD1 ASP D 484 " pdb=" OG SER D 571 " model vdw 2.192 2.440 nonbonded pdb=" OD1 ASP E 484 " pdb=" OG SER E 571 " model vdw 2.193 2.440 nonbonded pdb=" OD1 ASP C 588 " pdb=" OG SER C 715 " model vdw 2.222 2.440 nonbonded pdb=" N GLN F 285 " pdb=" OE1 GLN F 285 " model vdw 2.242 2.520 nonbonded pdb=" O SER D 380 " pdb=" NZ LYS D 420 " model vdw 2.259 2.520 ... (remaining 114211 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.820 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16551 Z= 0.178 Angle : 0.749 12.654 22407 Z= 0.384 Chirality : 0.041 0.218 2613 Planarity : 0.004 0.043 2856 Dihedral : 16.597 89.511 6228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.32 % Favored : 90.14 % Rotamer: Outliers : 0.11 % Allowed : 15.85 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 2049 helix: -0.47 (0.19), residues: 906 sheet: -0.49 (0.39), residues: 177 loop : -2.48 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.002 0.000 HIS E 579 PHE 0.011 0.001 PHE E 504 TYR 0.016 0.001 TYR E 294 ARG 0.005 0.000 ARG D 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: D 650 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7675 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 234 average time/residue: 0.2750 time to fit residues: 95.5596 Evaluate side-chains 228 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain B residue 661 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 0.0970 chunk 61 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** C 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 536 GLN B 608 HIS ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16551 Z= 0.198 Angle : 0.664 17.003 22407 Z= 0.309 Chirality : 0.041 0.191 2613 Planarity : 0.004 0.039 2856 Dihedral : 5.773 55.272 2316 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.05 % Favored : 89.41 % Rotamer: Outliers : 2.77 % Allowed : 15.79 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.19), residues: 2049 helix: -0.30 (0.19), residues: 918 sheet: -0.81 (0.35), residues: 201 loop : -2.46 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 292 HIS 0.003 0.000 HIS B 449 PHE 0.011 0.001 PHE E 504 TYR 0.014 0.001 TYR A 669 ARG 0.006 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 394 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 512 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: A 668 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8277 (ttpt) REVERT: A 736 ASP cc_start: 0.8446 (m-30) cc_final: 0.8222 (m-30) REVERT: D 375 THR cc_start: 0.8918 (t) cc_final: 0.8691 (p) REVERT: C 394 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 599 GLU cc_start: 0.7439 (tp30) cc_final: 0.7135 (tp30) REVERT: F 449 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8593 (t) REVERT: F 622 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6541 (tm-30) REVERT: B 455 ASP cc_start: 0.8502 (m-30) cc_final: 0.8243 (m-30) REVERT: B 736 ASP cc_start: 0.8373 (m-30) cc_final: 0.8158 (m-30) REVERT: E 374 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7808 (tp) REVERT: E 600 MET cc_start: 0.8102 (tpt) cc_final: 0.7867 (tpp) outliers start: 49 outliers final: 30 residues processed: 254 average time/residue: 0.2662 time to fit residues: 101.5631 Evaluate side-chains 249 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 520 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 576 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16551 Z= 0.217 Angle : 0.659 14.453 22407 Z= 0.308 Chirality : 0.041 0.179 2613 Planarity : 0.004 0.039 2856 Dihedral : 5.805 55.554 2314 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.30 % Favored : 89.17 % Rotamer: Outliers : 3.40 % Allowed : 17.77 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 2049 helix: -0.26 (0.19), residues: 924 sheet: -0.98 (0.35), residues: 207 loop : -2.44 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 292 HIS 0.003 0.001 HIS E 347 PHE 0.011 0.001 PHE E 504 TYR 0.015 0.001 TYR A 669 ARG 0.006 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 394 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 512 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: A 736 ASP cc_start: 0.8428 (m-30) cc_final: 0.8141 (m-30) REVERT: D 375 THR cc_start: 0.8990 (t) cc_final: 0.8710 (p) REVERT: D 424 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6955 (ttm-80) REVERT: D 600 MET cc_start: 0.8474 (tpp) cc_final: 0.8204 (tpt) REVERT: D 650 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7577 (ttm-80) REVERT: C 394 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 455 ASP cc_start: 0.8513 (m-30) cc_final: 0.8134 (m-30) REVERT: C 599 GLU cc_start: 0.7596 (tp30) cc_final: 0.7284 (tp30) REVERT: C 664 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7895 (tp40) REVERT: C 736 ASP cc_start: 0.8371 (m-30) cc_final: 0.8045 (m-30) REVERT: F 289 GLU cc_start: 0.8542 (tp30) cc_final: 0.8293 (tp30) REVERT: F 449 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8430 (t) REVERT: F 540 ASP cc_start: 0.8183 (t0) cc_final: 0.7657 (t0) REVERT: F 622 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6626 (tm-30) REVERT: F 650 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7480 (mtp85) REVERT: B 455 ASP cc_start: 0.8462 (m-30) cc_final: 0.8165 (m-30) REVERT: B 528 GLN cc_start: 0.8103 (tt0) cc_final: 0.7891 (tt0) REVERT: B 736 ASP cc_start: 0.8388 (m-30) cc_final: 0.8059 (m-30) REVERT: E 368 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8119 (mt) REVERT: E 374 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7875 (tp) REVERT: E 424 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6511 (ttm-80) outliers start: 60 outliers final: 39 residues processed: 254 average time/residue: 0.2548 time to fit residues: 97.7192 Evaluate side-chains 253 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 649 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 576 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16551 Z= 0.140 Angle : 0.612 13.160 22407 Z= 0.285 Chirality : 0.039 0.195 2613 Planarity : 0.003 0.036 2856 Dihedral : 5.581 53.185 2314 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.13 % Favored : 90.39 % Rotamer: Outliers : 3.17 % Allowed : 19.52 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 2049 helix: -0.00 (0.19), residues: 915 sheet: -0.93 (0.34), residues: 207 loop : -2.41 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.013 0.001 TYR D 294 ARG 0.007 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 1.615 Fit side-chains REVERT: A 394 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 424 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6905 (ttm-80) REVERT: D 600 MET cc_start: 0.8449 (tpp) cc_final: 0.8155 (tpt) REVERT: D 650 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7568 (mtp85) REVERT: C 394 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 455 ASP cc_start: 0.8488 (m-30) cc_final: 0.8123 (m-30) REVERT: C 512 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: C 599 GLU cc_start: 0.7433 (tp30) cc_final: 0.7149 (tp30) REVERT: C 664 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7749 (tp40) REVERT: C 736 ASP cc_start: 0.8314 (m-30) cc_final: 0.7996 (m-30) REVERT: F 289 GLU cc_start: 0.8316 (tp30) cc_final: 0.8071 (tp30) REVERT: F 449 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8479 (t) REVERT: F 622 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6608 (tm-30) REVERT: F 650 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7457 (mtp85) REVERT: B 455 ASP cc_start: 0.8453 (m-30) cc_final: 0.8126 (m-30) REVERT: B 736 ASP cc_start: 0.8388 (m-30) cc_final: 0.8038 (m-30) REVERT: E 371 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7266 (ttm110) REVERT: E 424 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6501 (ttm-80) REVERT: E 639 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6727 (pp) outliers start: 56 outliers final: 34 residues processed: 256 average time/residue: 0.2611 time to fit residues: 101.8681 Evaluate side-chains 244 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 576 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16551 Z= 0.233 Angle : 0.664 15.313 22407 Z= 0.309 Chirality : 0.041 0.185 2613 Planarity : 0.004 0.040 2856 Dihedral : 5.710 53.431 2314 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.54 % Favored : 88.97 % Rotamer: Outliers : 4.41 % Allowed : 19.35 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 2049 helix: -0.14 (0.19), residues: 924 sheet: -1.03 (0.34), residues: 207 loop : -2.39 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 292 HIS 0.002 0.001 HIS A 417 PHE 0.011 0.001 PHE B 429 TYR 0.015 0.001 TYR A 669 ARG 0.005 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 201 time to evaluate : 1.887 Fit side-chains REVERT: A 394 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 736 ASP cc_start: 0.8424 (m-30) cc_final: 0.8115 (m-30) REVERT: D 424 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6922 (ttm-80) REVERT: D 600 MET cc_start: 0.8519 (tpp) cc_final: 0.8205 (tpt) REVERT: D 650 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7569 (mtp85) REVERT: C 394 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 512 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: C 599 GLU cc_start: 0.7634 (tp30) cc_final: 0.7356 (tp30) REVERT: C 664 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7842 (tp40) REVERT: C 736 ASP cc_start: 0.8373 (m-30) cc_final: 0.8081 (m-30) REVERT: F 434 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: F 622 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6670 (tm-30) REVERT: F 650 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7516 (mtp85) REVERT: B 736 ASP cc_start: 0.8443 (m-30) cc_final: 0.8128 (m-30) REVERT: E 374 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7975 (tp) REVERT: E 424 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6476 (ttm-80) outliers start: 78 outliers final: 49 residues processed: 255 average time/residue: 0.2709 time to fit residues: 103.7129 Evaluate side-chains 250 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16551 Z= 0.202 Angle : 0.653 15.345 22407 Z= 0.304 Chirality : 0.040 0.184 2613 Planarity : 0.004 0.040 2856 Dihedral : 5.680 51.933 2314 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.91 % Favored : 89.65 % Rotamer: Outliers : 4.02 % Allowed : 19.98 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 2049 helix: -0.13 (0.19), residues: 945 sheet: -1.10 (0.34), residues: 207 loop : -2.47 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 292 HIS 0.003 0.000 HIS E 347 PHE 0.011 0.001 PHE E 504 TYR 0.014 0.001 TYR D 294 ARG 0.010 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 1.819 Fit side-chains REVERT: A 394 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 668 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8337 (ttmm) REVERT: A 736 ASP cc_start: 0.8500 (m-30) cc_final: 0.8187 (m-30) REVERT: D 424 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6987 (ttm-80) REVERT: D 600 MET cc_start: 0.8453 (tpp) cc_final: 0.8144 (tpt) REVERT: D 650 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7599 (mtp85) REVERT: C 394 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 512 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: C 530 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8181 (pp) REVERT: C 599 GLU cc_start: 0.7613 (tp30) cc_final: 0.7398 (tp30) REVERT: C 736 ASP cc_start: 0.8365 (m-30) cc_final: 0.8080 (m-30) REVERT: F 289 GLU cc_start: 0.8383 (tp30) cc_final: 0.8087 (tp30) REVERT: F 434 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: F 622 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6745 (tm-30) REVERT: F 650 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7453 (mtp85) REVERT: B 528 GLN cc_start: 0.8314 (tt0) cc_final: 0.8090 (tt0) REVERT: B 584 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8840 (tp) REVERT: B 736 ASP cc_start: 0.8447 (m-30) cc_final: 0.8137 (m-30) REVERT: E 374 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7948 (tp) REVERT: E 424 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6513 (ttm-80) outliers start: 71 outliers final: 52 residues processed: 254 average time/residue: 0.2704 time to fit residues: 103.0432 Evaluate side-chains 252 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 192 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.0020 chunk 22 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN E 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16551 Z= 0.154 Angle : 0.633 14.605 22407 Z= 0.292 Chirality : 0.039 0.199 2613 Planarity : 0.003 0.048 2856 Dihedral : 5.502 49.841 2314 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.42 % Favored : 90.14 % Rotamer: Outliers : 4.02 % Allowed : 20.43 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 2049 helix: 0.03 (0.19), residues: 939 sheet: -1.04 (0.34), residues: 207 loop : -2.47 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.015 0.001 TYR E 294 ARG 0.012 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 201 time to evaluate : 1.798 Fit side-chains REVERT: A 394 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 668 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8337 (ttmm) REVERT: A 736 ASP cc_start: 0.8466 (m-30) cc_final: 0.8141 (m-30) REVERT: D 424 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6991 (ttm-80) REVERT: D 600 MET cc_start: 0.8391 (tpp) cc_final: 0.8123 (tpt) REVERT: C 394 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 512 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: C 530 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8139 (pp) REVERT: C 599 GLU cc_start: 0.7517 (tp30) cc_final: 0.7314 (tp30) REVERT: C 736 ASP cc_start: 0.8326 (m-30) cc_final: 0.8033 (m-30) REVERT: F 289 GLU cc_start: 0.8373 (tp30) cc_final: 0.8062 (tp30) REVERT: F 434 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: F 449 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8477 (t) REVERT: F 622 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6691 (tm-30) REVERT: F 650 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7516 (mtp85) REVERT: F 653 GLU cc_start: 0.7937 (tp30) cc_final: 0.7541 (tt0) REVERT: B 464 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8180 (tt) REVERT: B 528 GLN cc_start: 0.8332 (tt0) cc_final: 0.8096 (tt0) REVERT: B 584 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8814 (tp) REVERT: B 736 ASP cc_start: 0.8398 (m-30) cc_final: 0.8190 (m-30) REVERT: E 371 ARG cc_start: 0.7398 (ttm110) cc_final: 0.6966 (ttm170) REVERT: E 424 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6412 (ttm-80) outliers start: 71 outliers final: 52 residues processed: 250 average time/residue: 0.2894 time to fit residues: 110.2278 Evaluate side-chains 252 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 191 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 0.0370 chunk 178 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16551 Z= 0.177 Angle : 0.643 14.601 22407 Z= 0.298 Chirality : 0.040 0.195 2613 Planarity : 0.003 0.042 2856 Dihedral : 5.467 49.030 2314 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.52 % Favored : 90.04 % Rotamer: Outliers : 3.74 % Allowed : 21.11 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 2049 helix: 0.07 (0.19), residues: 939 sheet: -1.04 (0.33), residues: 246 loop : -2.37 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.016 0.001 TYR D 294 ARG 0.010 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 193 time to evaluate : 1.807 Fit side-chains REVERT: A 394 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 668 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8344 (ttmm) REVERT: A 736 ASP cc_start: 0.8482 (m-30) cc_final: 0.8155 (m-30) REVERT: D 424 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6979 (ttm-80) REVERT: D 600 MET cc_start: 0.8443 (tpp) cc_final: 0.8182 (tpt) REVERT: D 601 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8049 (tt0) REVERT: D 650 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7562 (mtp85) REVERT: C 394 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 512 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: C 530 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8166 (pp) REVERT: C 599 GLU cc_start: 0.7611 (tp30) cc_final: 0.7377 (tp30) REVERT: C 736 ASP cc_start: 0.8271 (m-30) cc_final: 0.7954 (m-30) REVERT: F 289 GLU cc_start: 0.8390 (tp30) cc_final: 0.8062 (tp30) REVERT: F 434 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: F 449 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8456 (t) REVERT: F 622 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6712 (tm-30) REVERT: F 650 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7485 (mtp85) REVERT: F 653 GLU cc_start: 0.7900 (tp30) cc_final: 0.7465 (tt0) REVERT: B 464 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 528 GLN cc_start: 0.8297 (tt0) cc_final: 0.8092 (tt0) REVERT: B 579 MET cc_start: 0.7530 (mtt) cc_final: 0.7290 (mtt) REVERT: B 584 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8799 (tp) REVERT: B 736 ASP cc_start: 0.8355 (m-30) cc_final: 0.8117 (m-30) REVERT: E 374 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7927 (tp) REVERT: E 424 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6425 (ttm-80) outliers start: 66 outliers final: 52 residues processed: 243 average time/residue: 0.2588 time to fit residues: 95.4526 Evaluate side-chains 251 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 189 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN B 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16551 Z= 0.177 Angle : 0.641 14.667 22407 Z= 0.297 Chirality : 0.040 0.174 2613 Planarity : 0.003 0.050 2856 Dihedral : 5.424 47.810 2314 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.47 % Favored : 90.09 % Rotamer: Outliers : 3.68 % Allowed : 21.84 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 2049 helix: 0.14 (0.19), residues: 936 sheet: -1.01 (0.33), residues: 246 loop : -2.37 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.016 0.001 TYR E 294 ARG 0.014 0.000 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 195 time to evaluate : 1.637 Fit side-chains REVERT: A 394 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 668 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8347 (ttmm) REVERT: A 736 ASP cc_start: 0.8453 (m-30) cc_final: 0.8132 (m-30) REVERT: D 296 LYS cc_start: 0.8882 (tppp) cc_final: 0.8621 (tppt) REVERT: D 600 MET cc_start: 0.8451 (tpp) cc_final: 0.8179 (tpt) REVERT: D 650 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7529 (mtp85) REVERT: C 394 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 512 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: C 530 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7850 (pp) REVERT: C 599 GLU cc_start: 0.7611 (tp30) cc_final: 0.7370 (tp30) REVERT: C 736 ASP cc_start: 0.8319 (m-30) cc_final: 0.8052 (m-30) REVERT: F 289 GLU cc_start: 0.8402 (tp30) cc_final: 0.8068 (tp30) REVERT: F 449 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8448 (t) REVERT: F 622 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6722 (tm-30) REVERT: F 650 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7486 (mtp85) REVERT: F 653 GLU cc_start: 0.7960 (tp30) cc_final: 0.7517 (tt0) REVERT: B 464 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8259 (tt) REVERT: B 584 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (tp) REVERT: B 736 ASP cc_start: 0.8356 (m-30) cc_final: 0.8111 (m-30) REVERT: E 371 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7025 (ttm170) REVERT: E 374 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (tp) outliers start: 65 outliers final: 53 residues processed: 244 average time/residue: 0.2702 time to fit residues: 102.2012 Evaluate side-chains 249 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.0970 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.0040 chunk 99 optimal weight: 0.0570 chunk 128 optimal weight: 1.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 536 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16551 Z= 0.139 Angle : 0.628 14.220 22407 Z= 0.291 Chirality : 0.039 0.193 2613 Planarity : 0.003 0.056 2856 Dihedral : 5.295 45.743 2314 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.78 % Favored : 90.78 % Rotamer: Outliers : 3.06 % Allowed : 22.24 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 2049 helix: 0.30 (0.19), residues: 933 sheet: -0.95 (0.33), residues: 246 loop : -2.30 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 292 HIS 0.002 0.000 HIS B 527 PHE 0.010 0.001 PHE E 504 TYR 0.019 0.001 TYR D 294 ARG 0.013 0.000 ARG E 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 1.849 Fit side-chains REVERT: A 394 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 668 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8335 (ttmm) REVERT: A 736 ASP cc_start: 0.8410 (m-30) cc_final: 0.8078 (m-30) REVERT: D 296 LYS cc_start: 0.8852 (tppp) cc_final: 0.8631 (tppt) REVERT: D 600 MET cc_start: 0.8294 (tpp) cc_final: 0.7983 (tpt) REVERT: D 650 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7520 (mtp85) REVERT: C 394 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 512 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: C 530 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7819 (pp) REVERT: C 599 GLU cc_start: 0.7506 (tp30) cc_final: 0.7271 (tp30) REVERT: C 736 ASP cc_start: 0.8305 (m-30) cc_final: 0.8036 (m-30) REVERT: F 289 GLU cc_start: 0.8332 (tp30) cc_final: 0.7998 (tp30) REVERT: F 449 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8392 (t) REVERT: F 622 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6765 (tm-30) REVERT: F 650 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7472 (mtp85) REVERT: F 653 GLU cc_start: 0.7936 (tp30) cc_final: 0.7512 (tt0) REVERT: B 584 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8789 (tp) REVERT: E 371 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6976 (ttm170) outliers start: 54 outliers final: 47 residues processed: 239 average time/residue: 0.2691 time to fit residues: 97.9225 Evaluate side-chains 249 residues out of total 1767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.844 > 50: distance: 10 - 15: 33.376 distance: 16 - 17: 10.367 distance: 16 - 19: 55.545 distance: 17 - 18: 31.583 distance: 17 - 24: 8.900 distance: 19 - 20: 37.242 distance: 20 - 21: 40.391 distance: 25 - 26: 41.668 distance: 26 - 27: 31.217 distance: 26 - 28: 40.298 distance: 28 - 29: 19.760 distance: 29 - 30: 7.427 distance: 30 - 31: 42.665 distance: 32 - 33: 10.414 distance: 33 - 34: 40.133 distance: 34 - 36: 58.253 distance: 38 - 39: 40.192 distance: 38 - 41: 20.425 distance: 39 - 40: 6.583 distance: 39 - 49: 62.613 distance: 41 - 42: 18.317 distance: 43 - 45: 4.980 distance: 44 - 46: 23.316 distance: 45 - 47: 12.868 distance: 46 - 47: 8.496 distance: 47 - 48: 44.797 distance: 49 - 50: 41.217 distance: 50 - 51: 18.940 distance: 50 - 53: 69.380 distance: 51 - 52: 23.948 distance: 51 - 57: 19.816 distance: 53 - 54: 38.862 distance: 58 - 59: 14.032 distance: 59 - 60: 25.506 distance: 59 - 64: 47.228 distance: 64 - 65: 17.175 distance: 65 - 66: 37.494 distance: 65 - 68: 50.055 distance: 66 - 67: 46.581 distance: 66 - 73: 21.362 distance: 69 - 70: 14.831 distance: 70 - 71: 14.020 distance: 70 - 72: 25.004 distance: 73 - 74: 22.490 distance: 74 - 75: 6.741 distance: 74 - 77: 11.801 distance: 78 - 79: 6.888 distance: 79 - 80: 34.786 distance: 79 - 81: 6.333 distance: 83 - 84: 30.370 distance: 83 - 86: 22.130 distance: 84 - 85: 18.263 distance: 84 - 88: 19.864 distance: 86 - 87: 38.244 distance: 88 - 89: 34.589 distance: 89 - 90: 22.673 distance: 89 - 92: 9.987 distance: 90 - 91: 22.152 distance: 90 - 95: 14.281 distance: 91 - 116: 25.893 distance: 92 - 93: 8.486 distance: 92 - 94: 10.306