Starting phenix.real_space_refine on Fri May 10 13:40:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj8_38396/05_2024/8xj8_38396_updated.pdb" } resolution = 2.67 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= -0.002 sd= 0.159 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 15 5.49 5 Mg 3 5.21 5 S 78 5.16 5 C 10127 2.51 5 N 2691 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F GLU 460": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 15904 Number of models: 1 Model: "" Number of chains: 10 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3427 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2990 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 353} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3053 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 360} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2846 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2393 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.60, per 1000 atoms: 0.54 Number of scatterers: 15904 At special positions: 0 Unit cell: (116.748, 124.315, 135.125, 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 78 16.00 P 15 15.00 Mg 3 11.99 O 2990 8.00 N 2691 7.00 C 10127 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: 5.90 Conformation dependent library (CDL) restraints added in 2.8 seconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 24 sheets defined 37.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.726A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.554A pdb=" N ARG A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N HIS A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.584A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 384' Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.544A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 476 through 490 removed outlier: 5.145A pdb=" N LEU A 486 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER A 487 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER A 488 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N CYS A 489 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.511A pdb=" N LYS A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.633A pdb=" N THR A 533 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 4.691A pdb=" N MET A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.524A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 633 through 640 removed outlier: 3.586A pdb=" N ARG A 636 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 638 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 694 through 705 removed outlier: 4.755A pdb=" N PHE A 698 " --> pdb=" O ASP A 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.805A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.637A pdb=" N ARG B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.654A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 384' Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.505A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.529A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 435' Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.977A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.990A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.528A pdb=" N LYS B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.829A pdb=" N THR B 533 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 removed outlier: 5.066A pdb=" N MET B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.550A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 removed outlier: 3.510A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 620' Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.588A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 641' Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.782A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 377 through 384 removed outlier: 3.816A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 384' Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 456 through 468 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.898A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 523 removed outlier: 7.180A pdb=" N ASP C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.950A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 633 through 641 removed outlier: 3.519A pdb=" N ARG C 636 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 639 " --> pdb=" O ARG C 636 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 641 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 694 through 701 removed outlier: 4.704A pdb=" N PHE C 698 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 699 " --> pdb=" O PHE C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.940A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 3.602A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 386 through 397 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 476 through 490 removed outlier: 3.968A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 7.171A pdb=" N ASP D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 removed outlier: 4.430A pdb=" N MET D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 576 Processing helix chain 'D' and resid 615 through 620 removed outlier: 3.939A pdb=" N ARG D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 656 No H-bonds generated for 'chain 'D' and resid 654 through 656' Processing helix chain 'D' and resid 668 through 678 Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 694 through 701 removed outlier: 4.548A pdb=" N PHE D 698 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 699 " --> pdb=" O PHE D 696 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 700 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 4.075A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 381 through 384 removed outlier: 3.661A pdb=" N LEU E 384 " --> pdb=" O SER E 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 381 through 384' Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.505A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 removed outlier: 4.216A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 374 removed outlier: 3.625A pdb=" N ARG F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 384 removed outlier: 3.586A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU F 383 " --> pdb=" O TYR F 379 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 377 through 384' Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 462 through 467 Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 509 through 523 removed outlier: 3.715A pdb=" N GLY F 521 " --> pdb=" O LYS F 517 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N ASP F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F 523 " --> pdb=" O ALA F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.968A pdb=" N THR F 533 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 577 No H-bonds generated for 'chain 'F' and resid 574 through 577' Processing helix chain 'F' and resid 617 through 619 No H-bonds generated for 'chain 'F' and resid 617 through 619' Processing helix chain 'F' and resid 666 through 677 Processing sheet with id= A, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= B, first strand: chain 'A' and resid 412 through 414 Processing sheet with id= C, first strand: chain 'A' and resid 621 through 626 removed outlier: 6.259A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 600 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 501 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 602 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY A 503 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR A 604 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER A 556 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 581 through 583 Processing sheet with id= E, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.577A pdb=" N LYS A 647 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 631 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS A 649 " --> pdb=" O SER A 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= G, first strand: chain 'B' and resid 412 through 414 Processing sheet with id= H, first strand: chain 'B' and resid 621 through 626 removed outlier: 6.168A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 600 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE B 501 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 602 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY B 503 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 604 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= J, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.518A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 649 " --> pdb=" O SER B 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= L, first strand: chain 'C' and resid 412 through 414 Processing sheet with id= M, first strand: chain 'C' and resid 621 through 626 removed outlier: 6.229A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 600 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE C 501 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 602 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY C 503 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR C 604 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= O, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.452A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS C 649 " --> pdb=" O SER C 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 339 through 341 removed outlier: 4.623A pdb=" N HIS D 347 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 412 through 414 Processing sheet with id= R, first strand: chain 'D' and resid 621 through 626 removed outlier: 6.271A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= T, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= U, first strand: chain 'E' and resid 412 through 415 Processing sheet with id= V, first strand: chain 'F' and resid 339 through 341 Processing sheet with id= W, first strand: chain 'F' and resid 412 through 415 Processing sheet with id= X, first strand: chain 'F' and resid 600 through 603 417 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2604 1.30 - 1.43: 4061 1.43 - 1.56: 9429 1.56 - 1.69: 26 1.69 - 1.82: 116 Bond restraints: 16236 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C SER B 455 " pdb=" O SER B 455 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.34e+01 bond pdb=" C PRO B 456 " pdb=" O PRO B 456 " ideal model delta sigma weight residual 1.238 1.174 0.065 1.22e-02 6.72e+03 2.81e+01 ... (remaining 16231 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.58: 223 103.58 - 111.18: 6390 111.18 - 118.78: 6689 118.78 - 126.39: 8459 126.39 - 133.99: 220 Bond angle restraints: 21981 Sorted by residual: angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" CB PRO B 682 " ideal model delta sigma weight residual 103.25 112.09 -8.84 1.05e+00 9.07e-01 7.09e+01 angle pdb=" N PRO B 682 " pdb=" CA PRO B 682 " pdb=" C PRO B 682 " ideal model delta sigma weight residual 112.47 95.97 16.50 2.06e+00 2.36e-01 6.41e+01 angle pdb=" C ILE B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.98e+01 angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 110.35 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.59 16.36 3.00e+00 1.11e-01 2.97e+01 ... (remaining 21976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 8999 23.60 - 47.19: 724 47.19 - 70.79: 148 70.79 - 94.38: 30 94.38 - 117.98: 3 Dihedral angle restraints: 9904 sinusoidal: 4152 harmonic: 5752 Sorted by residual: dihedral pdb=" CA TYR F 428 " pdb=" C TYR F 428 " pdb=" N SER F 429 " pdb=" CA SER F 429 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LYS E 416 " pdb=" C LYS E 416 " pdb=" N ASN E 417 " pdb=" CA ASN E 417 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS F 678 " pdb=" C LYS F 678 " pdb=" N TYR F 679 " pdb=" CA TYR F 679 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2183 0.062 - 0.124: 286 0.124 - 0.186: 8 0.186 - 0.248: 3 0.248 - 0.310: 5 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CA ILE B 681 " pdb=" N ILE B 681 " pdb=" C ILE B 681 " pdb=" CB ILE B 681 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL F 423 " pdb=" CA VAL F 423 " pdb=" CG1 VAL F 423 " pdb=" CG2 VAL F 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' ANP C 801 " pdb=" C2' ANP C 801 " pdb=" C4' ANP C 801 " pdb=" O3' ANP C 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2482 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 450 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LYS B 450 " 0.074 2.00e-02 2.50e+03 pdb=" O LYS B 450 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 451 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 670 " -0.005 2.00e-02 2.50e+03 2.05e-02 8.41e+00 pdb=" CG TYR F 670 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 670 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 670 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR F 670 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR F 670 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 670 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 670 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 421 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C ASP F 421 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP F 421 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU F 422 " 0.015 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 122 2.59 - 3.17: 12520 3.17 - 3.75: 23552 3.75 - 4.32: 35748 4.32 - 4.90: 57040 Nonbonded interactions: 128982 Sorted by model distance: nonbonded pdb=" O3G ANP C 801 " pdb="MG MG C 802 " model vdw 2.015 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 2.061 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" O2B ANP A 801 " pdb="MG MG A 802 " model vdw 2.114 2.170 nonbonded pdb=" OG SER D 359 " pdb=" OE1 GLU D 360 " model vdw 2.175 2.440 ... (remaining 128977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 636 or (resid 637 \ through 641 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 2 through 681 or (resid 682 and (name N or name CA or name C or name O or name C \ B )) or resid 683 through 695 or resid 801 through 802)) selection = (chain 'B' and (resid 324 through 484 or resid 486 through 636 or (resid 637 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 695 or resid 801 through 802)) selection = (chain 'C' and (resid 324 through 452 or (resid 453 through 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 484 or resid 486 t \ hrough 681 or (resid 682 and (name N or name CA or name C or name O or name CB ) \ ) or resid 683 through 695 or resid 801 through 802)) } ncs_group { reference = (chain 'D' and (resid 324 through 423 or (resid 424 and (name N or name CA or na \ me C or name O or name CB )) or resid 425 or (resid 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 through 473 or (resid 474 and (nam \ e N or name CA or name C or name O or name CB )) or resid 475 or (resid 476 thro \ ugh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 th \ rough 503 or (resid 504 and (name N or name CA or name C or name O or name CB )) \ or resid 505 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 533 or (resid 534 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 through 557 or (resid 558 and (nam \ e N or name CA or name C or name O or name CB )) or resid 559 through 561 or (re \ sid 567 through 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) \ or resid 571 or (resid 572 and (name N or name CA or name C or name O or name C \ B )) or resid 573 through 574 or (resid 575 through 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 or (resid 578 through 579 and (nam \ e N or name CA or name C or name O or name CB )) or resid 596 through 611 or (re \ sid 612 and (name N or name CA or name C or name O or name CB )) or resid 613 or \ (resid 614 through 620 and (name N or name CA or name C or name O or name CB )) \ or resid 621 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 or (resid 627 and (name N or name CA or name C or \ name O or name CB )) or resid 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 655 through 684)) selection = (chain 'F' and (resid 324 through 559 or (resid 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 or resid 567 through 684)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.430 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.900 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 16236 Z= 0.286 Angle : 0.732 16.602 21981 Z= 0.394 Chirality : 0.044 0.310 2485 Planarity : 0.004 0.057 2761 Dihedral : 17.643 117.981 6160 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.00 % Favored : 95.28 % Rotamer: Outliers : 2.00 % Allowed : 16.35 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1927 helix: -0.02 (0.20), residues: 678 sheet: -0.19 (0.34), residues: 283 loop : -0.69 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS B 680 PHE 0.023 0.001 PHE B 451 TYR 0.045 0.001 TYR F 670 ARG 0.016 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ILE cc_start: 0.5818 (mm) cc_final: 0.5519 (mm) REVERT: B 415 PHE cc_start: 0.5596 (m-80) cc_final: 0.5367 (m-80) REVERT: B 432 ASP cc_start: 0.2521 (OUTLIER) cc_final: 0.2199 (t70) REVERT: C 547 MET cc_start: 0.4147 (mtm) cc_final: 0.3850 (pp-130) REVERT: D 495 LYS cc_start: 0.6093 (mppt) cc_final: 0.5531 (mmtt) REVERT: D 502 PHE cc_start: 0.4751 (t80) cc_final: 0.4543 (t80) REVERT: D 571 SER cc_start: 0.6315 (m) cc_final: 0.5952 (p) REVERT: E 354 SER cc_start: 0.5654 (t) cc_final: 0.5320 (t) REVERT: E 422 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2726 (tt) REVERT: E 444 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.5252 (p90) REVERT: F 354 SER cc_start: 0.4768 (t) cc_final: 0.4468 (t) REVERT: F 366 LYS cc_start: 0.7116 (mttt) cc_final: 0.6515 (mtpp) REVERT: F 413 LEU cc_start: 0.5054 (mt) cc_final: 0.4801 (mt) REVERT: F 423 VAL cc_start: 0.5991 (p) cc_final: 0.5737 (m) REVERT: F 465 ILE cc_start: 0.3814 (pp) cc_final: 0.3371 (mt) outliers start: 35 outliers final: 7 residues processed: 304 average time/residue: 1.1508 time to fit residues: 391.1508 Evaluate side-chains 158 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 444 PHE Chi-restraints excluded: chain F residue 556 SER Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 374 GLN A 573 ASN A 629 HIS A 641 ASN A 680 HIS B 596 ASN B 629 HIS C 548 HIS C 597 HIS D 548 HIS D 661 ASN F 347 HIS F 478 ASN F 546 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.8885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16236 Z= 0.372 Angle : 0.895 15.311 21981 Z= 0.466 Chirality : 0.051 0.312 2485 Planarity : 0.007 0.079 2761 Dihedral : 11.574 168.452 2278 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.67 % Favored : 94.81 % Rotamer: Outliers : 5.66 % Allowed : 17.04 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1927 helix: -0.81 (0.18), residues: 708 sheet: -0.61 (0.31), residues: 292 loop : -0.99 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 350 HIS 0.012 0.002 HIS C 680 PHE 0.022 0.003 PHE F 427 TYR 0.027 0.002 TYR A 670 ARG 0.026 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 346 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7874 (mtp85) REVERT: B 397 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.8569 (mtt-85) REVERT: B 593 ASN cc_start: 0.8931 (p0) cc_final: 0.8595 (p0) REVERT: C 377 LYS cc_start: 0.7512 (ttpp) cc_final: 0.7158 (mmtm) REVERT: C 469 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7358 (mm110) REVERT: D 371 ILE cc_start: 0.8449 (tt) cc_final: 0.8158 (tt) REVERT: D 426 MET cc_start: 0.5850 (tpp) cc_final: 0.5625 (mpp) REVERT: D 435 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (pttm) REVERT: D 463 ASN cc_start: 0.7422 (m-40) cc_final: 0.6938 (m110) REVERT: D 570 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.5628 (ttm-80) REVERT: D 684 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5031 (ptt) REVERT: F 403 SER cc_start: 0.5985 (m) cc_final: 0.5618 (p) REVERT: F 457 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5466 (mp0) REVERT: F 467 ASP cc_start: 0.2588 (OUTLIER) cc_final: 0.1944 (t70) REVERT: F 555 CYS cc_start: 0.5750 (OUTLIER) cc_final: 0.3090 (t) REVERT: F 679 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.4484 (m-80) outliers start: 99 outliers final: 14 residues processed: 407 average time/residue: 1.4400 time to fit residues: 640.0418 Evaluate side-chains 238 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 679 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS A 395 ASN A 680 HIS C 352 ASN C 573 ASN C 593 ASN C 596 ASN C 661 ASN D 478 ASN D 548 HIS D 593 ASN E 395 ASN F 352 ASN F 353 ASN F 374 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 1.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16236 Z= 0.214 Angle : 0.615 11.444 21981 Z= 0.322 Chirality : 0.043 0.162 2485 Planarity : 0.004 0.066 2761 Dihedral : 9.772 140.602 2263 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.68 % Favored : 95.90 % Rotamer: Outliers : 3.77 % Allowed : 21.67 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1927 helix: 0.23 (0.20), residues: 681 sheet: -0.32 (0.34), residues: 264 loop : -0.77 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 355 HIS 0.006 0.001 HIS B 597 PHE 0.013 0.001 PHE B 502 TYR 0.023 0.001 TYR A 670 ARG 0.005 0.001 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 269 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (mtm180) REVERT: A 448 ASP cc_start: 0.6855 (m-30) cc_final: 0.6314 (m-30) REVERT: A 451 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.5404 (m-80) REVERT: B 357 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7524 (t80) REVERT: B 547 MET cc_start: 0.8076 (ptm) cc_final: 0.7780 (ptm) REVERT: C 387 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7020 (mtp180) REVERT: C 684 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6432 (ttp) REVERT: D 426 MET cc_start: 0.6013 (tpp) cc_final: 0.5802 (mmt) REVERT: D 435 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7862 (pttm) REVERT: D 546 ASN cc_start: 0.7239 (t0) cc_final: 0.6952 (t0) REVERT: D 618 MET cc_start: 0.7031 (mmp) cc_final: 0.6574 (mmp) REVERT: D 620 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8226 (ttm170) REVERT: D 677 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8168 (tppt) REVERT: E 378 GLU cc_start: 0.7315 (mp0) cc_final: 0.7055 (pm20) REVERT: F 403 SER cc_start: 0.6305 (m) cc_final: 0.5722 (t) REVERT: F 555 CYS cc_start: 0.5587 (OUTLIER) cc_final: 0.3096 (t) outliers start: 66 outliers final: 12 residues processed: 312 average time/residue: 1.4983 time to fit residues: 514.8413 Evaluate side-chains 239 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 451 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 761 ASN C 475 ASN C 593 ASN D 347 HIS D 548 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 1.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 16236 Z= 0.295 Angle : 0.679 10.911 21981 Z= 0.357 Chirality : 0.045 0.193 2485 Planarity : 0.005 0.048 2761 Dihedral : 10.319 142.378 2259 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.26 % Favored : 95.28 % Rotamer: Outliers : 4.80 % Allowed : 20.81 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1927 helix: -0.08 (0.19), residues: 697 sheet: -0.30 (0.33), residues: 281 loop : -0.86 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 355 HIS 0.011 0.002 HIS B 597 PHE 0.017 0.002 PHE A 524 TYR 0.020 0.002 TYR B 482 ARG 0.007 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 267 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8591 (mmt180) cc_final: 0.8325 (mtp180) REVERT: A 641 ASN cc_start: 0.8001 (m-40) cc_final: 0.7752 (m-40) REVERT: A 658 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (mttp) REVERT: B 357 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8121 (t80) REVERT: B 382 GLU cc_start: 0.8232 (tp30) cc_final: 0.7999 (tp30) REVERT: B 426 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7894 (ttm) REVERT: B 529 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: B 547 MET cc_start: 0.8197 (ptm) cc_final: 0.7959 (ptm) REVERT: B 615 ASN cc_start: 0.9115 (m-40) cc_final: 0.8906 (m110) REVERT: B 692 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6306 (tp30) REVERT: C 448 ASP cc_start: 0.7689 (p0) cc_final: 0.7412 (p0) REVERT: C 618 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: C 684 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6970 (ttm) REVERT: D 517 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7620 (tptm) REVERT: D 546 ASN cc_start: 0.8132 (t0) cc_final: 0.7927 (t0) REVERT: D 570 ARG cc_start: 0.7169 (ttm-80) cc_final: 0.6702 (ttm-80) REVERT: D 591 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8326 (mmtm) REVERT: D 620 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8813 (ttm170) REVERT: D 625 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7229 (mtm-85) REVERT: D 628 THR cc_start: 0.6184 (OUTLIER) cc_final: 0.5790 (m) REVERT: E 434 LYS cc_start: 0.6525 (mtmt) cc_final: 0.6317 (mtpt) REVERT: F 461 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6700 (mt) REVERT: F 465 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6656 (pt) REVERT: F 525 VAL cc_start: 0.7409 (OUTLIER) cc_final: 0.7087 (p) outliers start: 84 outliers final: 18 residues processed: 313 average time/residue: 1.5062 time to fit residues: 514.4173 Evaluate side-chains 259 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 465 ILE Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 2 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 546 ASN C 593 ASN C 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 1.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16236 Z= 0.157 Angle : 0.538 11.651 21981 Z= 0.283 Chirality : 0.041 0.142 2485 Planarity : 0.004 0.051 2761 Dihedral : 9.611 140.423 2259 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.84 % Favored : 95.74 % Rotamer: Outliers : 4.00 % Allowed : 21.44 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1927 helix: 0.37 (0.20), residues: 695 sheet: -0.20 (0.33), residues: 281 loop : -0.70 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 355 HIS 0.005 0.001 HIS B 597 PHE 0.015 0.001 PHE F 427 TYR 0.018 0.001 TYR B 482 ARG 0.008 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 237 time to evaluate : 1.842 Fit side-chains REVERT: A 332 ARG cc_start: 0.8549 (mmt180) cc_final: 0.8292 (mtp180) REVERT: A 476 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8071 (ttmt) REVERT: A 658 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8725 (mttp) REVERT: B 357 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 382 GLU cc_start: 0.8186 (tp30) cc_final: 0.7977 (tp30) REVERT: B 529 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7764 (pp30) REVERT: C 343 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: C 387 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6924 (mtp180) REVERT: C 426 MET cc_start: 0.8261 (mmm) cc_final: 0.7994 (mmm) REVERT: C 448 ASP cc_start: 0.7738 (p0) cc_final: 0.7497 (p0) REVERT: C 604 THR cc_start: 0.8976 (p) cc_final: 0.8756 (p) REVERT: C 618 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: D 377 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7878 (tppp) REVERT: D 424 ASP cc_start: 0.7605 (t0) cc_final: 0.7357 (t0) REVERT: D 458 MET cc_start: 0.5493 (tpt) cc_final: 0.5187 (tpt) REVERT: D 516 LEU cc_start: 0.8578 (tp) cc_final: 0.8282 (tm) REVERT: D 517 LYS cc_start: 0.8073 (tptm) cc_final: 0.7483 (tppt) REVERT: D 534 ASP cc_start: 0.7662 (m-30) cc_final: 0.7440 (m-30) REVERT: D 546 ASN cc_start: 0.8182 (t0) cc_final: 0.7931 (t0) REVERT: D 570 ARG cc_start: 0.7201 (ttm-80) cc_final: 0.6858 (ttm-80) REVERT: D 576 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7957 (mttp) REVERT: D 591 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8292 (mmtm) REVERT: D 620 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8961 (mtt90) REVERT: D 625 ARG cc_start: 0.7491 (ptt-90) cc_final: 0.7222 (mtm-85) REVERT: D 628 THR cc_start: 0.6246 (OUTLIER) cc_final: 0.5839 (m) REVERT: E 426 MET cc_start: 0.4491 (OUTLIER) cc_final: 0.3984 (ppp) REVERT: E 428 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5088 (m-10) REVERT: F 375 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8085 (mt) REVERT: F 461 LEU cc_start: 0.7302 (pt) cc_final: 0.6354 (mt) outliers start: 70 outliers final: 28 residues processed: 274 average time/residue: 1.4872 time to fit residues: 445.0838 Evaluate side-chains 277 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 576 LYS Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 46 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 1.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16236 Z= 0.173 Angle : 0.539 11.524 21981 Z= 0.282 Chirality : 0.041 0.145 2485 Planarity : 0.004 0.052 2761 Dihedral : 9.446 139.828 2259 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.00 % Favored : 95.64 % Rotamer: Outliers : 3.95 % Allowed : 21.78 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1927 helix: 0.43 (0.20), residues: 713 sheet: -0.10 (0.34), residues: 268 loop : -0.65 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 355 HIS 0.006 0.001 HIS B 597 PHE 0.025 0.001 PHE A 752 TYR 0.019 0.001 TYR B 482 ARG 0.008 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 1.874 Fit side-chains REVERT: A 332 ARG cc_start: 0.8525 (mmt180) cc_final: 0.8276 (mtp180) REVERT: A 360 GLU cc_start: 0.7524 (mp0) cc_final: 0.7023 (pm20) REVERT: A 476 LYS cc_start: 0.8485 (tmmt) cc_final: 0.8096 (ttmt) REVERT: A 658 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8702 (mttp) REVERT: B 357 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 382 GLU cc_start: 0.8191 (tp30) cc_final: 0.7983 (tp30) REVERT: B 529 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7797 (pp30) REVERT: B 618 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7535 (mpp) REVERT: B 692 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 387 ARG cc_start: 0.7466 (mtm180) cc_final: 0.6896 (mtp180) REVERT: C 618 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: C 680 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.7002 (t70) REVERT: D 346 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6550 (t0) REVERT: D 424 ASP cc_start: 0.7666 (t0) cc_final: 0.7396 (t0) REVERT: D 458 MET cc_start: 0.5465 (tpt) cc_final: 0.5046 (tpt) REVERT: D 516 LEU cc_start: 0.8585 (tp) cc_final: 0.8306 (tm) REVERT: D 517 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7456 (tppt) REVERT: D 570 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6693 (ttt90) REVERT: D 591 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8253 (mmtm) REVERT: D 618 MET cc_start: 0.7903 (mpp) cc_final: 0.7542 (mmm) REVERT: D 620 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8637 (ttm170) REVERT: D 625 ARG cc_start: 0.7473 (ptt-90) cc_final: 0.7210 (mtm-85) REVERT: D 628 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6230 (m) REVERT: E 332 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.7209 (mtp85) REVERT: E 354 SER cc_start: 0.7719 (m) cc_final: 0.7193 (t) REVERT: E 402 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6275 (m-30) REVERT: E 426 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.4441 (ppp) REVERT: E 428 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.5039 (m-10) REVERT: F 375 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (mt) REVERT: F 461 LEU cc_start: 0.7127 (pt) cc_final: 0.6542 (mt) REVERT: F 525 VAL cc_start: 0.7511 (OUTLIER) cc_final: 0.7216 (p) outliers start: 69 outliers final: 31 residues processed: 284 average time/residue: 1.5377 time to fit residues: 477.2640 Evaluate side-chains 273 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 158 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS B 629 HIS C 593 ASN D 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 1.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16236 Z= 0.264 Angle : 0.611 10.806 21981 Z= 0.320 Chirality : 0.044 0.170 2485 Planarity : 0.004 0.047 2761 Dihedral : 9.873 136.278 2259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.36 % Favored : 95.28 % Rotamer: Outliers : 3.72 % Allowed : 23.04 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1927 helix: 0.20 (0.19), residues: 713 sheet: 0.05 (0.35), residues: 262 loop : -0.69 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 355 HIS 0.010 0.001 HIS B 597 PHE 0.018 0.002 PHE A 752 TYR 0.022 0.002 TYR B 482 ARG 0.007 0.001 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 257 time to evaluate : 2.552 Fit side-chains REVERT: A 332 ARG cc_start: 0.8530 (mmt180) cc_final: 0.8281 (mtp180) REVERT: A 360 GLU cc_start: 0.7561 (mp0) cc_final: 0.7017 (pm20) REVERT: A 476 LYS cc_start: 0.8459 (tmmt) cc_final: 0.8072 (ttmt) REVERT: A 566 SER cc_start: 0.7786 (t) cc_final: 0.7474 (m) REVERT: A 656 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: A 658 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8707 (mttp) REVERT: A 685 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6815 (mmmt) REVERT: B 356 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8466 (mttm) REVERT: B 504 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8104 (mm-30) REVERT: B 529 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: B 615 ASN cc_start: 0.9107 (m-40) cc_final: 0.8903 (m110) REVERT: C 618 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: C 660 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: C 680 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.7168 (t70) REVERT: D 460 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 517 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7518 (tptm) REVERT: D 570 ARG cc_start: 0.7023 (ttm-80) cc_final: 0.6599 (ttt90) REVERT: D 591 LYS cc_start: 0.8443 (mmtp) cc_final: 0.8242 (mmtm) REVERT: D 620 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8626 (ttm170) REVERT: E 332 ARG cc_start: 0.7533 (mtt-85) cc_final: 0.7308 (mtp85) REVERT: E 354 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7425 (t) REVERT: E 402 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: E 426 MET cc_start: 0.4849 (OUTLIER) cc_final: 0.4459 (ppp) REVERT: E 428 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.5239 (m-10) REVERT: F 382 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7964 (mt-10) REVERT: F 480 GLU cc_start: 0.5785 (mm-30) cc_final: 0.5150 (tm-30) REVERT: F 483 GLU cc_start: 0.6562 (pt0) cc_final: 0.6339 (pp20) REVERT: F 517 LYS cc_start: 0.6929 (tptt) cc_final: 0.6704 (tptt) REVERT: F 526 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7793 (mt-10) REVERT: F 553 VAL cc_start: 0.5997 (t) cc_final: 0.5727 (m) REVERT: F 604 THR cc_start: 0.5986 (p) cc_final: 0.5506 (t) outliers start: 65 outliers final: 32 residues processed: 297 average time/residue: 1.4639 time to fit residues: 476.4403 Evaluate side-chains 273 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 685 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 555 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 1.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16236 Z= 0.153 Angle : 0.526 11.088 21981 Z= 0.275 Chirality : 0.041 0.146 2485 Planarity : 0.004 0.047 2761 Dihedral : 9.360 139.619 2259 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.53 % Favored : 96.11 % Rotamer: Outliers : 2.80 % Allowed : 24.01 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1927 helix: 0.49 (0.20), residues: 705 sheet: 0.05 (0.35), residues: 264 loop : -0.59 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 355 HIS 0.004 0.001 HIS A 597 PHE 0.012 0.001 PHE F 427 TYR 0.018 0.001 TYR B 482 ARG 0.009 0.000 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 2.102 Fit side-chains REVERT: A 332 ARG cc_start: 0.8513 (mmt180) cc_final: 0.8263 (mtp180) REVERT: A 360 GLU cc_start: 0.7539 (mp0) cc_final: 0.7112 (pm20) REVERT: A 476 LYS cc_start: 0.8479 (tmmt) cc_final: 0.8096 (ttmt) REVERT: A 566 SER cc_start: 0.7767 (t) cc_final: 0.7455 (m) REVERT: A 656 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6927 (m-30) REVERT: A 658 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: B 356 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8486 (mttm) REVERT: B 529 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: C 387 ARG cc_start: 0.7507 (mtm180) cc_final: 0.6916 (mtp180) REVERT: C 612 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7572 (ttt90) REVERT: C 618 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (mtm) REVERT: C 660 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: C 680 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.7103 (t70) REVERT: D 460 GLU cc_start: 0.7259 (tm-30) cc_final: 0.7004 (tm-30) REVERT: D 517 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7446 (tppt) REVERT: D 570 ARG cc_start: 0.6939 (ttm-80) cc_final: 0.6554 (ttt90) REVERT: D 591 LYS cc_start: 0.8441 (mmtp) cc_final: 0.8238 (mmtm) REVERT: D 620 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8915 (mtt90) REVERT: E 332 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7280 (mtp85) REVERT: E 354 SER cc_start: 0.7784 (m) cc_final: 0.7411 (t) REVERT: E 426 MET cc_start: 0.4929 (OUTLIER) cc_final: 0.4553 (ppp) REVERT: E 428 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.5370 (m-10) REVERT: F 480 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5220 (tm-30) REVERT: F 514 ARG cc_start: 0.5963 (mtm-85) cc_final: 0.5221 (ptp90) REVERT: F 526 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7548 (mt-10) REVERT: F 555 CYS cc_start: 0.5547 (OUTLIER) cc_final: 0.4374 (p) REVERT: F 604 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5514 (t) outliers start: 49 outliers final: 21 residues processed: 272 average time/residue: 1.5332 time to fit residues: 455.2609 Evaluate side-chains 265 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 620 ARG Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 TYR Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0970 chunk 174 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 104 optimal weight: 0.0170 chunk 75 optimal weight: 0.0030 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 1.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16236 Z= 0.132 Angle : 0.506 10.742 21981 Z= 0.264 Chirality : 0.040 0.149 2485 Planarity : 0.004 0.046 2761 Dihedral : 9.116 141.516 2259 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.79 % Favored : 95.85 % Rotamer: Outliers : 1.83 % Allowed : 25.61 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1927 helix: 0.71 (0.20), residues: 705 sheet: 0.08 (0.37), residues: 239 loop : -0.55 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 675 HIS 0.003 0.000 HIS A 597 PHE 0.012 0.001 PHE A 752 TYR 0.016 0.001 TYR B 482 ARG 0.009 0.000 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 2.320 Fit side-chains REVERT: A 332 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8271 (mtp180) REVERT: A 360 GLU cc_start: 0.7522 (mp0) cc_final: 0.7129 (pm20) REVERT: A 476 LYS cc_start: 0.8470 (tmmt) cc_final: 0.8106 (ttmt) REVERT: A 566 SER cc_start: 0.7759 (t) cc_final: 0.7511 (m) REVERT: B 356 LYS cc_start: 0.8819 (ptpp) cc_final: 0.8528 (mttm) REVERT: B 529 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: C 387 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6807 (mtp180) REVERT: C 558 LEU cc_start: 0.7760 (mt) cc_final: 0.7545 (pp) REVERT: C 612 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7440 (ttt90) REVERT: C 660 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: C 680 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.7092 (t70) REVERT: D 460 GLU cc_start: 0.7251 (tm-30) cc_final: 0.7003 (tm-30) REVERT: D 465 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8161 (mp) REVERT: D 516 LEU cc_start: 0.8525 (tp) cc_final: 0.8309 (tm) REVERT: D 517 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7377 (tppt) REVERT: D 570 ARG cc_start: 0.6943 (ttm-80) cc_final: 0.6559 (ttt90) REVERT: D 591 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8264 (mmtm) REVERT: E 332 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.7241 (mtp85) REVERT: E 354 SER cc_start: 0.7873 (m) cc_final: 0.7373 (t) REVERT: E 426 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4574 (ppp) REVERT: F 448 ASP cc_start: 0.5706 (p0) cc_final: 0.5500 (m-30) REVERT: F 526 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7428 (mt-10) REVERT: F 555 CYS cc_start: 0.5461 (OUTLIER) cc_final: 0.4435 (p) REVERT: F 604 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5801 (t) outliers start: 32 outliers final: 13 residues processed: 265 average time/residue: 1.5907 time to fit residues: 459.1989 Evaluate side-chains 247 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 1.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16236 Z= 0.154 Angle : 0.528 10.219 21981 Z= 0.275 Chirality : 0.041 0.166 2485 Planarity : 0.004 0.049 2761 Dihedral : 9.213 140.413 2259 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.48 % Favored : 96.16 % Rotamer: Outliers : 1.77 % Allowed : 25.79 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1927 helix: 0.66 (0.20), residues: 708 sheet: 0.25 (0.36), residues: 251 loop : -0.53 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 355 HIS 0.004 0.001 HIS A 597 PHE 0.012 0.001 PHE F 427 TYR 0.018 0.001 TYR B 482 ARG 0.009 0.000 ARG D 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 1.939 Fit side-chains REVERT: A 360 GLU cc_start: 0.7515 (mp0) cc_final: 0.7131 (pm20) REVERT: A 372 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8276 (ttp-170) REVERT: A 476 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8112 (ttmt) REVERT: A 566 SER cc_start: 0.7748 (t) cc_final: 0.7524 (m) REVERT: B 356 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8499 (mttm) REVERT: B 504 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 529 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7844 (pp30) REVERT: B 692 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7096 (mt-10) REVERT: C 387 ARG cc_start: 0.7413 (mtm180) cc_final: 0.6836 (mtp180) REVERT: C 612 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7555 (ttt90) REVERT: C 618 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7969 (mtp) REVERT: C 660 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: C 680 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.7117 (t70) REVERT: D 460 GLU cc_start: 0.7274 (tm-30) cc_final: 0.7014 (tm-30) REVERT: D 465 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 516 LEU cc_start: 0.8557 (tp) cc_final: 0.8303 (tm) REVERT: D 517 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7424 (tppt) REVERT: D 570 ARG cc_start: 0.6897 (ttm-80) cc_final: 0.6502 (ttt90) REVERT: D 591 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8332 (mmtm) REVERT: D 627 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6519 (ttp-110) REVERT: E 332 ARG cc_start: 0.7494 (mtt-85) cc_final: 0.7285 (mtp85) REVERT: E 354 SER cc_start: 0.7845 (m) cc_final: 0.7367 (t) REVERT: F 555 CYS cc_start: 0.5641 (OUTLIER) cc_final: 0.4530 (p) REVERT: F 596 ASN cc_start: 0.5504 (m-40) cc_final: 0.4893 (t0) REVERT: F 604 THR cc_start: 0.5869 (OUTLIER) cc_final: 0.5625 (t) outliers start: 31 outliers final: 16 residues processed: 252 average time/residue: 1.5241 time to fit residues: 419.0961 Evaluate side-chains 246 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 680 HIS Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 0.0010 chunk 158 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121370 restraints weight = 17107.572| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.66 r_work: 0.3087 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16236 Z= 0.137 Angle : 0.516 10.343 21981 Z= 0.267 Chirality : 0.040 0.154 2485 Planarity : 0.004 0.054 2761 Dihedral : 9.112 140.365 2259 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.68 % Favored : 95.95 % Rotamer: Outliers : 1.83 % Allowed : 25.96 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1927 helix: 0.74 (0.20), residues: 707 sheet: 0.30 (0.37), residues: 234 loop : -0.46 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 355 HIS 0.003 0.001 HIS A 597 PHE 0.015 0.001 PHE E 427 TYR 0.017 0.001 TYR B 482 ARG 0.009 0.000 ARG D 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.47 seconds wall clock time: 133 minutes 13.08 seconds (7993.08 seconds total)