Starting phenix.real_space_refine on Sat Aug 10 11:16:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/08_2024/8s91_40234.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/08_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_40234/08_2024/8s91_40234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/08_2024/8s91_40234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/08_2024/8s91_40234.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s91_40234/08_2024/8s91_40234.cif" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 15.10, 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: 10.60 Conformation dependent library (CDL) restraints added in 4.8 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... Secondary structure from input PDB file: 139 helices and 28 sheets defined 40.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.585A pdb=" N TRP A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 79' Processing helix chain 'A' and resid 91 through 106 removed outlier: 4.280A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.589A pdb=" N ILE A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.618A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.996A pdb=" N THR A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.584A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.531A pdb=" N LYS A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.516A pdb=" N ALA A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.605A pdb=" N LEU A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.735A pdb=" N ARG A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 587' Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 662 through 674 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) Processing helix chain 'A' and resid 682 through 701 removed outlier: 3.512A pdb=" N ALA A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) 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 710 through 723 removed outlier: 3.542A pdb=" N GLU A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 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) removed outlier: 4.027A pdb=" N ILE A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.607A pdb=" N TYR A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.551A pdb=" N TRP B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 79' Processing helix chain 'B' and resid 91 through 106 removed outlier: 4.270A pdb=" N LYS B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.646A pdb=" N ILE B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 150 through 175 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 386 through 398 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.654A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.519A pdb=" N LYS B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.633A pdb=" N ALA B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.507A pdb=" N GLU B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 4.053A pdb=" N ARG B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 587' Processing helix chain 'B' and resid 599 through 612 removed outlier: 3.558A pdb=" N HIS B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.795A pdb=" N GLY B 671 " --> pdb=" O ARG B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 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 710 through 723 removed outlier: 3.534A pdb=" N GLU B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.516A pdb=" N ASP B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.527A pdb=" N TYR B 752 " --> pdb=" O MET B 748 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.527A pdb=" N TRP C 78 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 91 through 106 removed outlier: 4.265A pdb=" N LYS C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.753A pdb=" N ILE C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 148 through 175 removed outlier: 4.060A pdb=" N THR C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) 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 386 through 398 Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.606A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.630A pdb=" N LYS C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 536 Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 662 through 675 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) removed outlier: 3.523A pdb=" N GLN C 675 " --> pdb=" O GLY C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 701 removed outlier: 3.501A pdb=" N ALA C 686 " --> pdb=" O SER C 682 " (cutoff:3.500A) 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 710 through 723 removed outlier: 3.717A pdb=" N GLU C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 745 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) Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.446A pdb=" N SER C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.804A pdb=" N VAL D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 removed outlier: 3.892A pdb=" N ILE D 25 " --> pdb=" O HIS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 52 through 59 removed outlier: 4.231A pdb=" N GLU D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 83 removed outlier: 4.041A pdb=" N THR D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.608A pdb=" N TYR D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 removed outlier: 3.994A pdb=" N ARG D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.878A pdb=" N GLY D 330 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.850A 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) removed outlier: 3.988A pdb=" N THR D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.985A pdb=" N LEU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.787A pdb=" N ASP D 407 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.549A pdb=" N GLU D 432 " --> pdb=" O HIS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'D' and resid 496 through 507 Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 539 through 555 removed outlier: 3.969A pdb=" N ASN D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) 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: 3.581A pdb=" N GLU D 570 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 604 removed outlier: 3.609A pdb=" N ALA D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) 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 623 through 639 removed outlier: 3.883A pdb=" N GLN D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) 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) removed outlier: 3.903A pdb=" N LEU D 639 " --> pdb=" O ILE D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.732A pdb=" N LEU D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) 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) removed outlier: 3.575A pdb=" N ARG D 654 " --> pdb=" O ARG D 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.798A pdb=" N VAL E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 7 " --> pdb=" O SER E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 removed outlier: 3.736A pdb=" N ILE E 25 " --> pdb=" O HIS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 59 removed outlier: 4.297A pdb=" N GLY E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 56 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 83 removed outlier: 3.918A pdb=" N THR E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.785A pdb=" N GLN E 162 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E 163 " --> pdb=" O PHE E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.627A pdb=" N GLY E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 330 removed outlier: 3.920A pdb=" N GLY E 330 " --> pdb=" O MET E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.686A 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) removed outlier: 4.025A pdb=" N THR E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.873A pdb=" N LEU E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.694A pdb=" N ASP E 407 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 426 Processing helix chain 'E' and resid 427 through 433 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 468 through 473 Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.790A pdb=" N SER E 481 " --> pdb=" O PRO E 478 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 482 " --> pdb=" O LEU E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 478 through 482' Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 520 through 531 Processing helix chain 'E' and resid 539 through 544 removed outlier: 3.771A pdb=" N ASN E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 539 through 544' Processing helix chain 'E' and resid 545 through 555 removed outlier: 5.072A pdb=" N GLN E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 573 removed outlier: 3.693A pdb=" N GLU E 570 " --> pdb=" O ILE E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 589 through 604 removed outlier: 3.831A pdb=" N ALA E 593 " --> pdb=" O THR E 589 " (cutoff:3.500A) 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 623 through 639 removed outlier: 3.898A pdb=" N GLN E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) 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) removed outlier: 3.964A pdb=" N LEU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.754A pdb=" N LEU E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) 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 2 through 21 removed outlier: 3.854A pdb=" N VAL F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 3.902A pdb=" N ILE F 25 " --> pdb=" O HIS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 51 through 59 removed outlier: 4.498A pdb=" N GLY F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 83 removed outlier: 4.002A pdb=" N THR F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 298 through 310 removed outlier: 4.493A pdb=" N GLY F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 303 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 removed outlier: 3.514A pdb=" N LYS F 321 " --> pdb=" O MET F 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.557A pdb=" N PHE F 361 " --> pdb=" O GLY F 357 " (cutoff:3.500A) 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) removed outlier: 3.915A pdb=" N THR F 369 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.854A pdb=" N LEU F 385 " --> pdb=" O THR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.670A pdb=" N ASP F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 427 through 433 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 468 through 473 removed outlier: 3.625A pdb=" N ASN F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 508 removed outlier: 3.601A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 531 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.913A pdb=" N ASN F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) 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) Processing helix chain 'F' and resid 566 through 581 removed outlier: 3.561A pdb=" N GLU F 570 " --> pdb=" O ILE F 566 " (cutoff:3.500A) 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 589 through 604 removed outlier: 3.539A pdb=" N ALA F 593 " --> pdb=" O THR F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 639 removed outlier: 4.052A pdb=" N GLN F 627 " --> pdb=" O ASN F 623 " (cutoff:3.500A) 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) removed outlier: 3.961A pdb=" N LEU F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 removed outlier: 3.732A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) 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=AA1, 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=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 225 removed outlier: 3.577A pdb=" N THR A 224 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 294 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 311 " --> pdb=" O ILE A 293 " (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: 6.929A pdb=" N THR A 332 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 362 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR A 330 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 333 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 219 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.527A pdb=" N ALA A 559 " --> pdb=" O ILE A 517 " (cutoff:3.500A) 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) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.465A pdb=" N ARG B 197 " --> pdb=" O VAL B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, 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: 7.109A pdb=" N THR B 330 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 362 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR B 332 " --> pdb=" O ASN B 360 " (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=AA8, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AA9, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.507A pdb=" N ALA B 559 " --> pdb=" O ILE B 517 " (cutoff:3.500A) 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) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB2, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.510A pdb=" N ARG C 197 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.954A pdb=" N ILE C 219 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 333 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 332 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR C 310 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 357 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 312 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA C 359 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU C 314 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER C 361 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB5, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 478 removed outlier: 7.176A pdb=" N VAL C 477 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 559 " --> pdb=" O ILE C 517 " (cutoff:3.500A) 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) Processing sheet with id=AB7, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AB8, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.526A pdb=" N VAL D 40 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 240 removed outlier: 6.719A pdb=" N LYS D 203 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR D 133 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU D 201 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 224 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 202 " --> pdb=" O VAL D 222 " (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: 3.519A pdb=" N ARG D 247 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.840A pdb=" N ASP D 414 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 452 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 411 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 454 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 456 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 348 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR D 457 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 350 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU D 349 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU D 489 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 351 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, 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=AC4, first strand: chain 'E' and resid 126 through 133 removed outlier: 6.644A pdb=" N LYS E 203 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR E 133 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU E 201 " --> pdb=" O THR E 133 " (cutoff:3.500A) 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: 9.436A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR E 241 " --> pdb=" O ASN E 266 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 268 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR E 239 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 128 " --> pdb=" O LEU E 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 372 through 374 removed outlier: 6.874A pdb=" N VAL E 373 " --> pdb=" O CYS E 412 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASP E 414 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 452 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU E 454 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 456 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 352 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU E 349 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU E 489 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 351 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing sheet with id=AC6, 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=AC7, first strand: chain 'F' and resid 41 through 43 Processing sheet with id=AC8, first strand: chain 'F' and resid 123 through 133 removed outlier: 6.725A pdb=" N LYS F 203 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR F 133 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU F 201 " --> pdb=" O THR F 133 " (cutoff:3.500A) 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) removed outlier: 9.383A pdb=" N SER F 219 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N LEU F 263 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS F 221 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA F 265 " --> pdb=" O LYS F 221 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE F 223 " --> pdb=" O ALA F 265 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 126 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY F 242 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 372 through 374 removed outlier: 6.951A pdb=" N VAL F 373 " --> pdb=" O CYS F 412 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASP F 414 " --> pdb=" O VAL F 373 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR F 452 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS F 411 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 454 " --> pdb=" O CYS F 411 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 456 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY F 352 " --> pdb=" O THR F 457 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU F 349 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU F 489 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 351 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing sheet with id=AD1, 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) 907 hydrogen bonds defined for protein. 2595 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: 8.63 Time building geometry restraints manager: 11.61 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: 22344 3.14 - 3.73: 41622 3.73 - 4.31: 51829 4.31 - 4.90: 86673 Nonbonded interactions: 202665 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 3.040 nonbonded pdb=" OG SER C 461 " pdb="MG MG C2002 " model vdw 2.104 2.170 ... (remaining 202660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.560 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 68.950 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.050 ------------------------------------------------------------------------------- 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= 0.170 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 : 3.234 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: 0.3407 time to fit residues: 327.7111 Evaluate side-chains 425 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.159 ------------------------------------------------------------------------------- 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: 6.9990 chunk 277 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 213 ASN A 394 GLN A 462 GLN A 600 HIS A 608 HIS B 213 ASN B 394 GLN B 449 HIS B 603 HIS B 608 HIS C 213 ASN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS D 209 GLN D 433 GLN D 434 GLN E 5 GLN E 433 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1085 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= 0.200 Angle : 0.640 7.568 39930 Z= 0.319 Chirality : 0.043 0.182 4626 Planarity : 0.005 0.069 5091 Dihedral : 9.278 164.914 4032 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.83 % Favored : 89.73 % Rotamer: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.63 % 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: -1.59 (0.14), residues: 3603 helix: 0.76 (0.16), residues: 1275 sheet: -1.21 (0.23), residues: 519 loop : -2.44 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 292 HIS 0.007 0.001 HIS F 37 PHE 0.021 0.001 PHE E 13 TYR 0.018 0.001 TYR E 199 ARG 0.005 0.000 ARG E 32 *********************** 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 596 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 593 time to evaluate : 3.518 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 315 LEU cc_start: 0.8548 (mt) cc_final: 0.8229 (mp) REVERT: A 391 TYR cc_start: 0.8571 (t80) cc_final: 0.8244 (t80) REVERT: A 523 MET cc_start: 0.4886 (mtt) cc_final: 0.4649 (mtt) REVERT: A 538 SER cc_start: 0.8509 (m) cc_final: 0.8084 (p) REVERT: A 539 ILE cc_start: 0.8448 (tt) cc_final: 0.8136 (tt) REVERT: A 657 THR cc_start: 0.7908 (m) cc_final: 0.7658 (t) REVERT: B 113 ASP cc_start: 0.7117 (t70) cc_final: 0.6872 (t70) REVERT: B 258 TYR cc_start: 0.8206 (t80) cc_final: 0.7901 (t80) REVERT: B 352 MET cc_start: 0.6765 (mmm) cc_final: 0.6542 (tpp) REVERT: B 390 LEU cc_start: 0.9564 (mp) cc_final: 0.9311 (mp) REVERT: C 113 ASP cc_start: 0.7195 (t70) cc_final: 0.6697 (t70) REVERT: C 151 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8191 (ttmm) REVERT: D 52 MET cc_start: 0.8129 (pmm) cc_final: 0.7636 (tmm) REVERT: D 134 SER cc_start: 0.7846 (t) cc_final: 0.7430 (p) REVERT: D 287 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 317 MET cc_start: 0.6814 (mmm) cc_final: 0.6267 (mmp) REVERT: D 651 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7816 (tmm-80) REVERT: E 438 VAL cc_start: 0.7750 (m) cc_final: 0.7540 (p) REVERT: E 651 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7769 (tmm-80) REVERT: F 32 ARG cc_start: 0.7411 (tpt90) cc_final: 0.7133 (tpt90) REVERT: F 51 ASN cc_start: 0.8721 (t0) cc_final: 0.8238 (t0) REVERT: F 146 MET cc_start: 0.5158 (pmm) cc_final: 0.4734 (ppp) REVERT: F 166 PHE cc_start: 0.8288 (m-80) cc_final: 0.7306 (m-80) outliers start: 3 outliers final: 0 residues processed: 594 average time/residue: 0.3645 time to fit residues: 351.8604 Evaluate side-chains 428 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 3.186 ------------------------------------------------------------------------------- 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: 0.9980 chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 359 optimal weight: 0.5980 chunk 296 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 B 394 GLN C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN D 434 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29505 Z= 0.201 Angle : 0.646 7.890 39930 Z= 0.321 Chirality : 0.043 0.187 4626 Planarity : 0.004 0.067 5091 Dihedral : 8.877 168.550 4032 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.85 % Favored : 89.73 % Rotamer: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % 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: 0.70 (0.16), residues: 1284 sheet: -1.21 (0.23), residues: 519 loop : -2.36 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 519 HIS 0.010 0.001 HIS E 37 PHE 0.028 0.002 PHE E 13 TYR 0.016 0.001 TYR E 199 ARG 0.006 0.000 ARG B 170 *********************** 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 616 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 3.193 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 128 LEU cc_start: 0.8872 (mt) cc_final: 0.8671 (mp) REVERT: A 222 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6881 (ttp80) REVERT: A 231 ILE cc_start: 0.8561 (pt) cc_final: 0.8310 (pt) REVERT: A 315 LEU cc_start: 0.8583 (mt) cc_final: 0.8244 (mp) REVERT: A 391 TYR cc_start: 0.8592 (t80) cc_final: 0.8268 (t80) REVERT: A 538 SER cc_start: 0.8656 (m) cc_final: 0.8157 (p) REVERT: A 539 ILE cc_start: 0.8493 (tt) cc_final: 0.8232 (tt) REVERT: B 113 ASP cc_start: 0.7173 (t70) cc_final: 0.6927 (t70) REVERT: B 390 LEU cc_start: 0.9573 (mp) cc_final: 0.9343 (mp) REVERT: C 136 ASN cc_start: 0.9072 (m110) cc_final: 0.8793 (m-40) REVERT: C 151 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8225 (ttmm) REVERT: D 52 MET cc_start: 0.8113 (pmm) cc_final: 0.7546 (tmm) REVERT: D 134 SER cc_start: 0.8254 (t) cc_final: 0.7697 (p) REVERT: D 287 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7615 (tm-30) REVERT: D 317 MET cc_start: 0.6598 (mmm) cc_final: 0.5817 (mmp) REVERT: D 349 LEU cc_start: 0.7769 (tp) cc_final: 0.7359 (tp) REVERT: D 521 MET cc_start: 0.8262 (ppp) cc_final: 0.8037 (ppp) REVERT: D 651 ARG cc_start: 0.8211 (tmm-80) cc_final: 0.7842 (tmm-80) REVERT: E 92 MET cc_start: 0.6879 (ttm) cc_final: 0.6638 (tpp) REVERT: E 112 GLU cc_start: 0.8528 (mp0) cc_final: 0.7898 (tp30) REVERT: E 295 TYR cc_start: 0.8300 (m-80) cc_final: 0.8079 (m-80) REVERT: E 349 LEU cc_start: 0.7790 (tp) cc_final: 0.7511 (tp) REVERT: E 438 VAL cc_start: 0.7875 (m) cc_final: 0.7661 (p) REVERT: E 651 ARG cc_start: 0.8056 (tmm-80) cc_final: 0.7744 (tmm-80) REVERT: F 51 ASN cc_start: 0.8581 (t0) cc_final: 0.8098 (t0) REVERT: F 146 MET cc_start: 0.5386 (pmm) cc_final: 0.4955 (ppp) REVERT: F 349 LEU cc_start: 0.8108 (tp) cc_final: 0.7697 (tp) outliers start: 1 outliers final: 0 residues processed: 615 average time/residue: 0.3661 time to fit residues: 365.6683 Evaluate side-chains 419 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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: 0.7980 chunk 250 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 158 optimal weight: 0.0570 chunk 223 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 316 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 B 394 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29505 Z= 0.149 Angle : 0.619 8.088 39930 Z= 0.305 Chirality : 0.042 0.176 4626 Planarity : 0.004 0.066 5091 Dihedral : 8.648 175.943 4032 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.52 % Favored : 90.04 % Rotamer: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % 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: -1.46 (0.14), residues: 3603 helix: 0.75 (0.16), residues: 1302 sheet: -1.10 (0.22), residues: 546 loop : -2.35 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 519 HIS 0.007 0.001 HIS E 37 PHE 0.023 0.001 PHE D 13 TYR 0.014 0.001 TYR C 201 ARG 0.005 0.000 ARG E 32 *********************** 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 600 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 599 time to evaluate : 3.411 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 352 MET cc_start: 0.7781 (tpp) cc_final: 0.7524 (tpp) REVERT: A 390 LEU cc_start: 0.9461 (mt) cc_final: 0.9162 (mt) REVERT: A 538 SER cc_start: 0.8646 (m) cc_final: 0.8081 (p) REVERT: A 539 ILE cc_start: 0.8427 (tt) cc_final: 0.8152 (tt) REVERT: B 113 ASP cc_start: 0.7096 (t70) cc_final: 0.6860 (t70) REVERT: B 258 TYR cc_start: 0.8280 (t80) cc_final: 0.7936 (t80) REVERT: B 289 GLN cc_start: 0.8344 (pp30) cc_final: 0.7560 (pp30) REVERT: B 315 LEU cc_start: 0.8769 (mt) cc_final: 0.8362 (mp) REVERT: B 390 LEU cc_start: 0.9565 (mp) cc_final: 0.9350 (mp) REVERT: C 113 ASP cc_start: 0.6715 (t70) cc_final: 0.6498 (t70) REVERT: C 136 ASN cc_start: 0.9108 (m110) cc_final: 0.8843 (m-40) REVERT: C 151 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8307 (ttmm) REVERT: C 285 THR cc_start: 0.8467 (p) cc_final: 0.8242 (p) REVERT: D 51 ASN cc_start: 0.8642 (m-40) cc_final: 0.8354 (t0) REVERT: D 134 SER cc_start: 0.8210 (t) cc_final: 0.7618 (p) REVERT: D 220 MET cc_start: 0.8197 (tpp) cc_final: 0.7890 (tpt) REVERT: D 287 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 317 MET cc_start: 0.6433 (mmm) cc_final: 0.6033 (mmp) REVERT: D 349 LEU cc_start: 0.7709 (tp) cc_final: 0.7374 (tp) REVERT: D 451 THR cc_start: 0.9078 (p) cc_final: 0.8738 (m) REVERT: D 521 MET cc_start: 0.8091 (ppp) cc_final: 0.7819 (ppp) REVERT: D 641 LEU cc_start: 0.8952 (mm) cc_final: 0.8538 (mp) REVERT: D 651 ARG cc_start: 0.8230 (tmm-80) cc_final: 0.7807 (tmm-80) REVERT: E 45 MET cc_start: 0.6997 (mmp) cc_final: 0.6783 (mmp) REVERT: E 92 MET cc_start: 0.7019 (ttm) cc_final: 0.6786 (tpp) REVERT: E 112 GLU cc_start: 0.8513 (mp0) cc_final: 0.7897 (tp30) REVERT: E 166 PHE cc_start: 0.8572 (m-10) cc_final: 0.8337 (m-10) REVERT: E 295 TYR cc_start: 0.8300 (m-80) cc_final: 0.7897 (m-80) REVERT: E 349 LEU cc_start: 0.7770 (tp) cc_final: 0.7536 (tp) REVERT: E 438 VAL cc_start: 0.7917 (m) cc_final: 0.7682 (p) REVERT: E 651 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7794 (tmm-80) REVERT: F 51 ASN cc_start: 0.8511 (t0) cc_final: 0.8035 (t0) REVERT: F 146 MET cc_start: 0.5386 (pmm) cc_final: 0.5008 (ppp) REVERT: F 254 ASP cc_start: 0.9136 (m-30) cc_final: 0.8930 (m-30) REVERT: F 295 TYR cc_start: 0.8023 (m-80) cc_final: 0.6736 (m-80) REVERT: F 349 LEU cc_start: 0.8060 (tp) cc_final: 0.7699 (tp) REVERT: F 484 ASP cc_start: 0.7483 (m-30) cc_final: 0.7060 (m-30) REVERT: F 651 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7878 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 599 average time/residue: 0.3821 time to fit residues: 371.2638 Evaluate side-chains 432 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.177 ------------------------------------------------------------------------------- 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: 1.9990 chunk 200 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 180 optimal weight: 0.0770 chunk 317 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN B 394 GLN C 171 HIS ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29505 Z= 0.195 Angle : 0.647 8.737 39930 Z= 0.319 Chirality : 0.043 0.189 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.511 173.985 4032 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.02 % Favored : 89.56 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.77 % 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: -1.52 (0.14), residues: 3603 helix: 0.71 (0.15), residues: 1305 sheet: -1.24 (0.21), residues: 594 loop : -2.36 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 519 HIS 0.006 0.001 HIS F 617 PHE 0.025 0.002 PHE D 13 TYR 0.018 0.001 TYR B 391 ARG 0.007 0.000 ARG A 718 *********************** 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 591 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 588 time to evaluate : 3.015 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 387 LEU cc_start: 0.8881 (mt) cc_final: 0.8647 (pt) REVERT: A 538 SER cc_start: 0.8823 (m) cc_final: 0.8248 (p) REVERT: A 539 ILE cc_start: 0.8444 (tt) cc_final: 0.8224 (tt) REVERT: B 113 ASP cc_start: 0.7126 (t70) cc_final: 0.6896 (t70) REVERT: B 128 LEU cc_start: 0.7776 (mm) cc_final: 0.7502 (mp) REVERT: B 258 TYR cc_start: 0.8301 (t80) cc_final: 0.8066 (t80) REVERT: C 113 ASP cc_start: 0.6832 (t70) cc_final: 0.6591 (t70) REVERT: C 136 ASN cc_start: 0.9129 (m110) cc_final: 0.8847 (m-40) REVERT: C 151 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8349 (ttmm) REVERT: C 285 THR cc_start: 0.8523 (p) cc_final: 0.8302 (p) REVERT: C 394 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 134 SER cc_start: 0.8394 (t) cc_final: 0.7821 (p) REVERT: D 287 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 317 MET cc_start: 0.6658 (mmm) cc_final: 0.6271 (mmp) REVERT: D 349 LEU cc_start: 0.7845 (tp) cc_final: 0.7424 (tp) REVERT: D 519 TRP cc_start: 0.5030 (m-10) cc_final: 0.4699 (m-10) REVERT: D 521 MET cc_start: 0.8086 (ppp) cc_final: 0.7839 (ppp) REVERT: D 651 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.7887 (tmm-80) REVERT: E 92 MET cc_start: 0.7154 (ttm) cc_final: 0.6849 (tpp) REVERT: E 112 GLU cc_start: 0.8571 (mp0) cc_final: 0.7862 (tp30) REVERT: E 349 LEU cc_start: 0.8110 (tp) cc_final: 0.7813 (tp) REVERT: E 438 VAL cc_start: 0.7837 (m) cc_final: 0.7629 (p) REVERT: E 629 GLN cc_start: 0.8673 (tt0) cc_final: 0.7703 (tm-30) REVERT: E 651 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7743 (tmm-80) REVERT: F 1 MET cc_start: 0.3907 (mmt) cc_final: 0.3522 (mmp) REVERT: F 51 ASN cc_start: 0.8522 (t0) cc_final: 0.8084 (t0) REVERT: F 146 MET cc_start: 0.5544 (pmm) cc_final: 0.5037 (ppp) REVERT: F 166 PHE cc_start: 0.8539 (m-80) cc_final: 0.8256 (m-10) REVERT: F 254 ASP cc_start: 0.9167 (m-30) cc_final: 0.8951 (m-30) REVERT: F 295 TYR cc_start: 0.8069 (m-80) cc_final: 0.7780 (m-80) REVERT: F 349 LEU cc_start: 0.8187 (tp) cc_final: 0.7822 (tp) REVERT: F 493 LYS cc_start: 0.7884 (mppt) cc_final: 0.7582 (tmtt) REVERT: F 651 ARG cc_start: 0.8285 (ttt180) cc_final: 0.7835 (tmm-80) outliers start: 3 outliers final: 0 residues processed: 590 average time/residue: 0.3731 time to fit residues: 353.4324 Evaluate side-chains 422 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.519 ------------------------------------------------------------------------------- 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: 3.9990 chunk 318 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 207 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 354 optimal weight: 0.0980 chunk 293 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 536 GLN B 106 HIS ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 600 HIS C 480 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29505 Z= 0.153 Angle : 0.637 7.823 39930 Z= 0.312 Chirality : 0.043 0.196 4626 Planarity : 0.004 0.065 5091 Dihedral : 8.401 179.552 4032 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.35 % Favored : 90.20 % Rotamer: Outliers : 0.06 % Allowed : 1.96 % Favored : 97.98 % 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: -1.42 (0.14), residues: 3603 helix: 0.82 (0.16), residues: 1296 sheet: -1.12 (0.22), residues: 576 loop : -2.33 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 519 HIS 0.005 0.001 HIS F 617 PHE 0.024 0.001 PHE D 13 TYR 0.021 0.001 TYR F 38 ARG 0.007 0.000 ARG B 711 *********************** 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 597 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 595 time to evaluate : 3.267 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 295 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 538 SER cc_start: 0.8768 (m) cc_final: 0.8249 (p) REVERT: A 539 ILE cc_start: 0.8506 (tt) cc_final: 0.8277 (tt) REVERT: B 138 ILE cc_start: 0.8547 (tp) cc_final: 0.7915 (tp) REVERT: B 222 ARG cc_start: 0.6959 (tmm160) cc_final: 0.6745 (ttp80) REVERT: B 289 GLN cc_start: 0.8263 (pp30) cc_final: 0.7541 (pp30) REVERT: C 113 ASP cc_start: 0.6755 (t70) cc_final: 0.6508 (t70) REVERT: C 136 ASN cc_start: 0.9129 (m110) cc_final: 0.8828 (m-40) REVERT: C 151 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8326 (ttmm) REVERT: C 285 THR cc_start: 0.8499 (p) cc_final: 0.8270 (p) REVERT: C 394 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 736 ASP cc_start: 0.7336 (m-30) cc_final: 0.6404 (m-30) REVERT: D 134 SER cc_start: 0.8364 (t) cc_final: 0.7728 (p) REVERT: D 220 MET cc_start: 0.8079 (tpp) cc_final: 0.7814 (tpt) REVERT: D 287 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7893 (tm-30) REVERT: D 317 MET cc_start: 0.6489 (mmm) cc_final: 0.6142 (mmp) REVERT: D 349 LEU cc_start: 0.7786 (tp) cc_final: 0.7410 (tp) REVERT: D 521 MET cc_start: 0.8033 (ppp) cc_final: 0.7745 (ppp) REVERT: D 651 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7842 (tmm-80) REVERT: E 92 MET cc_start: 0.7137 (ttm) cc_final: 0.6839 (tpp) REVERT: E 112 GLU cc_start: 0.8568 (mp0) cc_final: 0.7895 (tp30) REVERT: E 349 LEU cc_start: 0.8031 (tp) cc_final: 0.7816 (tp) REVERT: E 438 VAL cc_start: 0.7724 (m) cc_final: 0.7462 (p) REVERT: E 629 GLN cc_start: 0.8710 (tt0) cc_final: 0.7589 (tm-30) REVERT: E 651 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7731 (tmm-80) REVERT: E 654 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7676 (ptp-170) REVERT: F 1 MET cc_start: 0.3771 (mmt) cc_final: 0.3305 (mmp) REVERT: F 51 ASN cc_start: 0.8438 (t0) cc_final: 0.7988 (t0) REVERT: F 60 MET cc_start: 0.7875 (tmm) cc_final: 0.6440 (tmm) REVERT: F 146 MET cc_start: 0.5378 (pmm) cc_final: 0.4963 (ppp) REVERT: F 254 ASP cc_start: 0.9150 (m-30) cc_final: 0.8930 (m-30) REVERT: F 295 TYR cc_start: 0.8154 (m-80) cc_final: 0.6608 (m-80) REVERT: F 349 LEU cc_start: 0.8116 (tp) cc_final: 0.7754 (tp) REVERT: F 493 LYS cc_start: 0.7849 (mppt) cc_final: 0.7570 (tmtt) REVERT: F 651 ARG cc_start: 0.8292 (ttt180) cc_final: 0.7838 (tmm-80) outliers start: 2 outliers final: 0 residues processed: 596 average time/residue: 0.3909 time to fit residues: 373.9879 Evaluate side-chains 421 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.406 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 258 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 162 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN B 394 GLN B 600 HIS C 171 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 59 ASN D 434 GLN E 448 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29505 Z= 0.159 Angle : 0.641 9.330 39930 Z= 0.313 Chirality : 0.043 0.180 4626 Planarity : 0.004 0.064 5091 Dihedral : 8.279 178.440 4032 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.58 % Favored : 89.95 % Rotamer: Outliers : 0.12 % Allowed : 1.21 % Favored : 98.67 % 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: -1.38 (0.14), residues: 3603 helix: 0.82 (0.15), residues: 1299 sheet: -1.06 (0.22), residues: 576 loop : -2.30 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 519 HIS 0.005 0.001 HIS F 617 PHE 0.024 0.001 PHE D 13 TYR 0.018 0.001 TYR F 38 ARG 0.008 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 584 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 580 time to evaluate : 2.956 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 297 MET cc_start: 0.7216 (tmm) cc_final: 0.6981 (tmm) REVERT: A 538 SER cc_start: 0.8767 (m) cc_final: 0.8234 (p) REVERT: A 539 ILE cc_start: 0.8525 (tt) cc_final: 0.8323 (tt) REVERT: B 258 TYR cc_start: 0.8362 (t80) cc_final: 0.8111 (t80) REVERT: B 391 TYR cc_start: 0.8357 (t80) cc_final: 0.7947 (t80) REVERT: C 136 ASN cc_start: 0.9131 (m110) cc_final: 0.8834 (m-40) REVERT: C 151 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8399 (ttmm) REVERT: C 249 GLN cc_start: 0.8400 (pp30) cc_final: 0.8175 (pp30) REVERT: C 285 THR cc_start: 0.8577 (p) cc_final: 0.8354 (p) REVERT: C 394 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 51 ASN cc_start: 0.7615 (t0) cc_final: 0.6428 (m-40) REVERT: D 60 MET cc_start: 0.7860 (ttp) cc_final: 0.7525 (ptm) REVERT: D 134 SER cc_start: 0.8417 (t) cc_final: 0.7792 (p) REVERT: D 220 MET cc_start: 0.8091 (tpp) cc_final: 0.7851 (tpt) REVERT: D 287 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 317 MET cc_start: 0.6480 (mmm) cc_final: 0.6126 (mmp) REVERT: D 349 LEU cc_start: 0.7741 (tp) cc_final: 0.7363 (tp) REVERT: D 519 TRP cc_start: 0.5015 (m-10) cc_final: 0.4521 (m-10) REVERT: D 521 MET cc_start: 0.8046 (ppp) cc_final: 0.7782 (ppp) REVERT: D 637 GLU cc_start: 0.8053 (tt0) cc_final: 0.7158 (tm-30) REVERT: D 651 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7845 (tmm-80) REVERT: E 92 MET cc_start: 0.7176 (ttm) cc_final: 0.6832 (tpp) REVERT: E 112 GLU cc_start: 0.8577 (mp0) cc_final: 0.7872 (tp30) REVERT: E 349 LEU cc_start: 0.8019 (tp) cc_final: 0.7759 (tp) REVERT: E 438 VAL cc_start: 0.7764 (m) cc_final: 0.7532 (p) REVERT: E 629 GLN cc_start: 0.8643 (tt0) cc_final: 0.7672 (tm-30) REVERT: E 654 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7623 (ptp-170) REVERT: F 1 MET cc_start: 0.3757 (mmt) cc_final: 0.3421 (mmp) REVERT: F 51 ASN cc_start: 0.8400 (t0) cc_final: 0.7951 (t0) REVERT: F 146 MET cc_start: 0.5364 (pmm) cc_final: 0.5016 (ppp) REVERT: F 254 ASP cc_start: 0.9159 (m-30) cc_final: 0.8938 (m-30) REVERT: F 295 TYR cc_start: 0.8133 (m-80) cc_final: 0.7695 (m-80) REVERT: F 349 LEU cc_start: 0.8268 (tp) cc_final: 0.7872 (tp) REVERT: F 493 LYS cc_start: 0.8000 (mppt) cc_final: 0.7793 (tmtt) REVERT: F 651 ARG cc_start: 0.8355 (ttt180) cc_final: 0.7844 (tmm-80) outliers start: 4 outliers final: 0 residues processed: 582 average time/residue: 0.3681 time to fit residues: 347.0963 Evaluate side-chains 402 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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: 3.9990 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 224 optimal weight: 0.3980 chunk 240 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 277 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 600 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 434 GLN E 448 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2738 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= 0.159 Angle : 0.650 10.872 39930 Z= 0.318 Chirality : 0.043 0.181 4626 Planarity : 0.004 0.063 5091 Dihedral : 8.171 176.410 4032 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.58 % Favored : 90.01 % Rotamer: Outliers : 0.12 % Allowed : 1.21 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3603 helix: 0.89 (0.16), residues: 1278 sheet: -1.07 (0.22), residues: 549 loop : -2.33 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 288 HIS 0.006 0.001 HIS B 663 PHE 0.023 0.001 PHE D 13 TYR 0.015 0.001 TYR A 391 ARG 0.007 0.000 ARG E 32 *********************** 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 572 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 568 time to evaluate : 3.880 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 295 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 297 MET cc_start: 0.7178 (tmm) cc_final: 0.6945 (tmm) REVERT: A 390 LEU cc_start: 0.9498 (mt) cc_final: 0.9263 (mt) REVERT: A 538 SER cc_start: 0.8773 (m) cc_final: 0.8246 (p) REVERT: A 539 ILE cc_start: 0.8581 (tt) cc_final: 0.8380 (tt) REVERT: B 289 GLN cc_start: 0.8233 (pp30) cc_final: 0.7489 (pp30) REVERT: B 391 TYR cc_start: 0.8343 (t80) cc_final: 0.7987 (t80) REVERT: B 650 LEU cc_start: 0.7042 (mt) cc_final: 0.6671 (mp) REVERT: C 101 LYS cc_start: 0.9197 (mttt) cc_final: 0.8698 (tppt) REVERT: C 136 ASN cc_start: 0.9111 (m110) cc_final: 0.8828 (m-40) REVERT: C 151 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8411 (ttmm) REVERT: C 249 GLN cc_start: 0.8464 (pp30) cc_final: 0.8219 (pp30) REVERT: C 285 THR cc_start: 0.8574 (p) cc_final: 0.8344 (p) REVERT: D 51 ASN cc_start: 0.7643 (t0) cc_final: 0.6439 (m-40) REVERT: D 134 SER cc_start: 0.8475 (t) cc_final: 0.7879 (p) REVERT: D 201 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7751 (tt0) REVERT: D 287 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7982 (tm-30) REVERT: D 317 MET cc_start: 0.6450 (mmm) cc_final: 0.6129 (mmp) REVERT: D 349 LEU cc_start: 0.7721 (tp) cc_final: 0.7367 (tp) REVERT: D 496 ASP cc_start: 0.7943 (t0) cc_final: 0.7720 (t0) REVERT: D 521 MET cc_start: 0.8031 (ppp) cc_final: 0.7734 (ppp) REVERT: D 637 GLU cc_start: 0.7999 (tt0) cc_final: 0.7111 (tm-30) REVERT: D 651 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7804 (tmm-80) REVERT: E 92 MET cc_start: 0.7259 (ttm) cc_final: 0.6835 (tpp) REVERT: E 112 GLU cc_start: 0.8537 (mp0) cc_final: 0.7878 (tp30) REVERT: E 349 LEU cc_start: 0.8030 (tp) cc_final: 0.7782 (tp) REVERT: E 438 VAL cc_start: 0.7811 (m) cc_final: 0.7580 (p) REVERT: E 629 GLN cc_start: 0.8648 (tt0) cc_final: 0.7675 (tm-30) REVERT: E 654 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7624 (ptp-170) REVERT: F 1 MET cc_start: 0.3806 (mmt) cc_final: 0.3373 (mmp) REVERT: F 51 ASN cc_start: 0.8370 (t0) cc_final: 0.7909 (t0) REVERT: F 60 MET cc_start: 0.7742 (tmm) cc_final: 0.6309 (tmm) REVERT: F 146 MET cc_start: 0.5380 (pmm) cc_final: 0.5009 (ppp) REVERT: F 254 ASP cc_start: 0.9162 (m-30) cc_final: 0.8946 (m-30) REVERT: F 295 TYR cc_start: 0.8274 (m-80) cc_final: 0.6672 (m-80) REVERT: F 349 LEU cc_start: 0.8182 (tp) cc_final: 0.7821 (tp) REVERT: F 438 VAL cc_start: 0.7518 (m) cc_final: 0.7311 (p) REVERT: F 493 LYS cc_start: 0.8093 (mppt) cc_final: 0.7845 (tmtt) REVERT: F 651 ARG cc_start: 0.8347 (ttt180) cc_final: 0.7778 (tmm-80) outliers start: 4 outliers final: 0 residues processed: 570 average time/residue: 0.3123 time to fit residues: 289.9186 Evaluate side-chains 403 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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: 0.8980 chunk 337 optimal weight: 3.9990 chunk 308 optimal weight: 0.0770 chunk 328 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 258 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 310 optimal weight: 0.0870 chunk 327 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: