Starting phenix.real_space_refine on Thu Mar 21 02:18:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/03_2024/8s91_40234_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 177 5.16 5 C 18309 2.51 5 N 4980 2.21 5 O 5535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 721": "OE1" <-> "OE2" Residue "B TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ASP 227": "OD1" <-> "OD2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "D TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 640": "OE1" <-> "OE2" Residue "D GLU 647": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E ASP 336": "OD1" <-> "OD2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 557": "OD1" <-> "OD2" Residue "E ASP 586": "OD1" <-> "OD2" Residue "E GLU 622": "OE1" <-> "OE2" Residue "E GLU 647": "OE1" <-> "OE2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 464": "OD1" <-> "OD2" Residue "F ASP 496": "OD1" <-> "OD2" Residue "F ASP 498": "OD1" <-> "OD2" Residue "F GLU 577": "OE1" <-> "OE2" Residue "F PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F GLU 622": "OE1" <-> "OE2" Residue "F GLU 637": "OE1" <-> "OE2" Residue "F GLU 647": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29019 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "B" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "C" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4703 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 29, 'TRANS': 572} Chain breaks: 5 Chain: "D" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "E" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "F" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4914 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 22, 'TRANS': 598} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.15, per 1000 atoms: 0.52 Number of scatterers: 29019 At special positions: 0 Unit cell: (153.18, 153.18, 127.65, 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 177 16.00 P 12 15.00 Mg 6 11.99 O 5535 8.00 N 4980 7.00 C 18309 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: 11.20 Conformation dependent library (CDL) restraints added in 5.3 seconds 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 23 sheets defined 34.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.646A pdb=" N GLU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 105 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 153 through 174 removed outlier: 4.005A pdb=" N GLY A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.534A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.516A pdb=" N ALA A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 506 through 509 No H-bonds generated for 'chain 'A' and resid 506 through 509' Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 583 through 586 No H-bonds generated for 'chain 'A' and resid 583 through 586' Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 663 through 675 removed outlier: 3.705A pdb=" N LYS A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 700 removed outlier: 3.986A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 4.134A pdb=" N ALA A 724 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 742 removed outlier: 3.832A pdb=" N ILE A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 749 through 752 No H-bonds generated for 'chain 'A' and resid 749 through 752' Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.631A pdb=" N GLU B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 151 through 174 removed outlier: 3.711A pdb=" N CYS B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.518A pdb=" N PHE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.633A pdb=" N ALA B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 506 through 509 No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.507A pdb=" N GLU B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 586 No H-bonds generated for 'chain 'B' and resid 583 through 586' Processing helix chain 'B' and resid 600 through 611 Processing helix chain 'B' and resid 663 through 673 removed outlier: 3.795A pdb=" N GLY B 671 " --> pdb=" O ARG B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.972A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.992A pdb=" N ALA B 724 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.516A pdb=" N ASP B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 749 through 752 No H-bonds generated for 'chain 'B' and resid 749 through 752' Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 91 through 105 removed outlier: 3.638A pdb=" N GLU C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 105 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 151 through 174 removed outlier: 3.841A pdb=" N CYS C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 506 through 509 No H-bonds generated for 'chain 'C' and resid 506 through 509' Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 663 through 674 removed outlier: 3.707A pdb=" N LYS C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C 671 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 672 " --> pdb=" O LYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 700 removed outlier: 3.923A pdb=" N ARG C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 724 removed outlier: 3.987A pdb=" N ALA C 724 " --> pdb=" O THR C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.977A pdb=" N ILE C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 745 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 752 No H-bonds generated for 'chain 'C' and resid 749 through 752' Processing helix chain 'D' and resid 3 through 20 removed outlier: 3.655A pdb=" N THR D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 29 Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 64 through 82 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 358 through 368 removed outlier: 3.850A pdb=" N LYS D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.549A pdb=" N GLU D 432 " --> pdb=" O HIS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 469 through 472 No H-bonds generated for 'chain 'D' and resid 469 through 472' Processing helix chain 'D' and resid 497 through 506 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 540 through 555 removed outlier: 4.378A pdb=" N GLN D 544 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 581 removed outlier: 4.464A pdb=" N ILE D 573 " --> pdb=" O GLU D 570 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 575 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 603 removed outlier: 3.933A pdb=" N SER D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 4.011A pdb=" N GLU D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 653 removed outlier: 3.768A pdb=" N SER D 646 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.657A pdb=" N THR E 7 " --> pdb=" O SER E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 52 through 58 removed outlier: 4.013A pdb=" N GLU E 56 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 82 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 282 through 294 Processing helix chain 'E' and resid 299 through 309 removed outlier: 4.001A pdb=" N ARG E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 329 Processing helix chain 'E' and resid 358 through 368 removed outlier: 3.686A pdb=" N LYS E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 469 through 472 No H-bonds generated for 'chain 'E' and resid 469 through 472' Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 497 through 506 Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 540 through 554 removed outlier: 4.251A pdb=" N GLN E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLN E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 572 Processing helix chain 'E' and resid 574 through 579 Processing helix chain 'E' and resid 590 through 603 removed outlier: 4.173A pdb=" N SER E 598 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 599 " --> pdb=" O THR E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 638 removed outlier: 4.147A pdb=" N GLU E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 653 removed outlier: 3.931A pdb=" N SER E 646 " --> pdb=" O GLN E 642 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU E 647 " --> pdb=" O SER E 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.694A pdb=" N THR F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 52 through 58 removed outlier: 4.198A pdb=" N GLU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 82 Processing helix chain 'F' and resid 226 through 228 No H-bonds generated for 'chain 'F' and resid 226 through 228' Processing helix chain 'F' and resid 282 through 294 Processing helix chain 'F' and resid 299 through 309 removed outlier: 3.899A pdb=" N ARG F 303 " --> pdb=" O PRO F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 329 Processing helix chain 'F' and resid 358 through 368 removed outlier: 3.858A pdb=" N LYS F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'F' and resid 428 through 432 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 469 through 472 No H-bonds generated for 'chain 'F' and resid 469 through 472' Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 497 through 507 Processing helix chain 'F' and resid 521 through 530 Processing helix chain 'F' and resid 540 through 555 removed outlier: 4.425A pdb=" N GLN F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN F 555 " --> pdb=" O GLN F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 581 removed outlier: 3.827A pdb=" N ARG F 574 " --> pdb=" O GLU F 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 581 " --> pdb=" O GLU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 603 Processing helix chain 'F' and resid 624 through 638 removed outlier: 3.992A pdb=" N GLU F 637 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS F 638 " --> pdb=" O LEU F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 653 removed outlier: 3.752A pdb=" N SER F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU F 647 " --> pdb=" O SER F 643 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 124 removed outlier: 8.075A pdb=" N HIS A 195 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL A 123 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 197 " --> pdb=" O VAL A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 219 through 223 removed outlier: 3.878A pdb=" N ILE A 219 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 333 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE A 334 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA A 359 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS A 336 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE A 357 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR A 310 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ILE A 357 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 312 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 359 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU A 314 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER A 361 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 311 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 557 through 560 removed outlier: 6.601A pdb=" N ILE A 450 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ALA A 560 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 452 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 589 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 453 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE A 591 " --> pdb=" O VAL A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 121 through 124 Processing sheet with id= E, first strand: chain 'B' and resid 219 through 223 removed outlier: 3.590A pdb=" N ILE B 219 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 331 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 332 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE B 334 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA B 359 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS B 336 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE B 357 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N THR B 310 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ILE B 357 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU B 312 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 359 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU B 314 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 361 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 311 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 557 through 560 removed outlier: 6.750A pdb=" N ILE B 450 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA B 560 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 452 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 589 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 453 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 591 " --> pdb=" O VAL B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.536A pdb=" N ARG C 197 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 291 through 294 removed outlier: 7.744A pdb=" N LEU C 355 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU C 312 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 332 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 557 through 560 removed outlier: 6.629A pdb=" N ILE C 450 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA C 560 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 452 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C 589 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 453 " --> pdb=" O LEU C 589 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE C 591 " --> pdb=" O VAL C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 38 through 43 removed outlier: 3.526A pdb=" N VAL D 40 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 126 through 128 removed outlier: 3.659A pdb=" N THR D 239 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 243 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA D 265 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N MET D 245 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU D 263 " --> pdb=" O MET D 245 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG D 247 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE D 261 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N SER D 219 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N LEU D 263 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS D 221 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA D 265 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 223 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TYR D 267 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N GLU D 225 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 12.384A pdb=" N GLN D 269 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 202 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 224 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 485 through 489 removed outlier: 4.208A pdb=" N GLY D 352 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY D 409 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU D 454 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS D 411 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA D 456 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 413 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 414 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 435 through 438 removed outlier: 3.743A pdb=" N LEU D 447 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 438 " --> pdb=" O CYS D 445 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 38 through 43 removed outlier: 3.578A pdb=" N HIS E 97 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 40 " --> pdb=" O HIS E 97 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.522A pdb=" N GLY E 128 " --> pdb=" O LEU E 238 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 199 through 205 removed outlier: 3.790A pdb=" N GLN E 200 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 224 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 202 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE E 261 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS E 221 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU E 263 " --> pdb=" O LYS E 221 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 485 through 489 removed outlier: 4.014A pdb=" N GLY E 352 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY E 409 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU E 454 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N CYS E 411 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA E 456 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE E 413 " --> pdb=" O ALA E 456 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 435 through 438 removed outlier: 3.806A pdb=" N LEU E 447 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 438 " --> pdb=" O CYS E 445 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 39 through 43 removed outlier: 6.698A pdb=" N HIS F 97 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL F 42 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG F 99 " --> pdb=" O VAL F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 123 through 128 removed outlier: 3.554A pdb=" N GLY F 242 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 126 " --> pdb=" O ILE F 240 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 199 through 205 removed outlier: 3.818A pdb=" N GLN F 200 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 224 " --> pdb=" O GLN F 200 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 485 through 489 removed outlier: 4.227A pdb=" N GLY F 352 " --> pdb=" O THR F 457 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY F 409 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU F 454 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS F 411 " --> pdb=" O LEU F 454 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ALA F 456 " --> pdb=" O CYS F 411 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE F 413 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 373 " --> pdb=" O LEU F 410 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 435 through 438 removed outlier: 3.671A pdb=" N LEU F 447 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 438 " --> pdb=" O CYS F 445 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2013 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: 8.09 Time building geometry restraints manager: 12.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9580 1.34 - 1.46: 6085 1.46 - 1.58: 13558 1.58 - 1.70: 18 1.70 - 1.82: 264 Bond restraints: 29505 Sorted by residual: bond pdb=" N ASP E 226 " pdb=" CA ASP E 226 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.84e+00 bond pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLU E 31 " pdb=" CG GLU E 31 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CA LEU F 480 " pdb=" CB LEU F 480 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.31e-02 5.83e+03 1.13e+00 bond pdb=" CA VAL B 210 " pdb=" CB VAL B 210 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.06e+00 ... (remaining 29500 not shown) Histogram of bond angle deviations from ideal: 99.28 - 107.10: 832 107.10 - 114.91: 18016 114.91 - 122.72: 17987 122.72 - 130.54: 2980 130.54 - 138.35: 115 Bond angle restraints: 39930 Sorted by residual: angle pdb=" C ALA C 560 " pdb=" N ASN C 561 " pdb=" CA ASN C 561 " ideal model delta sigma weight residual 122.31 138.35 -16.04 2.34e+00 1.83e-01 4.70e+01 angle pdb=" C LEU F 518 " pdb=" N TRP F 519 " pdb=" CA TRP F 519 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C LEU E 518 " pdb=" CA LEU E 518 " pdb=" CB LEU E 518 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" C LEU D 518 " pdb=" N TRP D 519 " pdb=" CA TRP D 519 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" C LEU E 518 " pdb=" N TRP E 519 " pdb=" CA TRP E 519 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 ... (remaining 39925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 17489 32.01 - 64.02: 492 64.02 - 96.03: 64 96.03 - 128.03: 11 128.03 - 160.04: 7 Dihedral angle restraints: 18063 sinusoidal: 7365 harmonic: 10698 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 100.05 -160.04 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 99.35 -159.35 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP C2001 " pdb=" O5' ADP C2001 " pdb=" PA ADP C2001 " pdb=" O2A ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 97.08 -157.08 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 18060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3434 0.043 - 0.086: 892 0.086 - 0.129: 270 0.129 - 0.172: 26 0.172 - 0.215: 4 Chirality restraints: 4626 Sorted by residual: chirality pdb=" CB ILE F 486 " pdb=" CA ILE F 486 " pdb=" CG1 ILE F 486 " pdb=" CG2 ILE F 486 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA GLU B 202 " pdb=" N GLU B 202 " pdb=" C GLU B 202 " pdb=" CB GLU B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CB THR E 338 " pdb=" CA THR E 338 " pdb=" OG1 THR E 338 " pdb=" CG2 THR E 338 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 4623 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 518 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LEU E 518 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU E 518 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP E 519 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 518 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C LEU F 518 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU F 518 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP F 519 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 266 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 267 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.041 5.00e-02 4.00e+02 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 197 2.55 - 3.14: 22477 3.14 - 3.73: 41718 3.73 - 4.31: 52228 4.31 - 4.90: 86745 Nonbonded interactions: 203365 Sorted by model distance: nonbonded pdb=" O1B ADP E2001 " pdb="MG MG E2002 " model vdw 1.964 2.170 nonbonded pdb=" O1B ADP D2001 " pdb="MG MG D2002 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP D2001 " pdb="MG MG D2002 " model vdw 2.057 2.170 nonbonded pdb=" O THR E 46 " pdb=" OG1 THR E 50 " model vdw 2.083 2.440 nonbonded pdb=" OG SER C 461 " pdb="MG MG C2002 " model vdw 2.104 2.170 ... (remaining 203360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.020 Extract box with map and model: 8.420 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 74.140 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29505 Z= 0.168 Angle : 0.711 16.038 39930 Z= 0.373 Chirality : 0.042 0.215 4626 Planarity : 0.005 0.073 5091 Dihedral : 15.789 160.042 11127 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.41 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3603 helix: 0.56 (0.16), residues: 1269 sheet: -0.96 (0.24), residues: 474 loop : -2.39 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 292 HIS 0.010 0.001 HIS F 37 PHE 0.022 0.001 PHE B 102 TYR 0.023 0.001 TYR B 391 ARG 0.010 0.001 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 586 time to evaluate : 4.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8559 (t80) cc_final: 0.8316 (t80) REVERT: B 113 ASP cc_start: 0.6985 (t70) cc_final: 0.6730 (t70) REVERT: B 258 TYR cc_start: 0.7986 (t80) cc_final: 0.7683 (t80) REVERT: C 151 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8079 (ttmm) REVERT: D 52 MET cc_start: 0.7995 (pmm) cc_final: 0.7638 (tmm) REVERT: D 134 SER cc_start: 0.7477 (t) cc_final: 0.7036 (p) REVERT: D 220 MET cc_start: 0.8190 (tpp) cc_final: 0.7965 (mmm) REVERT: D 524 MET cc_start: 0.7181 (tpp) cc_final: 0.6915 (mmt) REVERT: E 114 ILE cc_start: 0.8025 (mm) cc_final: 0.7543 (tp) REVERT: F 51 ASN cc_start: 0.8957 (t0) cc_final: 0.8520 (t0) REVERT: F 60 MET cc_start: 0.8116 (ttt) cc_final: 0.7647 (ttt) REVERT: F 146 MET cc_start: 0.5218 (pmm) cc_final: 0.4720 (ppp) REVERT: F 651 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7839 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.3668 time to fit residues: 352.8400 Evaluate side-chains 425 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 5.9990 chunk 277 optimal weight: 0.0870 chunk 153 optimal weight: 0.0030 chunk 94 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 162 GLN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 600 HIS A 608 HIS B 213 ASN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS C 213 ASN C 608 HIS ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 209 GLN D 433 GLN D 434 GLN D 551 GLN E 5 GLN E 209 GLN F 59 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29505 Z= 0.144 Angle : 0.597 6.965 39930 Z= 0.294 Chirality : 0.041 0.180 4626 Planarity : 0.004 0.069 5091 Dihedral : 9.313 169.569 4032 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.60 % Favored : 89.98 % Rotamer: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3603 helix: 0.65 (0.16), residues: 1269 sheet: -1.14 (0.23), residues: 495 loop : -2.33 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 519 HIS 0.007 0.001 HIS F 37 PHE 0.018 0.001 PHE E 13 TYR 0.014 0.001 TYR C 201 ARG 0.005 0.000 ARG C 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 586 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6720 (ptt180) cc_final: 0.5187 (mmm-85) REVERT: A 391 TYR cc_start: 0.8613 (t80) cc_final: 0.8264 (t80) REVERT: B 113 ASP cc_start: 0.7007 (t70) cc_final: 0.6780 (t70) REVERT: B 258 TYR cc_start: 0.8056 (t80) cc_final: 0.7771 (t80) REVERT: B 289 GLN cc_start: 0.8280 (pp30) cc_final: 0.7533 (pp30) REVERT: C 113 ASP cc_start: 0.7080 (t70) cc_final: 0.6585 (t70) REVERT: C 151 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8165 (ttmm) REVERT: D 20 TYR cc_start: 0.6676 (m-10) cc_final: 0.5922 (m-10) REVERT: D 52 MET cc_start: 0.8122 (pmm) cc_final: 0.7655 (tmm) REVERT: D 134 SER cc_start: 0.7587 (t) cc_final: 0.7152 (p) REVERT: D 287 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 317 MET cc_start: 0.6939 (mmm) cc_final: 0.6343 (mmp) REVERT: D 551 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: F 32 ARG cc_start: 0.7284 (tpt90) cc_final: 0.6872 (tpt90) REVERT: F 51 ASN cc_start: 0.8948 (t0) cc_final: 0.8435 (t0) REVERT: F 146 MET cc_start: 0.5202 (pmm) cc_final: 0.4583 (ppp) REVERT: F 166 PHE cc_start: 0.8283 (m-80) cc_final: 0.7302 (m-80) REVERT: F 521 MET cc_start: 0.7766 (ppp) cc_final: 0.7491 (tpt) REVERT: F 651 ARG cc_start: 0.8395 (ttt180) cc_final: 0.7894 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 588 average time/residue: 0.3666 time to fit residues: 352.3415 Evaluate side-chains 423 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 226 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 HIS D 59 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 433 GLN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29505 Z= 0.268 Angle : 0.688 9.326 39930 Z= 0.341 Chirality : 0.044 0.200 4626 Planarity : 0.005 0.066 5091 Dihedral : 8.899 162.154 4032 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.13 % Favored : 88.48 % Rotamer: Outliers : 0.12 % Allowed : 4.75 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3603 helix: 0.46 (0.16), residues: 1269 sheet: -1.27 (0.22), residues: 564 loop : -2.40 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 292 HIS 0.007 0.002 HIS F 617 PHE 0.038 0.002 PHE E 13 TYR 0.023 0.002 TYR E 199 ARG 0.006 0.001 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 576 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6815 (ttp80) REVERT: A 391 TYR cc_start: 0.8652 (t80) cc_final: 0.8173 (t80) REVERT: A 539 ILE cc_start: 0.8433 (tt) cc_final: 0.8218 (tt) REVERT: A 657 THR cc_start: 0.7831 (m) cc_final: 0.7605 (t) REVERT: B 113 ASP cc_start: 0.7155 (t70) cc_final: 0.6924 (t70) REVERT: B 258 TYR cc_start: 0.8321 (t80) cc_final: 0.8072 (t80) REVERT: B 390 LEU cc_start: 0.9567 (mp) cc_final: 0.9283 (mp) REVERT: B 391 TYR cc_start: 0.7955 (t80) cc_final: 0.7649 (t80) REVERT: C 151 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8194 (ttmm) REVERT: C 736 ASP cc_start: 0.8059 (m-30) cc_final: 0.7790 (m-30) REVERT: D 52 MET cc_start: 0.8132 (pmm) cc_final: 0.7594 (tmm) REVERT: D 134 SER cc_start: 0.8371 (t) cc_final: 0.7870 (p) REVERT: D 201 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7980 (tt0) REVERT: D 287 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 317 MET cc_start: 0.6826 (mmm) cc_final: 0.6224 (mmp) REVERT: D 451 THR cc_start: 0.9093 (p) cc_final: 0.8851 (m) REVERT: E 295 TYR cc_start: 0.7945 (m-80) cc_final: 0.7133 (m-80) REVERT: F 51 ASN cc_start: 0.8883 (t0) cc_final: 0.8510 (t0) REVERT: F 146 MET cc_start: 0.5368 (pmm) cc_final: 0.4709 (ppp) REVERT: F 405 LEU cc_start: 0.8625 (mt) cc_final: 0.8366 (mt) outliers start: 4 outliers final: 0 residues processed: 578 average time/residue: 0.3597 time to fit residues: 335.5777 Evaluate side-chains 396 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 334 optimal weight: 0.9990 chunk 353 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 316 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29505 Z= 0.159 Angle : 0.614 8.412 39930 Z= 0.301 Chirality : 0.042 0.185 4626 Planarity : 0.004 0.066 5091 Dihedral : 8.617 167.922 4032 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.46 % Favored : 90.12 % Rotamer: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3603 helix: 0.57 (0.16), residues: 1266 sheet: -1.03 (0.23), residues: 519 loop : -2.33 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 292 HIS 0.007 0.001 HIS E 37 PHE 0.026 0.001 PHE D 13 TYR 0.015 0.001 TYR F 38 ARG 0.006 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7048 (ttp80) cc_final: 0.6833 (ttp80) REVERT: A 339 ASN cc_start: 0.8208 (t0) cc_final: 0.7752 (t0) REVERT: A 391 TYR cc_start: 0.8650 (t80) cc_final: 0.8067 (t80) REVERT: A 657 THR cc_start: 0.7875 (m) cc_final: 0.7435 (t) REVERT: B 113 ASP cc_start: 0.7191 (t70) cc_final: 0.6971 (t70) REVERT: B 258 TYR cc_start: 0.8302 (t80) cc_final: 0.8073 (t80) REVERT: B 289 GLN cc_start: 0.8236 (pp30) cc_final: 0.7525 (pp30) REVERT: B 390 LEU cc_start: 0.9541 (mp) cc_final: 0.9304 (mp) REVERT: C 105 ARG cc_start: 0.7925 (ptm160) cc_final: 0.7427 (ptp90) REVERT: C 136 ASN cc_start: 0.9143 (m110) cc_final: 0.8840 (m-40) REVERT: C 151 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8297 (ttmm) REVERT: C 394 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 736 ASP cc_start: 0.7921 (m-30) cc_final: 0.7683 (m-30) REVERT: D 52 MET cc_start: 0.8085 (pmm) cc_final: 0.7608 (tmm) REVERT: D 134 SER cc_start: 0.8164 (t) cc_final: 0.7698 (p) REVERT: D 220 MET cc_start: 0.8283 (tpp) cc_final: 0.8037 (tpt) REVERT: D 287 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 317 MET cc_start: 0.6935 (mmm) cc_final: 0.6258 (mmp) REVERT: D 451 THR cc_start: 0.9008 (p) cc_final: 0.8786 (m) REVERT: D 566 ILE cc_start: 0.8146 (tt) cc_final: 0.7788 (mm) REVERT: D 651 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7941 (tmm-80) REVERT: E 45 MET cc_start: 0.6936 (mmp) cc_final: 0.6599 (mmp) REVERT: E 166 PHE cc_start: 0.8644 (m-10) cc_final: 0.8347 (m-10) REVERT: E 295 TYR cc_start: 0.7964 (m-80) cc_final: 0.7036 (m-80) REVERT: E 629 GLN cc_start: 0.8738 (tt0) cc_final: 0.7645 (tm-30) REVERT: E 651 ARG cc_start: 0.8100 (tmm-80) cc_final: 0.7834 (tmm-80) REVERT: F 51 ASN cc_start: 0.8872 (t0) cc_final: 0.8493 (t0) REVERT: F 146 MET cc_start: 0.5300 (pmm) cc_final: 0.4644 (ppp) REVERT: F 254 ASP cc_start: 0.9139 (m-30) cc_final: 0.8937 (m-30) REVERT: F 405 LEU cc_start: 0.8620 (mt) cc_final: 0.8319 (mt) REVERT: F 651 ARG cc_start: 0.8333 (ttt180) cc_final: 0.7874 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.3749 time to fit residues: 351.8363 Evaluate side-chains 411 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 263 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 301 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29505 Z= 0.147 Angle : 0.607 9.510 39930 Z= 0.297 Chirality : 0.042 0.184 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.425 172.255 4032 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.85 % Favored : 89.73 % Rotamer: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3603 helix: 0.63 (0.16), residues: 1260 sheet: -0.98 (0.23), residues: 522 loop : -2.27 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 519 HIS 0.006 0.001 HIS E 37 PHE 0.025 0.001 PHE D 13 TYR 0.013 0.001 TYR F 38 ARG 0.006 0.000 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 566 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASN cc_start: 0.8244 (t0) cc_final: 0.7716 (t0) REVERT: A 391 TYR cc_start: 0.8642 (t80) cc_final: 0.8069 (t80) REVERT: A 539 ILE cc_start: 0.8440 (tt) cc_final: 0.8232 (tt) REVERT: B 113 ASP cc_start: 0.7200 (t70) cc_final: 0.6972 (t70) REVERT: B 258 TYR cc_start: 0.8269 (t80) cc_final: 0.8029 (t80) REVERT: B 289 GLN cc_start: 0.8369 (pp30) cc_final: 0.7622 (pp30) REVERT: B 701 GLN cc_start: 0.8295 (mm110) cc_final: 0.8070 (mt0) REVERT: B 744 MET cc_start: 0.7489 (tpp) cc_final: 0.7239 (tpp) REVERT: C 105 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7422 (ptp90) REVERT: C 136 ASN cc_start: 0.9171 (m110) cc_final: 0.8900 (m-40) REVERT: C 151 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8341 (ttmm) REVERT: C 736 ASP cc_start: 0.7962 (m-30) cc_final: 0.7693 (m-30) REVERT: D 52 MET cc_start: 0.8121 (pmm) cc_final: 0.7663 (tmm) REVERT: D 134 SER cc_start: 0.8346 (t) cc_final: 0.7802 (p) REVERT: D 287 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 317 MET cc_start: 0.7065 (mmm) cc_final: 0.6501 (mmp) REVERT: D 451 THR cc_start: 0.9022 (p) cc_final: 0.8783 (m) REVERT: D 566 ILE cc_start: 0.8076 (tt) cc_final: 0.7694 (mm) REVERT: D 651 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7925 (tmm-80) REVERT: E 295 TYR cc_start: 0.7987 (m-80) cc_final: 0.7014 (m-80) REVERT: E 629 GLN cc_start: 0.8672 (tt0) cc_final: 0.7604 (tm-30) REVERT: E 651 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: F 51 ASN cc_start: 0.8880 (t0) cc_final: 0.8517 (t0) REVERT: F 146 MET cc_start: 0.5362 (pmm) cc_final: 0.4659 (ppp) REVERT: F 254 ASP cc_start: 0.9142 (m-30) cc_final: 0.8921 (m-30) REVERT: F 651 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7885 (tmm-80) outliers start: 2 outliers final: 2 residues processed: 568 average time/residue: 0.3746 time to fit residues: 341.5138 Evaluate side-chains 409 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 293 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 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 209 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN D 152 HIS D 434 GLN E 5 GLN E 246 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29505 Z= 0.211 Angle : 0.655 9.881 39930 Z= 0.322 Chirality : 0.044 0.204 4626 Planarity : 0.004 0.076 5091 Dihedral : 8.376 165.316 4032 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.85 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3603 helix: 0.49 (0.16), residues: 1254 sheet: -1.14 (0.22), residues: 570 loop : -2.30 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 292 HIS 0.005 0.001 HIS E 37 PHE 0.029 0.002 PHE D 13 TYR 0.023 0.001 TYR B 752 ARG 0.008 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8788 (t80) cc_final: 0.8559 (t80) REVERT: A 539 ILE cc_start: 0.8555 (tt) cc_final: 0.8325 (tt) REVERT: B 113 ASP cc_start: 0.7281 (t70) cc_final: 0.7041 (t70) REVERT: B 144 GLU cc_start: 0.7374 (tp30) cc_final: 0.7074 (tp30) REVERT: B 258 TYR cc_start: 0.8480 (t80) cc_final: 0.8264 (t80) REVERT: B 390 LEU cc_start: 0.9565 (mp) cc_final: 0.9337 (mp) REVERT: B 391 TYR cc_start: 0.8579 (t80) cc_final: 0.8113 (t80) REVERT: B 701 GLN cc_start: 0.8398 (mm110) cc_final: 0.8090 (mt0) REVERT: B 731 GLU cc_start: 0.7313 (tp30) cc_final: 0.7056 (tp30) REVERT: C 136 ASN cc_start: 0.9163 (m110) cc_final: 0.8926 (m-40) REVERT: C 151 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8456 (ttmm) REVERT: D 52 MET cc_start: 0.8122 (pmm) cc_final: 0.7666 (tmm) REVERT: D 134 SER cc_start: 0.8600 (t) cc_final: 0.8013 (p) REVERT: D 287 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 317 MET cc_start: 0.7075 (mmm) cc_final: 0.6549 (mmp) REVERT: D 349 LEU cc_start: 0.8278 (tp) cc_final: 0.7920 (tp) REVERT: D 637 GLU cc_start: 0.7947 (tt0) cc_final: 0.7175 (tm-30) REVERT: D 651 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7863 (tmm-80) REVERT: E 295 TYR cc_start: 0.8287 (m-80) cc_final: 0.6985 (m-80) REVERT: E 595 THR cc_start: 0.7388 (m) cc_final: 0.6760 (p) REVERT: E 629 GLN cc_start: 0.8707 (tt0) cc_final: 0.7622 (tm-30) REVERT: F 51 ASN cc_start: 0.8858 (t0) cc_final: 0.8491 (t0) REVERT: F 146 MET cc_start: 0.5475 (pmm) cc_final: 0.4787 (ppp) REVERT: F 493 LYS cc_start: 0.8071 (mppt) cc_final: 0.7852 (tmtt) REVERT: F 651 ARG cc_start: 0.8466 (ttt180) cc_final: 0.7859 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.3738 time to fit residues: 331.4509 Evaluate side-chains 384 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 258 optimal weight: 0.0030 chunk 200 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 197 optimal weight: 0.0010 chunk 352 optimal weight: 7.9990 chunk 220 optimal weight: 0.3980 chunk 215 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN D 152 HIS D 434 GLN E 5 GLN ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29505 Z= 0.157 Angle : 0.625 8.140 39930 Z= 0.306 Chirality : 0.042 0.188 4626 Planarity : 0.004 0.075 5091 Dihedral : 8.220 167.575 4032 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.91 % Favored : 89.65 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3603 helix: 0.62 (0.16), residues: 1239 sheet: -1.07 (0.22), residues: 570 loop : -2.29 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 497 HIS 0.005 0.001 HIS E 37 PHE 0.024 0.001 PHE D 13 TYR 0.015 0.001 TYR E 199 ARG 0.007 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASN cc_start: 0.8385 (t0) cc_final: 0.7911 (t0) REVERT: A 390 LEU cc_start: 0.9499 (mt) cc_final: 0.9206 (mt) REVERT: A 536 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7839 (mm-40) REVERT: A 539 ILE cc_start: 0.8559 (tt) cc_final: 0.8347 (tt) REVERT: B 113 ASP cc_start: 0.7232 (t70) cc_final: 0.7001 (t70) REVERT: B 144 GLU cc_start: 0.7242 (tp30) cc_final: 0.6850 (tp30) REVERT: B 258 TYR cc_start: 0.8457 (t80) cc_final: 0.8232 (t80) REVERT: B 286 MET cc_start: 0.8411 (ptp) cc_final: 0.8189 (ptp) REVERT: B 289 GLN cc_start: 0.8315 (pp30) cc_final: 0.7552 (pp30) REVERT: B 701 GLN cc_start: 0.8506 (mm110) cc_final: 0.8134 (mt0) REVERT: B 731 GLU cc_start: 0.7308 (tp30) cc_final: 0.7037 (tp30) REVERT: C 151 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8451 (ttmm) REVERT: C 285 THR cc_start: 0.8363 (p) cc_final: 0.8160 (p) REVERT: D 52 MET cc_start: 0.8135 (pmm) cc_final: 0.7758 (tmm) REVERT: D 134 SER cc_start: 0.8560 (t) cc_final: 0.7971 (p) REVERT: D 287 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 317 MET cc_start: 0.7031 (mmm) cc_final: 0.6555 (mmp) REVERT: D 552 MET cc_start: 0.8366 (tpp) cc_final: 0.8080 (tpt) REVERT: D 637 GLU cc_start: 0.7935 (tt0) cc_final: 0.7134 (tm-30) REVERT: D 651 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7894 (tmm-80) REVERT: E 92 MET cc_start: 0.7198 (ttm) cc_final: 0.6933 (tpp) REVERT: E 94 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8939 (tp-100) REVERT: E 166 PHE cc_start: 0.8638 (m-10) cc_final: 0.8312 (m-10) REVERT: E 629 GLN cc_start: 0.8682 (tt0) cc_final: 0.7606 (tm-30) REVERT: F 51 ASN cc_start: 0.8802 (t0) cc_final: 0.8461 (t0) REVERT: F 60 MET cc_start: 0.7964 (tmm) cc_final: 0.6640 (tmm) REVERT: F 146 MET cc_start: 0.5432 (pmm) cc_final: 0.4755 (ppp) REVERT: F 254 ASP cc_start: 0.9199 (m-30) cc_final: 0.8975 (m-30) REVERT: F 651 ARG cc_start: 0.8516 (ttt180) cc_final: 0.7829 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.3721 time to fit residues: 329.0234 Evaluate side-chains 391 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 210 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 240 optimal weight: 0.0370 chunk 174 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 209 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS D 152 HIS D 434 GLN E 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29505 Z= 0.189 Angle : 0.659 10.310 39930 Z= 0.322 Chirality : 0.043 0.221 4626 Planarity : 0.004 0.073 5091 Dihedral : 8.142 164.442 4032 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.91 % Favored : 88.68 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3603 helix: 0.49 (0.16), residues: 1239 sheet: -1.11 (0.22), residues: 570 loop : -2.29 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 292 HIS 0.004 0.001 HIS E 37 PHE 0.026 0.002 PHE D 13 TYR 0.017 0.001 TYR E 199 ARG 0.007 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 546 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.9579 (mt) cc_final: 0.9370 (mt) REVERT: A 394 GLN cc_start: 0.8506 (mp10) cc_final: 0.8213 (mp10) REVERT: A 536 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7869 (mm-40) REVERT: A 538 SER cc_start: 0.8184 (m) cc_final: 0.7803 (p) REVERT: A 539 ILE cc_start: 0.8616 (tt) cc_final: 0.8287 (tt) REVERT: B 113 ASP cc_start: 0.7274 (t70) cc_final: 0.7037 (t70) REVERT: B 144 GLU cc_start: 0.7270 (tp30) cc_final: 0.6841 (tp30) REVERT: B 222 ARG cc_start: 0.7083 (tmm160) cc_final: 0.6863 (ttp80) REVERT: B 258 TYR cc_start: 0.8510 (t80) cc_final: 0.8273 (t80) REVERT: B 701 GLN cc_start: 0.8463 (mm110) cc_final: 0.8211 (mt0) REVERT: B 731 GLU cc_start: 0.7366 (tp30) cc_final: 0.7074 (tp30) REVERT: C 113 ASP cc_start: 0.6455 (t70) cc_final: 0.6054 (t70) REVERT: C 151 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8516 (ttmm) REVERT: D 52 MET cc_start: 0.8072 (pmm) cc_final: 0.7649 (tmm) REVERT: D 134 SER cc_start: 0.8706 (t) cc_final: 0.8173 (p) REVERT: D 201 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7748 (tt0) REVERT: D 287 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 317 MET cc_start: 0.7007 (mmm) cc_final: 0.6469 (mmp) REVERT: D 349 LEU cc_start: 0.8318 (tp) cc_final: 0.7979 (tp) REVERT: D 552 MET cc_start: 0.8411 (tpp) cc_final: 0.8143 (tpt) REVERT: D 637 GLU cc_start: 0.7747 (tt0) cc_final: 0.7015 (tm-30) REVERT: D 651 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7797 (tmm-80) REVERT: E 92 MET cc_start: 0.7408 (ttm) cc_final: 0.7130 (tpp) REVERT: E 94 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8886 (tp-100) REVERT: E 295 TYR cc_start: 0.8322 (m-80) cc_final: 0.7019 (m-80) REVERT: E 629 GLN cc_start: 0.8684 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 51 ASN cc_start: 0.8861 (t0) cc_final: 0.8525 (t0) REVERT: F 146 MET cc_start: 0.5647 (pmm) cc_final: 0.4891 (ppp) REVERT: F 254 ASP cc_start: 0.9210 (m-30) cc_final: 0.8986 (m-30) REVERT: F 651 ARG cc_start: 0.8520 (ttt180) cc_final: 0.7832 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 548 average time/residue: 0.3756 time to fit residues: 331.1994 Evaluate side-chains 400 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.3980 chunk 337 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 chunk 197 optimal weight: 0.0020 chunk 143 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 310 optimal weight: 0.0060 chunk 327 optimal weight: 0.9980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS B 600 HIS C 480 ASN D 86 GLN D 152 HIS D 434 GLN E 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29505 Z= 0.141 Angle : 0.636 11.230 39930 Z= 0.310 Chirality : 0.043 0.194 4626 Planarity : 0.004 0.065 5091 Dihedral : 7.976 169.808 4032 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.46 % Favored : 90.12 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3603 helix: 0.54 (0.16), residues: 1257 sheet: -0.80 (0.24), residues: 510 loop : -2.28 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 519 HIS 0.004 0.000 HIS E 37 PHE 0.021 0.001 PHE D 13 TYR 0.015 0.001 TYR D 199 ARG 0.007 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 556 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7962 (mm-40) REVERT: A 538 SER cc_start: 0.8078 (m) cc_final: 0.7697 (p) REVERT: A 539 ILE cc_start: 0.8602 (tt) cc_final: 0.8265 (tt) REVERT: B 113 ASP cc_start: 0.7261 (t70) cc_final: 0.7018 (t70) REVERT: B 222 ARG cc_start: 0.7043 (tmm160) cc_final: 0.6790 (ttp80) REVERT: B 258 TYR cc_start: 0.8430 (t80) cc_final: 0.8208 (t80) REVERT: B 289 GLN cc_start: 0.8428 (pp30) cc_final: 0.7610 (pp30) REVERT: B 650 LEU cc_start: 0.7091 (mt) cc_final: 0.6779 (mp) REVERT: B 731 GLU cc_start: 0.7289 (tp30) cc_final: 0.6986 (tp30) REVERT: C 151 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8501 (ttmm) REVERT: C 249 GLN cc_start: 0.8509 (pp30) cc_final: 0.8236 (pp30) REVERT: D 52 MET cc_start: 0.8035 (pmm) cc_final: 0.7675 (tmm) REVERT: D 134 SER cc_start: 0.8553 (t) cc_final: 0.7980 (p) REVERT: D 201 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7684 (tt0) REVERT: D 287 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 289 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8472 (mt-10) REVERT: D 317 MET cc_start: 0.6967 (mmm) cc_final: 0.6521 (mmp) REVERT: D 630 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7850 (tpp-160) REVERT: D 637 GLU cc_start: 0.7768 (tt0) cc_final: 0.6948 (tm-30) REVERT: D 651 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7790 (tmm-80) REVERT: E 92 MET cc_start: 0.7427 (ttm) cc_final: 0.7131 (tpp) REVERT: E 94 GLN cc_start: 0.9343 (mm-40) cc_final: 0.8884 (tp-100) REVERT: E 295 TYR cc_start: 0.8227 (m-80) cc_final: 0.6990 (m-80) REVERT: E 629 GLN cc_start: 0.8655 (tt0) cc_final: 0.7682 (tm-30) REVERT: E 651 ARG cc_start: 0.8162 (tmm-80) cc_final: 0.7938 (tmm-80) REVERT: F 51 ASN cc_start: 0.8828 (t0) cc_final: 0.8469 (t0) REVERT: F 60 MET cc_start: 0.7891 (tmm) cc_final: 0.6664 (tmm) REVERT: F 146 MET cc_start: 0.5570 (pmm) cc_final: 0.4842 (ppp) REVERT: F 254 ASP cc_start: 0.9220 (m-30) cc_final: 0.8990 (m-30) REVERT: F 555 GLN cc_start: 0.8327 (pm20) cc_final: 0.7669 (pp30) REVERT: F 651 ARG cc_start: 0.8506 (ttt180) cc_final: 0.7814 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 558 average time/residue: 0.3739 time to fit residues: 336.3829 Evaluate side-chains 406 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 10.0000 chunk 347 optimal weight: 0.0020 chunk 212 optimal weight: 0.0050 chunk 164 optimal weight: 0.0470 chunk 241 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 chunk 290 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 209 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS C 171 HIS D 51 ASN D 152 HIS E 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29505 Z= 0.140 Angle : 0.645 11.085 39930 Z= 0.313 Chirality : 0.043 0.189 4626 Planarity : 0.004 0.062 5091 Dihedral : 7.877 175.275 4032 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.41 % Favored : 90.17 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3603 helix: 0.52 (0.16), residues: 1257 sheet: -0.86 (0.24), residues: 492 loop : -2.22 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 292 HIS 0.005 0.000 HIS C 317 PHE 0.024 0.001 PHE C 102 TYR 0.016 0.001 TYR D 199 ARG 0.010 0.000 ARG D 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7206 Ramachandran restraints generated. 3603 Oldfield, 0 Emsley, 3603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 561 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6043 (ttt90) REVERT: A 394 GLN cc_start: 0.8610 (mp10) cc_final: 0.8277 (mp10) REVERT: A 536 GLN cc_start: 0.8390 (tp-100) cc_final: 0.7970 (mm-40) REVERT: A 538 SER cc_start: 0.8006 (m) cc_final: 0.7676 (p) REVERT: A 539 ILE cc_start: 0.8597 (tt) cc_final: 0.8261 (tt) REVERT: B 113 ASP cc_start: 0.7247 (t70) cc_final: 0.6999 (t70) REVERT: B 222 ARG cc_start: 0.7082 (tmm160) cc_final: 0.6881 (ttp80) REVERT: B 258 TYR cc_start: 0.8421 (t80) cc_final: 0.8179 (t80) REVERT: B 394 GLN cc_start: 0.8677 (mp-120) cc_final: 0.8418 (mp10) REVERT: B 650 LEU cc_start: 0.7107 (mt) cc_final: 0.6835 (mp) REVERT: B 709 THR cc_start: 0.8952 (p) cc_final: 0.8749 (p) REVERT: B 731 GLU cc_start: 0.7275 (tp30) cc_final: 0.6963 (tp30) REVERT: C 151 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8500 (ttmm) REVERT: C 222 ARG cc_start: 0.7499 (tmm160) cc_final: 0.7139 (ttp80) REVERT: D 52 MET cc_start: 0.7886 (pmm) cc_final: 0.7611 (tmm) REVERT: D 134 SER cc_start: 0.8517 (t) cc_final: 0.7847 (p) REVERT: D 287 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8131 (tm-30) REVERT: D 317 MET cc_start: 0.6942 (mmm) cc_final: 0.6454 (mmp) REVERT: D 630 ARG cc_start: 0.8139 (tpp-160) cc_final: 0.7918 (tpp-160) REVERT: D 637 GLU cc_start: 0.7773 (tt0) cc_final: 0.6923 (tm-30) REVERT: D 651 ARG cc_start: 0.8083 (tmm-80) cc_final: 0.7819 (tmm-80) REVERT: E 92 MET cc_start: 0.7474 (ttm) cc_final: 0.7105 (tpp) REVERT: E 94 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8862 (tp-100) REVERT: E 295 TYR cc_start: 0.8220 (m-80) cc_final: 0.6959 (m-80) REVERT: E 629 GLN cc_start: 0.8634 (tt0) cc_final: 0.7646 (tm-30) REVERT: E 651 ARG cc_start: 0.8169 (tmm-80) cc_final: 0.7945 (tmm-80) REVERT: F 51 ASN cc_start: 0.8761 (t0) cc_final: 0.8354 (t0) REVERT: F 60 MET cc_start: 0.7783 (tmm) cc_final: 0.7108 (tmm) REVERT: F 146 MET cc_start: 0.5573 (pmm) cc_final: 0.4782 (ppp) REVERT: F 254 ASP cc_start: 0.9212 (m-30) cc_final: 0.8978 (m-30) REVERT: F 522 GLU cc_start: 0.8253 (pp20) cc_final: 0.8019 (pp20) REVERT: F 555 GLN cc_start: 0.8335 (pm20) cc_final: 0.7647 (pp30) REVERT: F 651 ARG cc_start: 0.8490 (ttt180) cc_final: 0.7805 (tmm-80) outliers start: 2 outliers final: 1 residues processed: 563 average time/residue: 0.3604 time to fit residues: 329.6159 Evaluate side-chains 424 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 298 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS C 480 ASN D 51 ASN D 152 HIS D 434 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120341 restraints weight = 48658.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121330 restraints weight = 38039.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122380 restraints weight = 31091.197| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29505 Z= 0.198 Angle : 0.671 10.033 39930 Z= 0.330 Chirality : 0.044 0.191 4626 Planarity : 0.004 0.063 5091 Dihedral : 7.850 166.025 4032 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.91 % Favored : 88.68 % Rotamer: Outliers : 0.03 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3603 helix: 0.47 (0.16), residues: 1236 sheet: -1.04 (0.23), residues: 552 loop : -2.24 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 519 HIS 0.004 0.001 HIS E 37 PHE 0.021 0.002 PHE F 166 TYR 0.018 0.001 TYR E 199 ARG 0.008 0.000 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6360.79 seconds wall clock time: 115 minutes 24.55 seconds (6924.55 seconds total)