Starting phenix.real_space_refine on Sat May 11 18:24:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj7_38395/05_2024/8xj7_38395_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.128 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 22 5.49 5 Mg 3 5.21 5 S 94 5.16 5 C 12486 2.51 5 N 3299 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 361": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 691": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 19595 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3035 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 358} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3601 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3666 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3611 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2934 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2447 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain breaks: 6 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 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: 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} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 10.22, per 1000 atoms: 0.52 Number of scatterers: 19595 At special positions: 0 Unit cell: (115.271, 128.199, 130.353, 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 94 16.00 P 22 15.00 Mg 3 11.99 O 3691 8.00 N 3299 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 3.5 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 31 sheets defined 37.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.544A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.519A pdb=" N ARG A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N HIS A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.038A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 383' Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.730A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 7.239A pdb=" N ASP A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.790A pdb=" N THR A 533 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 removed outlier: 4.709A pdb=" N MET A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.663A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.288A pdb=" N ASP A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY A 657 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 659 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.524A pdb=" N TYR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.749A pdb=" N PHE A 698 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.503A pdb=" N ARG B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 383' Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.847A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.840A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 7.551A pdb=" N ASP B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 533 No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 542 through 547 removed outlier: 5.262A pdb=" N MET B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.585A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 No H-bonds generated for 'chain 'B' and resid 637 through 640' Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.566A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 705 removed outlier: 4.417A pdb=" N PHE B 698 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 718 removed outlier: 4.236A pdb=" N THR B 718 " --> pdb=" O PRO B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 718' Processing helix chain 'B' and resid 736 through 745 removed outlier: 3.634A pdb=" N LYS B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 6.793A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.657A 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: 4.011A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 4.034A 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 431 through 434 No H-bonds generated for 'chain 'C' and resid 431 through 434' Processing helix chain 'C' and resid 456 through 468 removed outlier: 3.788A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 463 " --> pdb=" O GLU C 459 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 490 removed outlier: 3.854A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 7.125A pdb=" N ASP C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.780A pdb=" N THR C 533 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 545 No H-bonds generated for 'chain 'C' and resid 542 through 545' Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 615 through 620 removed outlier: 4.035A pdb=" N ARG C 620 " --> pdb=" O ALA C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 694 through 705 removed outlier: 4.351A pdb=" N PHE C 698 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 713 No H-bonds generated for 'chain 'C' and resid 711 through 713' Processing helix chain 'C' and resid 717 through 723 removed outlier: 4.405A pdb=" N LYS C 722 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 removed outlier: 3.917A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 removed outlier: 7.386A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.726A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.543A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 384 removed outlier: 3.530A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 384' Processing helix chain 'D' and resid 386 through 399 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 455 through 468 removed outlier: 3.736A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 490 removed outlier: 3.878A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 6.971A pdb=" N ASP D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 4.438A pdb=" N THR D 533 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 removed outlier: 4.537A 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 655 through 658 No H-bonds generated for 'chain 'D' and resid 655 through 658' Processing helix chain 'D' and resid 667 through 679 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 703 removed outlier: 4.630A pdb=" N PHE D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 removed outlier: 4.314A pdb=" N THR D 718 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 719 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS D 722 " --> pdb=" O ASP D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 759 through 762 No H-bonds generated for 'chain 'D' and resid 759 through 762' Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.879A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 373 removed outlier: 3.521A pdb=" N ARG E 372 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.896A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU E 383 " --> pdb=" O TYR E 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 383' Processing helix chain 'E' and resid 386 through 399 Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.983A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 468 removed outlier: 3.608A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 489 removed outlier: 3.703A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 523 removed outlier: 8.057A pdb=" N ASP E 522 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU E 523 " --> pdb=" O ALA E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 533 No H-bonds generated for 'chain 'E' and resid 530 through 533' Processing helix chain 'E' and resid 571 through 576 Processing helix chain 'E' and resid 633 through 640 removed outlier: 4.482A pdb=" N GLU E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 638 " --> pdb=" O GLY E 635 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA E 639 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 640 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 665 through 679 Processing helix chain 'E' and resid 694 through 703 removed outlier: 3.901A pdb=" N PHE E 698 " --> pdb=" O ASP E 695 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 701 " --> pdb=" O PHE E 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.746A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 374 removed outlier: 3.516A pdb=" N ARG F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 384 removed outlier: 3.683A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU F 383 " --> pdb=" O TYR F 379 " (cutoff:3.500A) removed outlier: 4.264A 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 431 through 433 No H-bonds generated for 'chain 'F' and resid 431 through 433' Processing helix chain 'F' and resid 455 through 468 removed outlier: 4.540A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 468 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 489 removed outlier: 3.875A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 523 removed outlier: 7.268A pdb=" N ASP F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU F 523 " --> pdb=" O ALA F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 547 No H-bonds generated for 'chain 'F' and resid 545 through 547' Processing helix chain 'F' and resid 571 through 578 removed outlier: 3.748A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 619 Processing helix chain 'F' and resid 655 through 658 No H-bonds generated for 'chain 'F' and resid 655 through 658' Processing helix chain 'F' and resid 665 through 679 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 415 removed outlier: 3.534A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 621 through 626 removed outlier: 6.197A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (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: 6.517A pdb=" N LYS A 647 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER A 631 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.118A 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: 6.141A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 600 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 501 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 602 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY B 503 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 5.755A 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: 6.445A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 6.066A 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: 6.173A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (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: 6.519A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 5.991A 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 'C' and resid 706 through 708 Processing sheet with id= Q, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.756A pdb=" N ILE C 726 " --> pdb=" O THR C 733 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 339 through 341 Processing sheet with id= S, first strand: chain 'D' and resid 412 through 414 Processing sheet with id= T, first strand: chain 'D' and resid 621 through 626 removed outlier: 6.168A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER D 556 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= V, first strand: chain 'D' and resid 629 through 631 Processing sheet with id= W, first strand: chain 'D' and resid 725 through 728 Processing sheet with id= X, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= Y, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.780A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET E 426 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 621 through 625 removed outlier: 5.957A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.207A pdb=" N LYS E 647 " --> pdb=" O HIS E 629 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER E 631 " --> pdb=" O LYS E 647 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS E 649 " --> pdb=" O SER E 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 339 through 341 removed outlier: 4.321A pdb=" N HIS F 347 " --> pdb=" O ASN F 358 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.849A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 621 through 625 removed outlier: 6.094A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 553 " --> pdb=" O THR F 599 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.180A pdb=" N LYS F 647 " --> pdb=" O HIS F 629 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER F 631 " --> pdb=" O LYS F 647 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS F 649 " --> pdb=" O SER F 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE 549 hydrogen bonds defined for protein. 1533 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: 6.04 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3194 1.30 - 1.43: 5063 1.43 - 1.56: 11577 1.56 - 1.69: 38 1.69 - 1.81: 141 Bond restraints: 20013 Sorted by residual: bond pdb=" O3A ANP C 801 " pdb=" PB ANP C 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" O3A ANP E 801 " pdb=" PB ANP E 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.08e+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 5.06e+01 bond pdb=" O3A ANP D 801 " pdb=" PB ANP D 801 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 20008 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 576 106.39 - 113.29: 10924 113.29 - 120.19: 7132 120.19 - 127.09: 8285 127.09 - 133.99: 209 Bond angle restraints: 27126 Sorted by residual: angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 109.00 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.17 17.78 3.00e+00 1.11e-01 3.51e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.19 17.76 3.00e+00 1.11e-01 3.50e+01 angle pdb=" PB ANP D 801 " pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 126.95 109.65 17.30 3.00e+00 1.11e-01 3.32e+01 angle pdb=" C SER B 708 " pdb=" N SER B 709 " pdb=" CA SER B 709 " ideal model delta sigma weight residual 121.90 115.35 6.55 1.26e+00 6.30e-01 2.71e+01 ... (remaining 27121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 11111 22.98 - 45.96: 858 45.96 - 68.94: 173 68.94 - 91.92: 63 91.92 - 114.90: 5 Dihedral angle restraints: 12210 sinusoidal: 5089 harmonic: 7121 Sorted by residual: dihedral pdb=" CA VAL D 707 " pdb=" C VAL D 707 " pdb=" N SER D 708 " pdb=" CA SER D 708 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL B 707 " pdb=" C VAL B 707 " pdb=" N SER B 708 " pdb=" CA SER B 708 " ideal model delta harmonic sigma weight residual 180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET C 462 " pdb=" C MET C 462 " pdb=" N ASN C 463 " pdb=" CA ASN C 463 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 12207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2546 0.054 - 0.108: 477 0.108 - 0.162: 44 0.162 - 0.217: 0 0.217 - 0.271: 8 Chirality restraints: 3075 Sorted by residual: chirality pdb=" CB ILE A 569 " pdb=" CA ILE A 569 " pdb=" CG1 ILE A 569 " pdb=" CG2 ILE A 569 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP F 801 " pdb=" C2' ANP F 801 " pdb=" C4' ANP F 801 " pdb=" O3' ANP F 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP E 801 " pdb=" C2' ANP E 801 " pdb=" C4' ANP E 801 " pdb=" O3' ANP E 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3072 not shown) Planarity restraints: 3398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 689 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO F 690 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO F 690 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 690 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 758 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER D 758 " 0.066 2.00e-02 2.50e+03 pdb=" O SER D 758 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE D 759 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 455 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C SER C 455 " -0.041 2.00e-02 2.50e+03 pdb=" O SER C 455 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO C 456 " 0.014 2.00e-02 2.50e+03 ... (remaining 3395 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 217 2.60 - 3.18: 16227 3.18 - 3.75: 29756 3.75 - 4.33: 44236 4.33 - 4.90: 70898 Nonbonded interactions: 161334 Sorted by model distance: nonbonded pdb=" OG SER C 510 " pdb="MG MG C 802 " model vdw 2.027 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A 802 " model vdw 2.070 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B 802 " model vdw 2.090 2.170 nonbonded pdb=" OE2 GLU C 653 " pdb=" OH TYR D 687 " model vdw 2.209 2.440 nonbonded pdb=" N GLU A 474 " pdb=" OE1 GLU A 474 " model vdw 2.220 2.520 ... (remaining 161329 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 359 or (resid 360 through 361 and (name N or n \ ame CA or name C or name O or name CB )) or resid 362 through 533 or (resid 534 \ and (name N or name CA or name C or name O or name CB )) or resid 542 through 56 \ 3 or resid 567 through 583 or resid 594 through 652 or (resid 653 and (name N or \ name CA or name C or name O or name CB )) or resid 654 through 691 or (resid 69 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 693 through \ 700)) selection = (chain 'E' and (resid 324 through 642 or (resid 643 through 644 and (name N or n \ ame CA or name C or name O or name CB )) or resid 645 through 697 or (resid 698 \ and (name N or name CA or name C or name O or name CB )) or resid 699 or (resid \ 700 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 324 through 635 or (resid 636 through 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 \ through 644 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 5 through 715 or (resid 716 and (name N or name CA or name C or name O or name C \ B )) or resid 717 through 718 or (resid 719 through 720 and (name N or name CA o \ r name C or name O or name CB )) or resid 721 through 728 or (resid 729 through \ 730 and (name N or name CA or name C or name O or name CB )) or resid 731 throug \ h 763 or (resid 764 and (name N or name CA or name C or name O or name CB )) or \ resid 773 through 779 or (resid 780 and (name N or name CA or name C or name O o \ r name CB )) or resid 781 through 782 or resid 801)) selection = (chain 'C' and (resid 324 through 635 or (resid 636 through 639 and (name N or n \ ame CA or name C or name O or name CB )) or resid 640 through 642 or (resid 643 \ through 644 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 5 through 708 or (resid 709 through 710 and (name N or name CA or name C or name \ O or name CB )) or resid 711 through 715 or (resid 716 and (name N or name CA o \ r name C or name O or name CB )) or resid 717 through 718 or (resid 719 through \ 720 and (name N or name CA or name C or name O or name CB )) or resid 721 or (re \ sid 722 through 723 and (name N or name CA or name C or name O or name CB )) or \ resid 724 through 727 or (resid 728 through 730 and (name N or name CA or name C \ or name O or name CB )) or resid 731 through 735 or (resid 736 and (name N or n \ ame CA or name C or name O or name CB )) or resid 737 through 740 or (resid 741 \ through 742 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 3 through 744 or (resid 745 and (name N or name CA or name C or name O or name C \ B )) or resid 746 through 750 or (resid 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB )) or resid 758 through 763 or (resid 764 and \ (name N or name CA or name C or name O or name CB )) or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 782 or resid 80 \ 1)) selection = (chain 'D' and (resid 324 through 708 or (resid 709 through 710 and (name N or n \ ame CA or name C or name O or name CB )) or resid 711 through 722 or (resid 723 \ and (name N or name CA or name C or name O or name CB )) or resid 724 through 72 \ 7 or (resid 728 through 730 and (name N or name CA or name C or name O or name C \ B )) or resid 731 through 735 or (resid 736 and (name N or name CA or name C or \ name O or name CB )) or resid 737 through 750 or (resid 751 and (name N or name \ CA or name C or name O or name CB )) or resid 752 through 756 or (resid 757 and \ (name N or name CA or name C or name O or name CB )) or resid 758 through 761 or \ (resid 762 and (name N or name CA or name C or name O or name CB )) or resid 76 \ 3 through 764 or (resid 773 and (name N or name CA or name C or name O or name C \ B )) or resid 774 through 779 or (resid 780 and (name N or name CA or name C or \ name O or name CB )) or resid 781 through 782 or resid 801)) } 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: 1.220 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: 5.940 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 51.690 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.005 0.143 20013 Z= 0.317 Angle : 0.729 17.951 27126 Z= 0.350 Chirality : 0.043 0.271 3075 Planarity : 0.005 0.118 3398 Dihedral : 17.625 114.902 7580 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.08 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 17.85 % Favored : 80.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.64 (0.17), residues: 2384 helix: 0.11 (0.18), residues: 857 sheet: 0.00 (0.32), residues: 289 loop : -0.87 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 675 HIS 0.004 0.001 HIS B 597 PHE 0.032 0.001 PHE C 698 TYR 0.017 0.001 TYR C 482 ARG 0.013 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 2.135 Fit side-chains REVERT: C 537 ASP cc_start: 0.7772 (p0) cc_final: 0.7274 (p0) REVERT: E 576 LYS cc_start: 0.8312 (tttt) cc_final: 0.7722 (tmmt) outliers start: 33 outliers final: 25 residues processed: 262 average time/residue: 1.2696 time to fit residues: 377.1536 Evaluate side-chains 256 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 458 MET Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 626 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 529 GLN B 660 GLN C 593 ASN F 597 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20013 Z= 0.195 Angle : 0.544 6.542 27126 Z= 0.281 Chirality : 0.042 0.179 3075 Planarity : 0.004 0.071 3398 Dihedral : 12.245 138.808 2887 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.12 % Favored : 94.59 % Rotamer: Outliers : 3.04 % Allowed : 16.53 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.60 (0.17), residues: 2384 helix: 0.27 (0.18), residues: 875 sheet: -0.13 (0.32), residues: 303 loop : -0.91 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 675 HIS 0.006 0.001 HIS B 597 PHE 0.024 0.001 PHE C 698 TYR 0.019 0.001 TYR B 482 ARG 0.006 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 250 time to evaluate : 2.339 Fit side-chains REVERT: A 618 MET cc_start: 0.6975 (mmm) cc_final: 0.6296 (tmm) REVERT: B 343 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 504 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: B 557 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: C 537 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7201 (p0) REVERT: D 757 GLU cc_start: 0.7199 (mp0) cc_final: 0.6943 (mp0) REVERT: E 461 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8044 (tm) REVERT: F 486 LEU cc_start: 0.6682 (mt) cc_final: 0.6251 (mm) REVERT: F 626 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5871 (m-10) outliers start: 65 outliers final: 35 residues processed: 290 average time/residue: 1.3284 time to fit residues: 435.1975 Evaluate side-chains 278 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 0.0070 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 529 GLN B 660 GLN F 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20013 Z= 0.303 Angle : 0.583 6.899 27126 Z= 0.304 Chirality : 0.044 0.191 3075 Planarity : 0.005 0.054 3398 Dihedral : 11.056 140.710 2867 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.75 % Favored : 93.96 % Rotamer: Outliers : 4.26 % Allowed : 16.96 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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 (0.17), residues: 2384 helix: 0.27 (0.18), residues: 860 sheet: -0.19 (0.30), residues: 321 loop : -0.95 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 675 HIS 0.013 0.001 HIS B 597 PHE 0.017 0.002 PHE D 524 TYR 0.023 0.001 TYR B 482 ARG 0.005 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 256 time to evaluate : 2.263 Fit side-chains REVERT: A 618 MET cc_start: 0.7154 (mmm) cc_final: 0.6501 (tmm) REVERT: B 343 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: B 504 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: C 537 ASP cc_start: 0.8010 (p0) cc_final: 0.7357 (p0) REVERT: D 757 GLU cc_start: 0.7239 (mp0) cc_final: 0.6815 (mp0) REVERT: D 780 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6722 (pp20) REVERT: E 461 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8014 (tm) REVERT: F 486 LEU cc_start: 0.6934 (mt) cc_final: 0.6537 (mm) REVERT: F 664 TYR cc_start: 0.5679 (m-80) cc_final: 0.5317 (m-80) outliers start: 91 outliers final: 48 residues processed: 322 average time/residue: 1.2868 time to fit residues: 470.0811 Evaluate side-chains 290 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 104 optimal weight: 0.0980 chunk 146 optimal weight: 0.7980 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 529 GLN B 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20013 Z= 0.134 Angle : 0.494 6.396 27126 Z= 0.262 Chirality : 0.040 0.183 3075 Planarity : 0.004 0.048 3398 Dihedral : 10.416 143.347 2863 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.03 % Favored : 94.67 % Rotamer: Outliers : 3.23 % Allowed : 18.36 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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 (0.17), residues: 2384 helix: 0.50 (0.18), residues: 873 sheet: 0.00 (0.32), residues: 303 loop : -0.89 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 675 HIS 0.003 0.000 HIS F 548 PHE 0.011 0.001 PHE D 451 TYR 0.017 0.001 TYR C 482 ARG 0.007 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 256 time to evaluate : 2.087 Fit side-chains REVERT: A 377 LYS cc_start: 0.8768 (mppt) cc_final: 0.8497 (tmmt) REVERT: A 618 MET cc_start: 0.7083 (mmm) cc_final: 0.6511 (tmm) REVERT: B 343 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: B 504 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: C 537 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7196 (p0) REVERT: D 649 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7792 (mptm) REVERT: E 560 ASP cc_start: 0.6369 (m-30) cc_final: 0.5919 (t70) REVERT: E 576 LYS cc_start: 0.8327 (tttt) cc_final: 0.7799 (tmmt) REVERT: F 351 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6800 (mt) REVERT: F 486 LEU cc_start: 0.6896 (mt) cc_final: 0.6685 (mm) REVERT: F 532 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6225 (tt) REVERT: F 664 TYR cc_start: 0.5756 (m-80) cc_final: 0.5424 (m-80) outliers start: 69 outliers final: 24 residues processed: 308 average time/residue: 1.2821 time to fit residues: 447.6304 Evaluate side-chains 272 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.0570 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN B 529 GLN B 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20013 Z= 0.150 Angle : 0.500 7.794 27126 Z= 0.263 Chirality : 0.041 0.264 3075 Planarity : 0.004 0.048 3398 Dihedral : 10.208 141.787 2859 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 3.19 % Allowed : 19.11 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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 (0.17), residues: 2384 helix: 0.64 (0.18), residues: 871 sheet: -0.05 (0.32), residues: 313 loop : -0.84 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 675 HIS 0.005 0.001 HIS B 597 PHE 0.024 0.001 PHE C 698 TYR 0.017 0.001 TYR B 482 ARG 0.007 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 248 time to evaluate : 2.265 Fit side-chains REVERT: A 377 LYS cc_start: 0.8815 (mppt) cc_final: 0.8545 (tmmt) REVERT: A 390 LYS cc_start: 0.8733 (mptt) cc_final: 0.8490 (mptt) REVERT: A 618 MET cc_start: 0.7107 (mmm) cc_final: 0.6528 (tmm) REVERT: A 690 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: B 504 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: C 537 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7290 (p0) REVERT: D 649 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7823 (mptm) REVERT: D 757 GLU cc_start: 0.7143 (mp0) cc_final: 0.6751 (mp0) REVERT: E 390 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: E 560 ASP cc_start: 0.6512 (m-30) cc_final: 0.6035 (t70) REVERT: E 576 LYS cc_start: 0.8366 (tttt) cc_final: 0.7780 (tmmt) REVERT: F 335 ASP cc_start: 0.6897 (m-30) cc_final: 0.6697 (m-30) REVERT: F 351 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6862 (mt) REVERT: F 532 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6216 (tt) REVERT: F 664 TYR cc_start: 0.5778 (m-80) cc_final: 0.5429 (m-80) outliers start: 68 outliers final: 37 residues processed: 301 average time/residue: 1.2881 time to fit residues: 439.9156 Evaluate side-chains 280 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 121 optimal weight: 0.0670 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20013 Z= 0.175 Angle : 0.512 6.671 27126 Z= 0.268 Chirality : 0.041 0.223 3075 Planarity : 0.004 0.063 3398 Dihedral : 10.194 141.756 2859 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.16 % Favored : 94.59 % Rotamer: Outliers : 3.23 % Allowed : 19.58 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.27 (0.17), residues: 2384 helix: 0.66 (0.18), residues: 874 sheet: -0.07 (0.31), residues: 316 loop : -0.81 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 675 HIS 0.006 0.001 HIS B 597 PHE 0.013 0.001 PHE B 357 TYR 0.019 0.001 TYR B 482 ARG 0.008 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 250 time to evaluate : 2.341 Fit side-chains REVERT: A 377 LYS cc_start: 0.8851 (mppt) cc_final: 0.8567 (tmmt) REVERT: A 618 MET cc_start: 0.7126 (mmm) cc_final: 0.6560 (tmm) REVERT: A 690 PRO cc_start: 0.7538 (Cg_endo) cc_final: 0.7113 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: B 504 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: C 537 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7137 (p0) REVERT: D 649 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7813 (mptm) REVERT: D 757 GLU cc_start: 0.7178 (mp0) cc_final: 0.6796 (mp0) REVERT: E 390 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (mtmt) REVERT: E 560 ASP cc_start: 0.6327 (m-30) cc_final: 0.5892 (t70) REVERT: E 576 LYS cc_start: 0.8393 (tttt) cc_final: 0.7804 (tmmt) REVERT: F 335 ASP cc_start: 0.6858 (m-30) cc_final: 0.6630 (m-30) REVERT: F 351 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6869 (mt) REVERT: F 532 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6216 (tt) REVERT: F 664 TYR cc_start: 0.5945 (m-80) cc_final: 0.5581 (m-80) outliers start: 69 outliers final: 46 residues processed: 300 average time/residue: 1.2896 time to fit residues: 438.8544 Evaluate side-chains 287 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 0.0040 chunk 131 optimal weight: 0.5980 chunk 195 optimal weight: 0.0370 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20013 Z= 0.150 Angle : 0.506 8.149 27126 Z= 0.265 Chirality : 0.041 0.223 3075 Planarity : 0.004 0.052 3398 Dihedral : 10.094 141.967 2859 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 3.23 % Allowed : 19.67 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.21 (0.17), residues: 2384 helix: 0.76 (0.18), residues: 865 sheet: -0.02 (0.32), residues: 316 loop : -0.80 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 675 HIS 0.006 0.001 HIS F 548 PHE 0.027 0.001 PHE C 698 TYR 0.017 0.001 TYR C 482 ARG 0.009 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 246 time to evaluate : 2.234 Fit side-chains REVERT: A 377 LYS cc_start: 0.8791 (mppt) cc_final: 0.8515 (tmmt) REVERT: A 618 MET cc_start: 0.7025 (mmm) cc_final: 0.6555 (tmm) REVERT: A 690 PRO cc_start: 0.7542 (Cg_endo) cc_final: 0.7101 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: B 504 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: C 390 LYS cc_start: 0.8650 (mppt) cc_final: 0.8445 (mptt) REVERT: C 537 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7277 (p0) REVERT: C 557 GLU cc_start: 0.6934 (mm-30) cc_final: 0.5931 (tp30) REVERT: D 649 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7926 (mptm) REVERT: D 757 GLU cc_start: 0.7135 (mp0) cc_final: 0.6722 (mp0) REVERT: E 390 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: E 560 ASP cc_start: 0.6313 (m-30) cc_final: 0.5873 (t70) REVERT: E 576 LYS cc_start: 0.8448 (tttt) cc_final: 0.7833 (tmmt) REVERT: F 335 ASP cc_start: 0.6783 (m-30) cc_final: 0.6543 (m-30) REVERT: F 351 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6868 (mt) REVERT: F 532 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6236 (tt) outliers start: 69 outliers final: 42 residues processed: 304 average time/residue: 1.2297 time to fit residues: 425.9616 Evaluate side-chains 286 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN B 632 GLN B 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20013 Z= 0.226 Angle : 0.544 7.402 27126 Z= 0.284 Chirality : 0.042 0.165 3075 Planarity : 0.004 0.056 3398 Dihedral : 10.233 141.656 2859 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 3.56 % Allowed : 19.53 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.33 (0.17), residues: 2384 helix: 0.65 (0.18), residues: 861 sheet: -0.08 (0.32), residues: 312 loop : -0.86 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 675 HIS 0.007 0.001 HIS B 597 PHE 0.018 0.001 PHE B 698 TYR 0.021 0.001 TYR B 482 ARG 0.009 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 240 time to evaluate : 2.191 Fit side-chains REVERT: A 377 LYS cc_start: 0.8814 (mppt) cc_final: 0.8524 (tmmt) REVERT: A 618 MET cc_start: 0.7054 (mmm) cc_final: 0.6631 (tmm) REVERT: A 690 PRO cc_start: 0.7560 (Cg_endo) cc_final: 0.7084 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: B 504 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 537 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7126 (p0) REVERT: C 557 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6080 (pm20) REVERT: D 649 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7905 (mptm) REVERT: D 757 GLU cc_start: 0.7192 (mp0) cc_final: 0.6781 (mp0) REVERT: E 390 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8354 (mtmt) REVERT: E 560 ASP cc_start: 0.6402 (m-30) cc_final: 0.5953 (t70) REVERT: E 576 LYS cc_start: 0.8482 (tttt) cc_final: 0.7861 (tmmt) REVERT: F 335 ASP cc_start: 0.6798 (m-30) cc_final: 0.6557 (m-30) REVERT: F 351 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6923 (mt) REVERT: F 532 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6232 (tt) outliers start: 76 outliers final: 49 residues processed: 297 average time/residue: 1.2807 time to fit residues: 431.5633 Evaluate side-chains 289 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 234 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 660 GLN B 632 GLN B 660 GLN D 713 HIS D 763 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20013 Z= 0.431 Angle : 0.667 9.470 27126 Z= 0.344 Chirality : 0.047 0.209 3075 Planarity : 0.005 0.057 3398 Dihedral : 10.746 138.088 2859 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.96 % Favored : 93.79 % Rotamer: Outliers : 3.51 % Allowed : 19.72 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.70 (0.17), residues: 2384 helix: 0.19 (0.18), residues: 873 sheet: -0.04 (0.31), residues: 306 loop : -1.03 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 675 HIS 0.014 0.002 HIS B 597 PHE 0.033 0.002 PHE B 698 TYR 0.026 0.002 TYR B 482 ARG 0.007 0.001 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 244 time to evaluate : 2.197 Fit side-chains REVERT: A 377 LYS cc_start: 0.8870 (mppt) cc_final: 0.8542 (tmmt) REVERT: A 618 MET cc_start: 0.7039 (mmm) cc_final: 0.6662 (tmm) REVERT: A 690 PRO cc_start: 0.7761 (Cg_endo) cc_final: 0.7327 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: B 504 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: C 537 ASP cc_start: 0.8137 (p0) cc_final: 0.7468 (p0) REVERT: C 653 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: D 649 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7901 (mptm) REVERT: D 665 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8015 (ttp-170) REVERT: E 560 ASP cc_start: 0.6595 (m-30) cc_final: 0.6127 (t70) REVERT: E 576 LYS cc_start: 0.8380 (tttt) cc_final: 0.7791 (tmmt) REVERT: F 335 ASP cc_start: 0.6846 (m-30) cc_final: 0.6631 (m-30) REVERT: F 351 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7022 (mt) REVERT: F 486 LEU cc_start: 0.7054 (mt) cc_final: 0.6717 (mm) outliers start: 75 outliers final: 50 residues processed: 302 average time/residue: 1.3604 time to fit residues: 464.8092 Evaluate side-chains 290 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN B 632 GLN B 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 20013 Z= 0.290 Angle : 0.855 59.196 27126 Z= 0.460 Chirality : 0.045 0.674 3075 Planarity : 0.006 0.202 3398 Dihedral : 10.749 138.763 2859 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.83 % Favored : 93.88 % Rotamer: Outliers : 2.81 % Allowed : 20.89 % Favored : 76.30 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.71 (0.17), residues: 2384 helix: 0.21 (0.18), residues: 873 sheet: -0.05 (0.31), residues: 306 loop : -1.06 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 675 HIS 0.012 0.001 HIS B 597 PHE 0.025 0.002 PHE B 698 TYR 0.025 0.001 TYR B 482 ARG 0.010 0.000 ARG A 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 236 time to evaluate : 2.409 Fit side-chains REVERT: A 332 ARG cc_start: 0.8338 (mtt-85) cc_final: 0.8058 (mtp85) REVERT: A 377 LYS cc_start: 0.8865 (mppt) cc_final: 0.8535 (tmmt) REVERT: A 618 MET cc_start: 0.7030 (mmm) cc_final: 0.6655 (tmm) REVERT: A 690 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: B 343 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 504 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: C 537 ASP cc_start: 0.8128 (p0) cc_final: 0.7456 (p0) REVERT: C 653 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: D 649 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7896 (mptm) REVERT: D 665 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7995 (ttp-170) REVERT: E 560 ASP cc_start: 0.6586 (m-30) cc_final: 0.6122 (t70) REVERT: E 576 LYS cc_start: 0.8373 (tttt) cc_final: 0.7788 (tmmt) REVERT: F 335 ASP cc_start: 0.6831 (m-30) cc_final: 0.6620 (m-30) REVERT: F 351 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7029 (mt) REVERT: F 486 LEU cc_start: 0.7070 (mt) cc_final: 0.6737 (mm) outliers start: 60 outliers final: 48 residues processed: 284 average time/residue: 1.3506 time to fit residues: 433.0189 Evaluate side-chains 285 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain D residue 555 CYS Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 605 ASN Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122515 restraints weight = 22863.557| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.84 r_work: 0.3006 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 20013 Z= 0.290 Angle : 0.855 59.196 27126 Z= 0.460 Chirality : 0.045 0.674 3075 Planarity : 0.006 0.202 3398 Dihedral : 10.749 138.763 2859 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.83 % Favored : 93.88 % Rotamer: Outliers : 2.53 % Allowed : 21.31 % Favored : 76.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.04 % 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: -0.71 (0.17), residues: 2384 helix: 0.21 (0.18), residues: 873 sheet: -0.05 (0.31), residues: 306 loop : -1.06 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 675 HIS 0.012 0.001 HIS B 597 PHE 0.025 0.002 PHE B 698 TYR 0.025 0.001 TYR B 482 ARG 0.010 0.000 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7012.03 seconds wall clock time: 126 minutes 53.07 seconds (7613.07 seconds total)