Starting phenix.real_space_refine on Sat Feb 24 21:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dag_30625/02_2024/7dag_30625_neut.pdb" } resolution = 4.37 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= 0.007 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 203 5.16 5 C 29218 2.51 5 N 7833 2.21 5 O 8722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A ASP 823": "OD1" <-> "OD2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 796": "NH1" <-> "NH2" Residue "B ASP 823": "OD1" <-> "OD2" Residue "B PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 796": "NH1" <-> "NH2" Residue "C ASP 823": "OD1" <-> "OD2" Residue "C PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 796": "NH1" <-> "NH2" Residue "D ASP 823": "OD1" <-> "OD2" Residue "D PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E ARG 265": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ASP 315": "OD1" <-> "OD2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E ASP 377": "OD1" <-> "OD2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 796": "NH1" <-> "NH2" Residue "E ASP 823": "OD1" <-> "OD2" Residue "E PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ASP 377": "OD1" <-> "OD2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 796": "NH1" <-> "NH2" Residue "F ASP 823": "OD1" <-> "OD2" Residue "F PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 508": "OE1" <-> "OE2" Residue "G PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 796": "NH1" <-> "NH2" Residue "G GLU 834": "OE1" <-> "OE2" Residue "G PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H GLU 257": "OE1" <-> "OE2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ASP 315": "OD1" <-> "OD2" Residue "H TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 332": "OE1" <-> "OE2" Residue "H TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "B" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "C" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "D" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "E" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "F" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6568 Classifications: {'peptide': 867} Link IDs: {'CIS': 6, 'PTRANS': 38, 'TRANS': 822} Chain: "G" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3250 Classifications: {'peptide': 419} Link IDs: {'CIS': 5, 'PTRANS': 21, 'TRANS': 392} Chain: "H" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3318 Classifications: {'peptide': 448} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 429} Time building chain proxies: 22.78, per 1000 atoms: 0.50 Number of scatterers: 45976 At special positions: 0 Unit cell: (169.148, 192.449, 174.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 203 16.00 O 8722 8.00 N 7833 7.00 C 29218 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: 18.67 Conformation dependent library (CDL) restraints added in 9.7 seconds 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11256 Finding SS restraints... Secondary structure from input PDB file: 231 helices and 30 sheets defined 49.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 195 through 204 removed outlier: 3.512A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL A 244 " --> pdb=" O ASP A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 473 removed outlier: 4.301A pdb=" N ILE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 624 through 627 Processing helix chain 'A' and resid 644 through 663 Processing helix chain 'A' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP A 671 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN A 673 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 697 through 713 Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.761A pdb=" N SER A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.981A pdb=" N LEU B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.701A pdb=" N LYS B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 4.002A pdb=" N ALA B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 removed outlier: 3.525A pdb=" N VAL B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 365 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 435 through 438 Processing helix chain 'B' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL B 498 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 624 through 627 Processing helix chain 'B' and resid 644 through 663 Processing helix chain 'B' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP B 671 " --> pdb=" O ASN B 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) Proline residue: B 686 - end of helix Processing helix chain 'B' and resid 697 through 713 Processing helix chain 'B' and resid 719 through 733 removed outlier: 3.763A pdb=" N SER B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 742 Processing helix chain 'B' and resid 743 through 752 Processing helix chain 'B' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU B 830 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 27 through 45 removed outlier: 4.801A pdb=" N LYS C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.703A pdb=" N LYS C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 4.004A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.525A pdb=" N VAL C 244 " --> pdb=" O ASP C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 307 Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.982A pdb=" N ILE C 363 " --> pdb=" O THR C 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 365 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 Processing helix chain 'C' and resid 435 through 438 Processing helix chain 'C' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 Processing helix chain 'C' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL C 498 " --> pdb=" O TYR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 624 through 627 Processing helix chain 'C' and resid 644 through 663 Processing helix chain 'C' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP C 671 " --> pdb=" O ASN C 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU C 683 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR C 684 " --> pdb=" O MET C 680 " (cutoff:3.500A) Proline residue: C 686 - end of helix Processing helix chain 'C' and resid 697 through 713 Processing helix chain 'C' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER C 723 " --> pdb=" O GLY C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 742 Processing helix chain 'C' and resid 743 through 752 Processing helix chain 'C' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 838 removed outlier: 4.408A pdb=" N ASP C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 837 " --> pdb=" O VAL C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL D 244 " --> pdb=" O ASP D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 241 through 244' Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 277 through 287 removed outlier: 4.887A pdb=" N VAL D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY D 365 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 435 through 438 Processing helix chain 'D' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL D 498 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 560 removed outlier: 3.851A pdb=" N ASP D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 624 through 627 Processing helix chain 'D' and resid 644 through 663 Processing helix chain 'D' and resid 667 through 691 removed outlier: 3.907A pdb=" N ASP D 671 " --> pdb=" O ASN D 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 672 " --> pdb=" O GLU D 668 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN D 673 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU D 683 " --> pdb=" O LYS D 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D 684 " --> pdb=" O MET D 680 " (cutoff:3.500A) Proline residue: D 686 - end of helix Processing helix chain 'D' and resid 697 through 713 Processing helix chain 'D' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER D 723 " --> pdb=" O GLY D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 742 Processing helix chain 'D' and resid 743 through 752 Processing helix chain 'D' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 808 removed outlier: 3.668A pdb=" N LEU D 808 " --> pdb=" O LEU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU D 830 " --> pdb=" O ALA D 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 837 " --> pdb=" O VAL D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU D 853 " --> pdb=" O LEU D 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 27 through 45 removed outlier: 4.800A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 80 removed outlier: 3.703A pdb=" N LYS E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 143 through 159 Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.513A pdb=" N ALA E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 4.003A pdb=" N ALA E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 244' Processing helix chain 'E' and resid 258 through 268 Processing helix chain 'E' and resid 277 through 287 removed outlier: 4.886A pdb=" N VAL E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'E' and resid 349 through 365 removed outlier: 3.982A pdb=" N ILE E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY E 364 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 435 through 438 Processing helix chain 'E' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE E 470 " --> pdb=" O GLY E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 492 Processing helix chain 'E' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL E 498 " --> pdb=" O TYR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS E 526 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP E 549 " --> pdb=" O GLY E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 624 through 627 Processing helix chain 'E' and resid 644 through 663 Processing helix chain 'E' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP E 671 " --> pdb=" O ASN E 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY E 672 " --> pdb=" O GLU E 668 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN E 673 " --> pdb=" O TYR E 669 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS E 682 " --> pdb=" O LEU E 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU E 683 " --> pdb=" O LYS E 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR E 684 " --> pdb=" O MET E 680 " (cutoff:3.500A) Proline residue: E 686 - end of helix Processing helix chain 'E' and resid 697 through 713 Processing helix chain 'E' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER E 723 " --> pdb=" O GLY E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 742 Processing helix chain 'E' and resid 743 through 752 Processing helix chain 'E' and resid 769 through 781 removed outlier: 3.558A pdb=" N ARG E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 808 removed outlier: 3.668A pdb=" N LEU E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP E 829 " --> pdb=" O LEU E 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU E 830 " --> pdb=" O ALA E 826 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 862 removed outlier: 3.529A pdb=" N LEU E 853 " --> pdb=" O LEU E 849 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 24 Processing helix chain 'F' and resid 27 through 45 removed outlier: 4.801A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 58 removed outlier: 3.982A pdb=" N LEU F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 80 removed outlier: 3.702A pdb=" N LYS F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'F' and resid 174 through 183 Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.512A pdb=" N ALA F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 240 removed outlier: 4.004A pdb=" N ALA F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 244 removed outlier: 3.524A pdb=" N VAL F 244 " --> pdb=" O ASP F 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 241 through 244' Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 277 through 287 removed outlier: 4.886A pdb=" N VAL F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 307 Processing helix chain 'F' and resid 349 through 365 removed outlier: 3.981A pdb=" N ILE F 363 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY F 364 " --> pdb=" O MET F 360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 365 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 435 through 438 Processing helix chain 'F' and resid 466 through 473 removed outlier: 4.302A pdb=" N ILE F 470 " --> pdb=" O GLY F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 492 Processing helix chain 'F' and resid 494 through 504 removed outlier: 3.605A pdb=" N VAL F 498 " --> pdb=" O TYR F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 535 removed outlier: 3.723A pdb=" N LYS F 526 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 560 removed outlier: 3.852A pdb=" N ASP F 549 " --> pdb=" O GLY F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 Processing helix chain 'F' and resid 624 through 627 Processing helix chain 'F' and resid 644 through 663 Processing helix chain 'F' and resid 667 through 691 removed outlier: 3.906A pdb=" N ASP F 671 " --> pdb=" O ASN F 667 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY F 672 " --> pdb=" O GLU F 668 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN F 673 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 682 " --> pdb=" O LEU F 678 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU F 683 " --> pdb=" O LYS F 679 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR F 684 " --> pdb=" O MET F 680 " (cutoff:3.500A) Proline residue: F 686 - end of helix Processing helix chain 'F' and resid 697 through 713 Processing helix chain 'F' and resid 719 through 733 removed outlier: 3.762A pdb=" N SER F 723 " --> pdb=" O GLY F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 742 Processing helix chain 'F' and resid 743 through 752 Processing helix chain 'F' and resid 769 through 781 removed outlier: 3.559A pdb=" N ARG F 773 " --> pdb=" O GLN F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 808 removed outlier: 3.669A pdb=" N LEU F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 838 removed outlier: 4.407A pdb=" N ASP F 829 " --> pdb=" O LEU F 825 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU F 830 " --> pdb=" O ALA F 826 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP F 837 " --> pdb=" O VAL F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 862 removed outlier: 3.528A pdb=" N LEU F 853 " --> pdb=" O LEU F 849 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 474 removed outlier: 4.543A pdb=" N ASP G 474 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 492 Processing helix chain 'G' and resid 494 through 506 removed outlier: 3.523A pdb=" N VAL G 498 " --> pdb=" O TYR G 494 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN G 505 " --> pdb=" O LEU G 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 535 Processing helix chain 'G' and resid 545 through 560 Processing helix chain 'G' and resid 564 through 572 removed outlier: 4.014A pdb=" N LEU G 568 " --> pdb=" O HIS G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 627 Processing helix chain 'G' and resid 644 through 662 removed outlier: 3.705A pdb=" N VAL G 662 " --> pdb=" O LEU G 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 667 through 691 removed outlier: 4.151A pdb=" N ASP G 671 " --> pdb=" O ASN G 667 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY G 672 " --> pdb=" O GLU G 668 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN G 673 " --> pdb=" O TYR G 669 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 682 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU G 683 " --> pdb=" O LYS G 679 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR G 684 " --> pdb=" O MET G 680 " (cutoff:3.500A) Proline residue: G 686 - end of helix Processing helix chain 'G' and resid 697 through 714 Processing helix chain 'G' and resid 719 through 733 removed outlier: 3.595A pdb=" N SER G 723 " --> pdb=" O GLY G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 743 through 752 Processing helix chain 'G' and resid 769 through 781 Processing helix chain 'G' and resid 789 through 808 Processing helix chain 'G' and resid 820 through 837 removed outlier: 4.434A pdb=" N ASP G 829 " --> pdb=" O LEU G 825 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU G 830 " --> pdb=" O ALA G 826 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP G 837 " --> pdb=" O VAL G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 863 removed outlier: 3.613A pdb=" N LEU G 853 " --> pdb=" O LEU G 849 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS G 854 " --> pdb=" O ILE G 850 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 855 " --> pdb=" O ALA G 851 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 24 Processing helix chain 'H' and resid 27 through 45 removed outlier: 4.348A pdb=" N LYS H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 58 removed outlier: 3.897A pdb=" N LEU H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 80 Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'H' and resid 143 through 159 Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.525A pdb=" N VAL H 199 " --> pdb=" O GLY H 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 240 removed outlier: 3.720A pdb=" N ALA H 230 " --> pdb=" O ASP H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 244 Processing helix chain 'H' and resid 258 through 268 removed outlier: 3.651A pdb=" N VAL H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 287 removed outlier: 3.886A pdb=" N ASP H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 297 removed outlier: 4.067A pdb=" N ILE H 296 " --> pdb=" O ASN H 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL H 297 " --> pdb=" O ALA H 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 293 through 297' Processing helix chain 'H' and resid 300 through 309 Processing helix chain 'H' and resid 349 through 365 removed outlier: 4.034A pdb=" N ILE H 363 " --> pdb=" O THR H 359 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY H 364 " --> pdb=" O MET H 360 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 365 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 390 removed outlier: 3.631A pdb=" N ILE H 383 " --> pdb=" O ASN H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 438 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.655A pdb=" N THR A 99 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 91 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 97 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE B 395 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 444 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL B 397 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA A 446 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER B 370 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR B 373 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 220 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 217 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA B 252 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 219 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL B 254 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 221 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN B 250 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE B 345 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 252 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 319 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU B 344 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY B 321 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG B 346 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS B 272 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE A 107 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 137 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 109 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 106 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE A 190 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS A 108 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A 192 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 110 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE A 210 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS A 272 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 319 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 344 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG A 346 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN A 250 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE A 345 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 252 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 217 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A 252 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 219 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 254 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 221 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR A 373 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 220 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 370 " --> pdb=" O LEU A 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER A 460 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 633 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 462 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 595 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 482 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU A 542 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 484 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 607 through 611 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 92 removed outlier: 6.654A pdb=" N THR B 99 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 91 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 97 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.564A pdb=" N ILE B 107 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 137 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 109 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 106 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE B 190 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS B 108 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA B 192 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 110 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE B 210 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER B 460 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 633 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B 462 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 595 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 482 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU B 542 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 484 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 607 through 611 Processing sheet with id=AB1, first strand: chain 'C' and resid 88 through 92 removed outlier: 6.655A pdb=" N THR C 99 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU C 91 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 97 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 397 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER D 370 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR D 373 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 220 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 217 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA D 252 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 219 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL D 254 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 221 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 250 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE D 345 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA D 252 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 319 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU D 344 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY D 321 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ARG D 346 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS D 272 " --> pdb=" O VAL D 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE C 107 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER C 137 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY C 109 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 106 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE C 190 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS C 108 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA C 192 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 110 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE C 210 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 190 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL C 212 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA C 192 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS C 272 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU C 319 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU C 344 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY C 321 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG C 346 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN C 250 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE C 345 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 252 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 217 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 252 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 219 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL C 254 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 221 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR C 373 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 220 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 370 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 397 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 97 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU D 91 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 99 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 460 through 463 removed outlier: 6.406A pdb=" N SER C 460 " --> pdb=" O ALA C 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 633 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C 462 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 595 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 482 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU C 542 " --> pdb=" O PHE C 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 484 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 607 through 611 Processing sheet with id=AB6, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.562A pdb=" N ILE D 107 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER D 137 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY D 109 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 106 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE D 190 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS D 108 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA D 192 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 110 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE D 210 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE D 190 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL D 212 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA D 192 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 481 through 484 removed outlier: 6.451A pdb=" N PHE D 482 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 542 " --> pdb=" O PHE D 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 484 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR D 595 " --> pdb=" O ILE D 632 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER D 460 " --> pdb=" O ALA D 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL D 633 " --> pdb=" O SER D 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR D 462 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE D 461 " --> pdb=" O HIS E 455 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N HIS E 455 " --> pdb=" O ILE D 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 607 through 611 Processing sheet with id=AB9, first strand: chain 'E' and resid 88 through 92 removed outlier: 6.654A pdb=" N THR E 99 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU E 91 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 97 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 395 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 446 " --> pdb=" O ILE F 395 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL F 397 " --> pdb=" O ALA E 446 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER F 370 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR F 373 " --> pdb=" O PRO F 218 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 220 " --> pdb=" O TYR F 373 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL F 217 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA F 252 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 219 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL F 254 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE F 221 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN F 250 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE F 345 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 252 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU F 319 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU F 344 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY F 321 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG F 346 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS F 272 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 167 through 169 removed outlier: 6.563A pdb=" N ILE E 107 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER E 137 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY E 109 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE E 106 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE E 190 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS E 108 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA E 192 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 110 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ILE E 210 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 190 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL E 212 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA E 192 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.674A pdb=" N HIS E 272 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 319 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU E 344 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY E 321 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG E 346 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN E 250 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE E 345 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA E 252 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 217 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA E 252 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL E 219 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL E 254 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 221 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N TYR E 373 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 220 " --> pdb=" O TYR E 373 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER E 370 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE E 395 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR F 97 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU F 91 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR F 99 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER E 460 " --> pdb=" O ALA E 631 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL E 633 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR E 462 " --> pdb=" O VAL E 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 595 " --> pdb=" O ILE E 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE E 482 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 542 " --> pdb=" O PHE E 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 484 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 607 through 611 Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.562A pdb=" N ILE F 107 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER F 137 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY F 109 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 106 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 190 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS F 108 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA F 192 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE F 110 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ILE F 210 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 190 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL F 212 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA F 192 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 460 through 463 removed outlier: 6.407A pdb=" N SER F 460 " --> pdb=" O ALA F 631 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL F 633 " --> pdb=" O SER F 460 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR F 462 " --> pdb=" O VAL F 633 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F 595 " --> pdb=" O ILE F 632 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE F 482 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU F 542 " --> pdb=" O PHE F 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 484 " --> pdb=" O LEU F 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 607 through 611 Processing sheet with id=AC8, first strand: chain 'G' and resid 460 through 462 removed outlier: 3.597A pdb=" N THR G 595 " --> pdb=" O ILE G 632 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE G 539 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE G 594 " --> pdb=" O ILE G 539 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA G 541 " --> pdb=" O ILE G 594 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE G 482 " --> pdb=" O LEU G 540 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU G 542 " --> pdb=" O PHE G 482 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 484 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 483 " --> pdb=" O PHE G 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 607 through 611 Processing sheet with id=AD1, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.125A pdb=" N ILE H 88 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA H 101 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 167 through 169 removed outlier: 6.290A pdb=" N ILE H 134 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR H 193 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE H 190 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL H 212 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA H 192 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 272 through 274 removed outlier: 6.693A pdb=" N HIS H 272 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN H 250 " --> pdb=" O GLY H 343 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE H 345 " --> pdb=" O GLN H 250 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA H 252 " --> pdb=" O PHE H 345 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 217 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE H 253 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL H 219 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR H 373 " --> pdb=" O PRO H 218 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL H 220 " --> pdb=" O TYR H 373 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER H 370 " --> pdb=" O LEU H 396 " (cutoff:3.500A) 2081 hydrogen bonds defined for protein. 6132 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: 19.40 Time building geometry restraints manager: 20.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15081 1.34 - 1.46: 9924 1.46 - 1.59: 21482 1.59 - 1.71: 6 1.71 - 1.83: 357 Bond restraints: 46850 Sorted by residual: bond pdb=" CG GLU G 590 " pdb=" CD GLU G 590 " ideal model delta sigma weight residual 1.516 1.411 0.105 2.50e-02 1.60e+03 1.78e+01 bond pdb=" CG GLU B 90 " pdb=" CD GLU B 90 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.35e+01 bond pdb=" CG GLU E 90 " pdb=" CD GLU E 90 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU F 90 " pdb=" CD GLU F 90 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.34e+01 bond pdb=" CG GLU C 90 " pdb=" CD GLU C 90 " ideal model delta sigma weight residual 1.516 1.425 0.091 2.50e-02 1.60e+03 1.32e+01 ... (remaining 46845 not shown) Histogram of bond angle deviations from ideal: 95.25 - 104.92: 977 104.92 - 114.58: 27937 114.58 - 124.25: 33699 124.25 - 133.91: 903 133.91 - 143.58: 20 Bond angle restraints: 63536 Sorted by residual: angle pdb=" CB ARG C 464 " pdb=" CG ARG C 464 " pdb=" CD ARG C 464 " ideal model delta sigma weight residual 111.30 143.58 -32.28 2.30e+00 1.89e-01 1.97e+02 angle pdb=" CB ARG D 464 " pdb=" CG ARG D 464 " pdb=" CD ARG D 464 " ideal model delta sigma weight residual 111.30 143.54 -32.24 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG E 464 " pdb=" CG ARG E 464 " pdb=" CD ARG E 464 " ideal model delta sigma weight residual 111.30 143.52 -32.22 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG F 464 " pdb=" CG ARG F 464 " pdb=" CD ARG F 464 " ideal model delta sigma weight residual 111.30 143.51 -32.21 2.30e+00 1.89e-01 1.96e+02 angle pdb=" CB ARG A 464 " pdb=" CG ARG A 464 " pdb=" CD ARG A 464 " ideal model delta sigma weight residual 111.30 143.50 -32.20 2.30e+00 1.89e-01 1.96e+02 ... (remaining 63531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 24260 17.17 - 34.35: 2703 34.35 - 51.52: 1042 51.52 - 68.70: 320 68.70 - 85.87: 31 Dihedral angle restraints: 28356 sinusoidal: 10864 harmonic: 17492 Sorted by residual: dihedral pdb=" CA LYS C 447 " pdb=" C LYS C 447 " pdb=" N ARG C 448 " pdb=" CA ARG C 448 " ideal model delta harmonic sigma weight residual 180.00 135.12 44.88 0 5.00e+00 4.00e-02 8.06e+01 dihedral pdb=" CA LYS E 447 " pdb=" C LYS E 447 " pdb=" N ARG E 448 " pdb=" CA ARG E 448 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA LYS B 447 " pdb=" C LYS B 447 " pdb=" N ARG B 448 " pdb=" CA ARG B 448 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 28353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 6850 0.118 - 0.236: 410 0.236 - 0.353: 31 0.353 - 0.471: 18 0.471 - 0.589: 6 Chirality restraints: 7315 Sorted by residual: chirality pdb=" CB ILE A 67 " pdb=" CA ILE A 67 " pdb=" CG1 ILE A 67 " pdb=" CG2 ILE A 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CB ILE F 67 " pdb=" CA ILE F 67 " pdb=" CG1 ILE F 67 " pdb=" CG2 ILE F 67 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.65e+00 ... (remaining 7312 not shown) Planarity restraints: 8252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 90 " -0.041 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" CD GLU F 90 " 0.138 2.00e-02 2.50e+03 pdb=" OE1 GLU F 90 " -0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU F 90 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 90 " 0.041 2.00e-02 2.50e+03 7.94e-02 6.30e+01 pdb=" CD GLU D 90 " -0.137 2.00e-02 2.50e+03 pdb=" OE1 GLU D 90 " 0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU D 90 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 90 " -0.041 2.00e-02 2.50e+03 7.93e-02 6.29e+01 pdb=" CD GLU B 90 " 0.137 2.00e-02 2.50e+03 pdb=" OE1 GLU B 90 " -0.048 2.00e-02 2.50e+03 pdb=" OE2 GLU B 90 " -0.048 2.00e-02 2.50e+03 ... (remaining 8249 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1111 2.57 - 3.16: 45926 3.16 - 3.74: 78832 3.74 - 4.32: 107218 4.32 - 4.90: 159755 Nonbonded interactions: 392842 Sorted by model distance: nonbonded pdb=" N GLN C 44 " pdb=" OE1 GLN C 44 " model vdw 1.992 2.520 nonbonded pdb=" N GLN B 44 " pdb=" OE1 GLN B 44 " model vdw 1.992 2.520 nonbonded pdb=" N GLN D 44 " pdb=" OE1 GLN D 44 " model vdw 1.993 2.520 nonbonded pdb=" N GLN A 44 " pdb=" OE1 GLN A 44 " model vdw 1.993 2.520 nonbonded pdb=" N GLN E 44 " pdb=" OE1 GLN E 44 " model vdw 1.993 2.520 ... (remaining 392837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 10.920 Check model and map are aligned: 0.670 Set scattering table: 0.400 Process input model: 123.120 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.007 0.111 46850 Z= 0.497 Angle : 1.472 32.280 63536 Z= 0.772 Chirality : 0.067 0.589 7315 Planarity : 0.007 0.087 8252 Dihedral : 17.807 85.869 17100 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 39.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 15.66 % Allowed : 8.84 % Favored : 75.50 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 2.26 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.10), residues: 6053 helix: -1.53 (0.09), residues: 2702 sheet: -1.66 (0.16), residues: 964 loop : -2.52 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.008 TRP B 425 HIS 0.012 0.002 HIS F 780 PHE 0.048 0.004 PHE C 824 TYR 0.049 0.004 TYR C 259 ARG 0.057 0.004 ARG G 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 753 poor density : 653 time to evaluate : 5.698 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: 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: 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: 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 307 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7840 (ppp) REVERT: A 386 PHE cc_start: 0.8926 (t80) cc_final: 0.8627 (t80) REVERT: A 413 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: A 452 MET cc_start: 0.3902 (OUTLIER) cc_final: 0.3258 (tpp) REVERT: A 464 ARG cc_start: -0.2464 (OUTLIER) cc_final: -0.2967 (mtm110) REVERT: A 548 MET cc_start: -0.0075 (OUTLIER) cc_final: -0.0436 (mtt) REVERT: A 557 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.4971 (mmm) REVERT: A 582 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8414 (m-10) REVERT: A 585 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8622 (mpp) REVERT: A 614 LYS cc_start: 0.9389 (mptt) cc_final: 0.8908 (pttp) REVERT: A 708 ILE cc_start: 0.2480 (OUTLIER) cc_final: 0.2189 (mm) REVERT: B 86 CYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5841 (m) REVERT: B 523 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 531 MET cc_start: 0.9262 (ppp) cc_final: 0.8792 (ppp) REVERT: B 718 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4453 (pp) REVERT: C 46 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (ptp-170) REVERT: C 76 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 123 LYS cc_start: 0.8988 (mttt) cc_final: 0.8637 (mtpt) REVERT: C 182 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8597 (ptm) REVERT: C 233 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8970 (p) REVERT: C 238 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7748 (tptt) REVERT: C 413 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: C 452 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7006 (tpp) REVERT: D 22 GLU cc_start: 0.8827 (pm20) cc_final: 0.8542 (pm20) REVERT: D 452 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.4711 (tpp) REVERT: D 618 LYS cc_start: 0.5434 (tttt) cc_final: 0.4811 (mttt) REVERT: D 638 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8595 (p) REVERT: E 89 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8897 (mm) REVERT: E 198 MET cc_start: 0.9664 (mmp) cc_final: 0.9331 (mtt) REVERT: E 296 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (mp) REVERT: E 360 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9222 (mmm) REVERT: E 389 LYS cc_start: 0.3302 (OUTLIER) cc_final: 0.2762 (ttpt) REVERT: E 390 LEU cc_start: 0.6132 (mm) cc_final: 0.5556 (mm) REVERT: E 478 LYS cc_start: 0.6857 (mppt) cc_final: 0.6505 (mtmm) REVERT: E 523 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8184 (p) REVERT: E 554 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: E 613 ASP cc_start: 0.7870 (m-30) cc_final: 0.7365 (m-30) REVERT: E 680 MET cc_start: 0.8285 (ppp) cc_final: 0.7868 (ppp) REVERT: E 751 ASN cc_start: 0.8553 (m-40) cc_final: 0.8210 (t0) REVERT: F 46 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8247 (ptt180) REVERT: F 89 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9071 (mt) REVERT: F 182 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: F 198 MET cc_start: 0.9163 (mmp) cc_final: 0.8873 (mtp) REVERT: F 260 ASP cc_start: 0.9495 (OUTLIER) cc_final: 0.9232 (p0) REVERT: F 272 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (m-70) REVERT: F 307 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8422 (ptt) REVERT: F 413 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9107 (p0) REVERT: F 442 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (mmmt) REVERT: F 452 MET cc_start: 0.3730 (OUTLIER) cc_final: 0.3371 (tpt) REVERT: F 552 LYS cc_start: 0.9455 (mttt) cc_final: 0.9214 (mttt) REVERT: F 573 MET cc_start: 0.5703 (mtm) cc_final: 0.3324 (tmm) REVERT: F 585 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6348 (pmm) REVERT: G 566 GLU cc_start: 0.9188 (mp0) cc_final: 0.8960 (mp0) REVERT: G 570 MET cc_start: 0.8774 (tpt) cc_final: 0.8412 (ttt) REVERT: G 573 MET cc_start: 0.1689 (tmm) cc_final: 0.1014 (tpt) REVERT: G 580 TYR cc_start: 0.8490 (m-80) cc_final: 0.8186 (m-80) REVERT: G 581 LYS cc_start: 0.9719 (mtmm) cc_final: 0.9375 (tmtt) REVERT: G 691 ASN cc_start: 0.8709 (m-40) cc_final: 0.8258 (m-40) REVERT: H 78 ASN cc_start: 0.9250 (m-40) cc_final: 0.8855 (t0) outliers start: 753 outliers final: 170 residues processed: 1155 average time/residue: 0.5941 time to fit residues: 1101.7145 Evaluate side-chains 648 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 441 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 507 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 155 optimal weight: 0.0030 chunk 307 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 545 optimal weight: 20.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 172 GLN A 272 HIS A 560 HIS ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS A 736 HIS A 759 GLN A 780 HIS ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 HIS ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 807 ASN C 30 GLN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 272 HIS C 560 HIS ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 HIS ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 GLN E 560 HIS E 715 ASN ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 807 ASN F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 676 GLN ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 HIS F 736 HIS F 780 HIS ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 HIS ** H 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46850 Z= 0.271 Angle : 0.834 13.308 63536 Z= 0.428 Chirality : 0.048 0.270 7315 Planarity : 0.006 0.146 8252 Dihedral : 6.522 40.484 6439 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.35 % Allowed : 5.72 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 2.26 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.10), residues: 6053 helix: -0.83 (0.09), residues: 2792 sheet: -1.33 (0.16), residues: 977 loop : -2.40 (0.13), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 425 HIS 0.008 0.002 HIS E 272 PHE 0.030 0.002 PHE C 35 TYR 0.024 0.002 TYR G 774 ARG 0.025 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 567 time to evaluate : 4.952 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: 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: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.9312 (ptp) cc_final: 0.8320 (tmm) REVERT: A 307 MET cc_start: 0.8283 (ppp) cc_final: 0.8048 (ppp) REVERT: A 386 PHE cc_start: 0.8880 (t80) cc_final: 0.8648 (t80) REVERT: A 585 MET cc_start: 0.9125 (mpp) cc_final: 0.7509 (mmt) REVERT: A 614 LYS cc_start: 0.9549 (mppt) cc_final: 0.9314 (pttp) REVERT: A 639 MET cc_start: 0.1004 (mmt) cc_final: -0.0058 (mmm) REVERT: B 260 ASP cc_start: 0.8935 (m-30) cc_final: 0.8718 (m-30) REVERT: B 445 VAL cc_start: 0.8795 (t) cc_final: 0.8581 (t) REVERT: B 452 MET cc_start: 0.6312 (tpp) cc_final: 0.5517 (tpt) REVERT: B 531 MET cc_start: 0.9310 (ppp) cc_final: 0.8849 (ppp) REVERT: C 123 LYS cc_start: 0.8765 (mttt) cc_final: 0.8260 (mtpt) REVERT: C 182 MET cc_start: 0.8961 (ttt) cc_final: 0.8571 (ptm) REVERT: C 829 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.8806 (p0) REVERT: D 52 MET cc_start: 0.9343 (ppp) cc_final: 0.8968 (ppp) REVERT: D 91 GLU cc_start: 0.7304 (mp0) cc_final: 0.6935 (mp0) REVERT: D 182 MET cc_start: 0.9227 (ppp) cc_final: 0.8987 (ppp) REVERT: D 236 MET cc_start: 0.9179 (mpp) cc_final: 0.8861 (mtt) REVERT: D 452 MET cc_start: 0.5625 (tpp) cc_final: 0.5282 (tpt) REVERT: D 618 LYS cc_start: 0.4666 (tttt) cc_final: 0.4015 (mttt) REVERT: E 182 MET cc_start: 0.6855 (ppp) cc_final: 0.6414 (ppp) REVERT: E 266 PHE cc_start: 0.9558 (m-10) cc_final: 0.9328 (m-10) REVERT: E 307 MET cc_start: 0.8258 (ppp) cc_final: 0.7923 (ppp) REVERT: E 360 MET cc_start: 0.9747 (mmm) cc_final: 0.9441 (mmm) REVERT: E 613 ASP cc_start: 0.7784 (m-30) cc_final: 0.7329 (m-30) REVERT: E 797 LEU cc_start: 0.9502 (tt) cc_final: 0.9202 (mt) REVERT: F 182 MET cc_start: 0.9187 (ttt) cc_final: 0.8840 (ppp) REVERT: F 236 MET cc_start: 0.9330 (mpp) cc_final: 0.9115 (mmm) REVERT: F 307 MET cc_start: 0.8738 (ppp) cc_final: 0.8356 (ppp) REVERT: F 573 MET cc_start: 0.5903 (mtm) cc_final: 0.3646 (tmm) REVERT: G 524 VAL cc_start: 0.9455 (m) cc_final: 0.9203 (p) REVERT: G 566 GLU cc_start: 0.9145 (mp0) cc_final: 0.8883 (mp0) REVERT: G 573 MET cc_start: 0.2005 (tmm) cc_final: 0.1506 (tpt) REVERT: G 636 ASN cc_start: 0.7544 (p0) cc_final: 0.7232 (p0) REVERT: H 78 ASN cc_start: 0.9267 (m-40) cc_final: 0.8913 (t0) REVERT: H 80 TYR cc_start: 0.9193 (m-10) cc_final: 0.8839 (m-80) outliers start: 17 outliers final: 1 residues processed: 584 average time/residue: 0.6409 time to fit residues: 611.1541 Evaluate side-chains 394 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 392 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 303 optimal weight: 0.0040 chunk 169 optimal weight: 8.9990 chunk 454 optimal weight: 40.0000 chunk 371 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 546 optimal weight: 0.9990 chunk 590 optimal weight: 7.9990 chunk 486 optimal weight: 0.8980 chunk 542 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 438 optimal weight: 0.7980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 172 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 722 HIS B 736 HIS ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 115 ASN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 ASN D 30 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 HIS D 736 HIS ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 GLN ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 715 ASN ** F 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 GLN F 807 ASN G 691 ASN ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 759 GLN G 792 GLN ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46850 Z= 0.203 Angle : 0.730 13.521 63536 Z= 0.369 Chirality : 0.046 0.271 7315 Planarity : 0.005 0.078 8252 Dihedral : 5.776 35.651 6439 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.23 % Allowed : 4.35 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 1.50 % 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: -1.75 (0.11), residues: 6053 helix: -0.29 (0.10), residues: 2768 sheet: -1.09 (0.17), residues: 939 loop : -2.19 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 555 HIS 0.007 0.001 HIS D 726 PHE 0.026 0.002 PHE C 35 TYR 0.026 0.002 TYR E 77 ARG 0.009 0.001 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 532 time to evaluate : 5.134 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: 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 307 MET cc_start: 0.8179 (ppp) cc_final: 0.7901 (ppp) REVERT: A 507 MET cc_start: 0.1508 (mtp) cc_final: 0.0750 (ttt) REVERT: A 557 MET cc_start: 0.7105 (mmp) cc_final: 0.6810 (tpt) REVERT: A 585 MET cc_start: 0.9300 (mpp) cc_final: 0.8580 (mmt) REVERT: A 614 LYS cc_start: 0.9550 (mppt) cc_final: 0.9334 (pttp) REVERT: A 639 MET cc_start: 0.0796 (mmt) cc_final: 0.0239 (mmt) REVERT: A 785 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8516 (tt0) REVERT: B 59 MET cc_start: 0.6620 (pmm) cc_final: 0.6412 (pmm) REVERT: B 98 MET cc_start: 0.9345 (mmp) cc_final: 0.9114 (mmp) REVERT: B 198 MET cc_start: 0.8054 (ptt) cc_final: 0.7573 (tpt) REVERT: B 386 PHE cc_start: 0.9218 (t80) cc_final: 0.8859 (t80) REVERT: B 445 VAL cc_start: 0.8921 (t) cc_final: 0.8719 (t) REVERT: B 480 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7892 (mtp85) REVERT: B 531 MET cc_start: 0.9279 (ppp) cc_final: 0.8735 (ppp) REVERT: C 68 LYS cc_start: 0.9130 (pttp) cc_final: 0.8832 (pptt) REVERT: C 123 LYS cc_start: 0.8636 (mttt) cc_final: 0.7933 (ptmt) REVERT: C 182 MET cc_start: 0.8858 (ttt) cc_final: 0.8543 (ptm) REVERT: C 307 MET cc_start: 0.9086 (ptt) cc_final: 0.8732 (ppp) REVERT: C 557 MET cc_start: 0.8846 (mmp) cc_final: 0.8635 (mmm) REVERT: C 823 ASP cc_start: 0.9528 (m-30) cc_final: 0.9087 (p0) REVERT: D 262 VAL cc_start: 0.9762 (t) cc_final: 0.9407 (p) REVERT: D 452 MET cc_start: 0.5444 (tpp) cc_final: 0.5180 (tpt) REVERT: D 618 LYS cc_start: 0.4616 (tttt) cc_final: 0.3788 (mttt) REVERT: D 774 TYR cc_start: 0.7495 (m-80) cc_final: 0.7283 (m-80) REVERT: E 182 MET cc_start: 0.6845 (ppp) cc_final: 0.6350 (ppp) REVERT: E 236 MET cc_start: 0.9471 (tmm) cc_final: 0.9247 (mmt) REVERT: E 266 PHE cc_start: 0.9577 (m-10) cc_final: 0.9336 (m-10) REVERT: E 307 MET cc_start: 0.8156 (ppp) cc_final: 0.7935 (ppp) REVERT: E 360 MET cc_start: 0.9728 (mmm) cc_final: 0.9376 (ttp) REVERT: E 390 LEU cc_start: 0.6704 (mm) cc_final: 0.6441 (mm) REVERT: E 613 ASP cc_start: 0.7721 (m-30) cc_final: 0.7249 (m-30) REVERT: E 797 LEU cc_start: 0.9462 (tt) cc_final: 0.9207 (mt) REVERT: F 182 MET cc_start: 0.9176 (ttt) cc_final: 0.8723 (ppp) REVERT: F 236 MET cc_start: 0.9361 (mpp) cc_final: 0.9118 (mmm) REVERT: F 307 MET cc_start: 0.8752 (ppp) cc_final: 0.8135 (ppp) REVERT: F 573 MET cc_start: 0.5858 (mtm) cc_final: 0.3484 (tmm) REVERT: F 585 MET cc_start: 0.6668 (mmt) cc_final: 0.6355 (mmm) REVERT: G 512 PHE cc_start: 0.8921 (t80) cc_final: 0.8181 (t80) REVERT: G 524 VAL cc_start: 0.9374 (m) cc_final: 0.9012 (p) REVERT: G 566 GLU cc_start: 0.9165 (mp0) cc_final: 0.8930 (mp0) REVERT: G 573 MET cc_start: 0.1966 (tmm) cc_final: 0.1494 (tpt) REVERT: G 637 LEU cc_start: 0.8982 (mt) cc_final: 0.8716 (pp) REVERT: H 78 ASN cc_start: 0.9254 (m-40) cc_final: 0.8819 (t0) REVERT: H 80 TYR cc_start: 0.9168 (m-10) cc_final: 0.8779 (m-80) outliers start: 11 outliers final: 3 residues processed: 543 average time/residue: 0.5806 time to fit residues: 519.7058 Evaluate side-chains 401 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 5.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 540 optimal weight: 20.0000 chunk 411 optimal weight: 7.9990 chunk 283 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 260 optimal weight: 7.9990 chunk 367 optimal weight: 30.0000 chunk 548 optimal weight: 9.9990 chunk 580 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 520 optimal weight: 40.0000 chunk 156 optimal weight: 5.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 172 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 HIS ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 69 ASN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 ASN ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN ** H 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 46850 Z= 0.219 Angle : 0.691 13.890 63536 Z= 0.352 Chirality : 0.045 0.282 7315 Planarity : 0.004 0.073 8252 Dihedral : 5.473 33.136 6439 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.21 % Allowed : 4.35 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 1.13 % 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 (0.11), residues: 6053 helix: -0.10 (0.10), residues: 2824 sheet: -1.07 (0.17), residues: 915 loop : -2.10 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 555 HIS 0.008 0.001 HIS B 455 PHE 0.032 0.002 PHE E 717 TYR 0.020 0.002 TYR E 77 ARG 0.010 0.001 ARG D 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 505 time to evaluate : 5.232 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: 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 52 MET cc_start: 0.8124 (ptm) cc_final: 0.7727 (tmm) REVERT: A 172 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: A 307 MET cc_start: 0.8163 (ppp) cc_final: 0.7947 (ppp) REVERT: A 507 MET cc_start: 0.2224 (mtp) cc_final: 0.1316 (ttt) REVERT: A 557 MET cc_start: 0.7123 (mmp) cc_final: 0.6639 (tpt) REVERT: A 585 MET cc_start: 0.9276 (mpp) cc_final: 0.8467 (mmp) REVERT: A 614 LYS cc_start: 0.9585 (mppt) cc_final: 0.9367 (pttp) REVERT: A 639 MET cc_start: 0.0610 (mmt) cc_final: -0.0349 (mmt) REVERT: B 59 MET cc_start: 0.6824 (pmm) cc_final: 0.5885 (pmm) REVERT: B 98 MET cc_start: 0.9328 (mmp) cc_final: 0.9082 (mmp) REVERT: B 198 MET cc_start: 0.7926 (ptt) cc_final: 0.7561 (tpt) REVERT: B 307 MET cc_start: -0.2846 (ptm) cc_final: -0.4215 (tpt) REVERT: B 386 PHE cc_start: 0.9188 (t80) cc_final: 0.8798 (t80) REVERT: B 531 MET cc_start: 0.9234 (ppp) cc_final: 0.8835 (ppp) REVERT: C 52 MET cc_start: 0.8908 (ptp) cc_final: 0.8688 (ptp) REVERT: C 68 LYS cc_start: 0.9137 (pttp) cc_final: 0.8841 (pptt) REVERT: C 79 LYS cc_start: 0.9328 (mmmt) cc_final: 0.9102 (mmmm) REVERT: C 123 LYS cc_start: 0.8697 (mttt) cc_final: 0.8120 (mtpt) REVERT: C 182 MET cc_start: 0.8856 (ttt) cc_final: 0.8577 (ptm) REVERT: C 307 MET cc_start: 0.9163 (ptt) cc_final: 0.8795 (ppp) REVERT: C 834 GLU cc_start: 0.8724 (tp30) cc_final: 0.7901 (tp30) REVERT: D 52 MET cc_start: 0.9092 (ppp) cc_final: 0.8880 (ppp) REVERT: D 189 LEU cc_start: 0.9071 (tp) cc_final: 0.8865 (tp) REVERT: D 262 VAL cc_start: 0.9819 (t) cc_final: 0.9538 (t) REVERT: D 266 PHE cc_start: 0.9440 (m-80) cc_final: 0.9233 (m-80) REVERT: D 452 MET cc_start: 0.5893 (tpp) cc_final: 0.5604 (tpt) REVERT: D 618 LYS cc_start: 0.4888 (tttt) cc_final: 0.4122 (mttt) REVERT: D 774 TYR cc_start: 0.7648 (m-80) cc_final: 0.7422 (m-80) REVERT: E 182 MET cc_start: 0.7055 (ppp) cc_final: 0.6490 (ppp) REVERT: E 266 PHE cc_start: 0.9604 (m-10) cc_final: 0.9361 (m-10) REVERT: E 307 MET cc_start: 0.8064 (ppp) cc_final: 0.7811 (ppp) REVERT: E 360 MET cc_start: 0.9740 (mmm) cc_final: 0.9459 (mmm) REVERT: E 390 LEU cc_start: 0.6971 (mm) cc_final: 0.6717 (mm) REVERT: E 452 MET cc_start: 0.6799 (tpp) cc_final: 0.6300 (tpp) REVERT: E 613 ASP cc_start: 0.7943 (m-30) cc_final: 0.7454 (m-30) REVERT: E 797 LEU cc_start: 0.9491 (tt) cc_final: 0.9238 (mt) REVERT: F 182 MET cc_start: 0.9215 (ttt) cc_final: 0.8659 (ppp) REVERT: F 307 MET cc_start: 0.8809 (ppp) cc_final: 0.8184 (ppp) REVERT: F 342 LEU cc_start: 0.9182 (tp) cc_final: 0.8948 (tp) REVERT: F 573 MET cc_start: 0.6049 (mtm) cc_final: 0.3719 (tmm) REVERT: F 623 ASP cc_start: 0.8304 (p0) cc_final: 0.7788 (p0) REVERT: G 512 PHE cc_start: 0.8895 (t80) cc_final: 0.8321 (t80) REVERT: G 524 VAL cc_start: 0.9339 (m) cc_final: 0.8978 (p) REVERT: G 554 MET cc_start: 0.9194 (ptp) cc_final: 0.8979 (ptp) REVERT: G 566 GLU cc_start: 0.9191 (mp0) cc_final: 0.8970 (mp0) REVERT: G 573 MET cc_start: 0.1971 (tmm) cc_final: 0.1512 (tpt) REVERT: G 637 LEU cc_start: 0.8946 (mt) cc_final: 0.8682 (pt) REVERT: H 78 ASN cc_start: 0.9294 (m-40) cc_final: 0.8841 (t0) REVERT: H 80 TYR cc_start: 0.9209 (m-10) cc_final: 0.8804 (m-80) outliers start: 10 outliers final: 0 residues processed: 514 average time/residue: 0.5627 time to fit residues: 478.6632 Evaluate side-chains 380 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 5.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 483 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 432 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 495 optimal weight: 20.0000 chunk 401 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 296 optimal weight: 7.9990 chunk 521 optimal weight: 0.9980 chunk 146 optimal weight: 0.0170 overall best weight: 4.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 ASN A 792 GLN B 30 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 ASN F 807 ASN G 691 ASN ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 46850 Z= 0.208 Angle : 0.691 13.068 63536 Z= 0.352 Chirality : 0.045 0.272 7315 Planarity : 0.005 0.074 8252 Dihedral : 5.250 31.651 6439 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.75 % 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: -1.35 (0.11), residues: 6053 helix: 0.07 (0.10), residues: 2826 sheet: -0.94 (0.17), residues: 910 loop : -2.03 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 555 HIS 0.008 0.001 HIS F 564 PHE 0.040 0.002 PHE E 717 TYR 0.019 0.002 TYR B 580 ARG 0.009 0.001 ARG C 772 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 492 time to evaluate : 4.945 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: 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 52 MET cc_start: 0.8170 (ptm) cc_final: 0.7819 (tmm) REVERT: A 307 MET cc_start: 0.8247 (ppp) cc_final: 0.8019 (ppp) REVERT: A 507 MET cc_start: 0.2685 (mtp) cc_final: 0.1939 (ttt) REVERT: A 557 MET cc_start: 0.7169 (mmp) cc_final: 0.6680 (tpt) REVERT: A 585 MET cc_start: 0.9097 (mpp) cc_final: 0.8323 (mmt) REVERT: A 639 MET cc_start: 0.0510 (mmt) cc_final: -0.0326 (mmt) REVERT: A 641 MET cc_start: 0.7126 (ptm) cc_final: 0.6882 (ptt) REVERT: B 59 MET cc_start: 0.6856 (pmm) cc_final: 0.6577 (pmm) REVERT: B 98 MET cc_start: 0.9337 (mmp) cc_final: 0.9015 (mmp) REVERT: B 198 MET cc_start: 0.7933 (ptt) cc_final: 0.7584 (tpt) REVERT: B 307 MET cc_start: -0.2826 (ptm) cc_final: -0.4273 (tpt) REVERT: B 386 PHE cc_start: 0.9172 (t80) cc_final: 0.8755 (t80) REVERT: B 445 VAL cc_start: 0.9055 (t) cc_final: 0.8684 (p) REVERT: B 452 MET cc_start: 0.5322 (tpt) cc_final: 0.4657 (tpp) REVERT: B 531 MET cc_start: 0.9088 (ppp) cc_final: 0.8740 (ppp) REVERT: C 68 LYS cc_start: 0.9169 (pttp) cc_final: 0.8862 (pptt) REVERT: C 79 LYS cc_start: 0.9294 (mmmt) cc_final: 0.9086 (mmmm) REVERT: C 123 LYS cc_start: 0.8723 (mttt) cc_final: 0.8063 (mtpt) REVERT: C 266 PHE cc_start: 0.8337 (m-10) cc_final: 0.8092 (m-80) REVERT: C 307 MET cc_start: 0.9210 (ptt) cc_final: 0.8900 (ppp) REVERT: C 747 VAL cc_start: 0.9174 (t) cc_final: 0.8932 (p) REVERT: C 834 GLU cc_start: 0.8743 (tp30) cc_final: 0.7959 (tp30) REVERT: D 182 MET cc_start: 0.9208 (ppp) cc_final: 0.9007 (ppp) REVERT: D 262 VAL cc_start: 0.9827 (t) cc_final: 0.9547 (t) REVERT: D 452 MET cc_start: 0.6175 (tpp) cc_final: 0.5973 (tpt) REVERT: D 618 LYS cc_start: 0.4996 (tttt) cc_final: 0.4259 (mttt) REVERT: E 182 MET cc_start: 0.7131 (ppp) cc_final: 0.6510 (ppp) REVERT: E 266 PHE cc_start: 0.9634 (m-10) cc_final: 0.9386 (m-10) REVERT: E 307 MET cc_start: 0.8060 (ppp) cc_final: 0.7692 (ppp) REVERT: E 360 MET cc_start: 0.9771 (mmm) cc_final: 0.9484 (mmm) REVERT: E 390 LEU cc_start: 0.7108 (mm) cc_final: 0.6845 (mm) REVERT: E 452 MET cc_start: 0.6263 (tpp) cc_final: 0.5850 (tpp) REVERT: E 613 ASP cc_start: 0.7964 (m-30) cc_final: 0.7563 (m-30) REVERT: F 182 MET cc_start: 0.9228 (ttt) cc_final: 0.8606 (ppp) REVERT: F 236 MET cc_start: 0.9349 (mmp) cc_final: 0.9090 (mmm) REVERT: F 307 MET cc_start: 0.8866 (ppp) cc_final: 0.8290 (ppp) REVERT: F 342 LEU cc_start: 0.9219 (tp) cc_final: 0.8952 (tp) REVERT: F 573 MET cc_start: 0.6195 (mtm) cc_final: 0.4108 (tmm) REVERT: F 585 MET cc_start: 0.5306 (tpt) cc_final: 0.3580 (tpt) REVERT: F 717 PHE cc_start: 0.7319 (t80) cc_final: 0.7025 (t80) REVERT: G 566 GLU cc_start: 0.9205 (mp0) cc_final: 0.8991 (mp0) REVERT: G 573 MET cc_start: 0.2065 (tmm) cc_final: 0.1578 (tpt) REVERT: G 704 ASN cc_start: 0.9418 (m110) cc_final: 0.9203 (t0) REVERT: H 78 ASN cc_start: 0.9281 (m-40) cc_final: 0.8892 (t0) REVERT: H 80 TYR cc_start: 0.9282 (m-10) cc_final: 0.8838 (m-80) outliers start: 5 outliers final: 1 residues processed: 496 average time/residue: 0.5676 time to fit residues: 467.8110 Evaluate side-chains 376 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 375 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 195 optimal weight: 9.9990 chunk 523 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 581 optimal weight: 50.0000 chunk 482 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 48 optimal weight: 50.0000 chunk 192 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 172 GLN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN ** C 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 455 HIS ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 691 ASN ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 46850 Z= 0.196 Angle : 0.679 12.902 63536 Z= 0.342 Chirality : 0.045 0.263 7315 Planarity : 0.004 0.063 8252 Dihedral : 5.082 29.874 6439 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.18 (0.11), residues: 6053 helix: 0.21 (0.10), residues: 2838 sheet: -0.95 (0.17), residues: 958 loop : -1.91 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 555 HIS 0.008 0.001 HIS E 70 PHE 0.030 0.002 PHE E 717 TYR 0.015 0.002 TYR C 259 ARG 0.009 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 478 time to evaluate : 5.142 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: 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 52 MET cc_start: 0.8339 (ptm) cc_final: 0.7896 (tmm) REVERT: A 69 ASN cc_start: 0.9448 (m-40) cc_final: 0.9183 (m-40) REVERT: A 307 MET cc_start: 0.8209 (ppp) cc_final: 0.7979 (ppp) REVERT: A 396 LEU cc_start: 0.9023 (mm) cc_final: 0.8639 (tp) REVERT: A 507 MET cc_start: 0.2653 (mtp) cc_final: 0.1909 (ttt) REVERT: A 557 MET cc_start: 0.7137 (mmp) cc_final: 0.6839 (tpp) REVERT: A 585 MET cc_start: 0.9117 (mpp) cc_final: 0.8041 (mmp) REVERT: A 639 MET cc_start: 0.0435 (mmt) cc_final: -0.0380 (mmt) REVERT: B 59 MET cc_start: 0.6938 (pmm) cc_final: 0.6683 (pmm) REVERT: B 98 MET cc_start: 0.9341 (mmp) cc_final: 0.9010 (mmp) REVERT: B 198 MET cc_start: 0.7986 (ptt) cc_final: 0.7609 (tpt) REVERT: B 307 MET cc_start: -0.2970 (ptm) cc_final: -0.4439 (tpt) REVERT: B 386 PHE cc_start: 0.9154 (t80) cc_final: 0.8731 (t80) REVERT: B 445 VAL cc_start: 0.9099 (t) cc_final: 0.8709 (p) REVERT: B 531 MET cc_start: 0.9109 (ppp) cc_final: 0.8803 (ppp) REVERT: C 68 LYS cc_start: 0.9176 (pttp) cc_final: 0.8872 (pptt) REVERT: C 123 LYS cc_start: 0.8715 (mttt) cc_final: 0.8089 (mtpt) REVERT: C 266 PHE cc_start: 0.8361 (m-10) cc_final: 0.8138 (m-80) REVERT: C 307 MET cc_start: 0.9235 (ptt) cc_final: 0.8982 (ppp) REVERT: C 747 VAL cc_start: 0.9169 (t) cc_final: 0.8939 (p) REVERT: C 834 GLU cc_start: 0.8746 (tp30) cc_final: 0.7964 (tp30) REVERT: D 98 MET cc_start: 0.7462 (mmp) cc_final: 0.7240 (mmp) REVERT: D 182 MET cc_start: 0.9276 (ppp) cc_final: 0.9029 (ppp) REVERT: D 241 ASP cc_start: 0.8585 (m-30) cc_final: 0.8326 (p0) REVERT: D 262 VAL cc_start: 0.9820 (t) cc_final: 0.9516 (t) REVERT: D 452 MET cc_start: 0.6548 (tpp) cc_final: 0.6259 (tpt) REVERT: D 618 LYS cc_start: 0.4951 (tttt) cc_final: 0.4732 (tttt) REVERT: E 182 MET cc_start: 0.7198 (ppp) cc_final: 0.6564 (ppp) REVERT: E 307 MET cc_start: 0.8063 (ppp) cc_final: 0.7684 (ppp) REVERT: E 360 MET cc_start: 0.9787 (mmm) cc_final: 0.9496 (mmm) REVERT: E 390 LEU cc_start: 0.7301 (mm) cc_final: 0.7029 (mm) REVERT: E 613 ASP cc_start: 0.8037 (m-30) cc_final: 0.7545 (m-30) REVERT: F 182 MET cc_start: 0.9312 (ttt) cc_final: 0.8680 (ppp) REVERT: F 236 MET cc_start: 0.9345 (mmp) cc_final: 0.9109 (mmm) REVERT: F 307 MET cc_start: 0.8915 (ppp) cc_final: 0.8383 (ppp) REVERT: F 342 LEU cc_start: 0.9168 (tp) cc_final: 0.8890 (tp) REVERT: F 573 MET cc_start: 0.6234 (mtm) cc_final: 0.3987 (tmm) REVERT: F 585 MET cc_start: 0.5474 (tpt) cc_final: 0.3569 (tpt) REVERT: F 717 PHE cc_start: 0.7396 (t80) cc_final: 0.7074 (t80) REVERT: G 566 GLU cc_start: 0.9214 (mp0) cc_final: 0.9004 (mp0) REVERT: G 573 MET cc_start: 0.2269 (tmm) cc_final: 0.1822 (tpt) REVERT: G 636 ASN cc_start: 0.8041 (p0) cc_final: 0.7818 (p0) REVERT: G 704 ASN cc_start: 0.9429 (m110) cc_final: 0.9179 (t0) REVERT: H 78 ASN cc_start: 0.9298 (m-40) cc_final: 0.8881 (t0) REVERT: H 80 TYR cc_start: 0.9289 (m-10) cc_final: 0.8814 (m-80) outliers start: 4 outliers final: 1 residues processed: 482 average time/residue: 0.5580 time to fit residues: 447.7730 Evaluate side-chains 389 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 560 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 424 optimal weight: 8.9990 chunk 329 optimal weight: 20.0000 chunk 489 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 579 optimal weight: 0.0470 chunk 362 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 267 optimal weight: 4.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 807 ASN E 30 GLN E 69 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46850 Z= 0.197 Angle : 0.681 12.599 63536 Z= 0.344 Chirality : 0.045 0.267 7315 Planarity : 0.004 0.088 8252 Dihedral : 4.994 29.000 6439 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.08 (0.11), residues: 6053 helix: 0.30 (0.10), residues: 2838 sheet: -0.94 (0.16), residues: 999 loop : -1.87 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 555 HIS 0.013 0.001 HIS E 70 PHE 0.028 0.001 PHE E 717 TYR 0.014 0.001 TYR D 684 ARG 0.008 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 5.214 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: 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 52 MET cc_start: 0.8418 (ptm) cc_final: 0.7952 (tmm) REVERT: A 69 ASN cc_start: 0.9468 (m-40) cc_final: 0.9223 (m-40) REVERT: A 307 MET cc_start: 0.8202 (ppp) cc_final: 0.7976 (ppp) REVERT: A 396 LEU cc_start: 0.9041 (mm) cc_final: 0.8688 (tp) REVERT: A 507 MET cc_start: 0.2884 (mtp) cc_final: 0.2135 (ttt) REVERT: A 557 MET cc_start: 0.7137 (mmp) cc_final: 0.6912 (tpp) REVERT: A 581 LYS cc_start: 0.8900 (tptp) cc_final: 0.8695 (tppt) REVERT: A 585 MET cc_start: 0.9033 (mpp) cc_final: 0.8342 (mmt) REVERT: A 639 MET cc_start: 0.0328 (mmt) cc_final: -0.0504 (mmt) REVERT: A 641 MET cc_start: 0.5722 (ptt) cc_final: 0.5408 (ptt) REVERT: B 98 MET cc_start: 0.9353 (mmp) cc_final: 0.9057 (mmp) REVERT: B 198 MET cc_start: 0.8065 (ptt) cc_final: 0.7647 (tpt) REVERT: B 307 MET cc_start: -0.2903 (ptm) cc_final: -0.4412 (tpt) REVERT: B 386 PHE cc_start: 0.9132 (t80) cc_final: 0.8677 (t80) REVERT: B 445 VAL cc_start: 0.9087 (t) cc_final: 0.8704 (p) REVERT: B 502 LEU cc_start: 0.9569 (pp) cc_final: 0.9051 (pp) REVERT: B 531 MET cc_start: 0.9165 (ppp) cc_final: 0.8942 (ppp) REVERT: C 68 LYS cc_start: 0.9205 (pttp) cc_final: 0.8900 (pptt) REVERT: C 123 LYS cc_start: 0.8701 (mttt) cc_final: 0.8095 (mtpt) REVERT: C 266 PHE cc_start: 0.8370 (m-10) cc_final: 0.8140 (m-80) REVERT: C 307 MET cc_start: 0.9242 (ptt) cc_final: 0.9011 (ppp) REVERT: C 747 VAL cc_start: 0.9159 (t) cc_final: 0.8941 (p) REVERT: C 834 GLU cc_start: 0.8764 (tp30) cc_final: 0.8028 (tp30) REVERT: D 182 MET cc_start: 0.9255 (ppp) cc_final: 0.9023 (ppp) REVERT: D 241 ASP cc_start: 0.8604 (m-30) cc_final: 0.8403 (p0) REVERT: D 262 VAL cc_start: 0.9805 (t) cc_final: 0.9499 (t) REVERT: D 452 MET cc_start: 0.6898 (tpp) cc_final: 0.6553 (tpt) REVERT: D 618 LYS cc_start: 0.4875 (tttt) cc_final: 0.4607 (tttt) REVERT: E 182 MET cc_start: 0.7281 (ppp) cc_final: 0.6629 (ppp) REVERT: E 307 MET cc_start: 0.8036 (ppp) cc_final: 0.7787 (ppp) REVERT: E 360 MET cc_start: 0.9791 (mmm) cc_final: 0.9500 (mmm) REVERT: E 390 LEU cc_start: 0.7544 (mm) cc_final: 0.7253 (mm) REVERT: E 585 MET cc_start: 0.6523 (pmm) cc_final: 0.5917 (pmm) REVERT: E 613 ASP cc_start: 0.8061 (m-30) cc_final: 0.7552 (m-30) REVERT: F 182 MET cc_start: 0.9324 (ttt) cc_final: 0.8661 (ppp) REVERT: F 236 MET cc_start: 0.9371 (mmp) cc_final: 0.9162 (mmm) REVERT: F 307 MET cc_start: 0.8918 (ppp) cc_final: 0.8377 (ppp) REVERT: F 342 LEU cc_start: 0.9186 (tp) cc_final: 0.8959 (tp) REVERT: F 573 MET cc_start: 0.6157 (mtm) cc_final: 0.3853 (tmm) REVERT: F 585 MET cc_start: 0.5343 (tpt) cc_final: 0.3649 (tpt) REVERT: F 590 GLU cc_start: 0.8531 (pm20) cc_final: 0.8176 (pm20) REVERT: F 623 ASP cc_start: 0.8463 (p0) cc_final: 0.8226 (p0) REVERT: F 717 PHE cc_start: 0.7571 (t80) cc_final: 0.7302 (t80) REVERT: H 78 ASN cc_start: 0.9295 (m-40) cc_final: 0.9004 (t0) REVERT: H 80 TYR cc_start: 0.9313 (m-10) cc_final: 0.8833 (m-80) REVERT: H 307 MET cc_start: 0.2895 (ptm) cc_final: 0.2469 (ppp) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.5667 time to fit residues: 452.8075 Evaluate side-chains 383 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 5.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 358 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 345 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 368 optimal weight: 0.7980 chunk 394 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 455 optimal weight: 0.5980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN C 30 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN E 147 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46850 Z= 0.190 Angle : 0.679 12.446 63536 Z= 0.341 Chirality : 0.044 0.259 7315 Planarity : 0.004 0.079 8252 Dihedral : 4.905 25.986 6439 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.02 % Allowed : 1.50 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.02 (0.11), residues: 6053 helix: 0.35 (0.10), residues: 2851 sheet: -0.86 (0.17), residues: 964 loop : -1.87 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 555 HIS 0.007 0.001 HIS C 70 PHE 0.026 0.001 PHE E 717 TYR 0.018 0.001 TYR C 77 ARG 0.008 0.001 ARG G 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 5.119 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8449 (ptm) cc_final: 0.7971 (tmm) REVERT: A 69 ASN cc_start: 0.9479 (m-40) cc_final: 0.9245 (m-40) REVERT: A 307 MET cc_start: 0.8247 (ppp) cc_final: 0.8011 (ppp) REVERT: A 396 LEU cc_start: 0.9070 (mm) cc_final: 0.8705 (tp) REVERT: A 507 MET cc_start: 0.2951 (mtp) cc_final: 0.2191 (ttt) REVERT: A 557 MET cc_start: 0.7139 (mmp) cc_final: 0.6925 (tpp) REVERT: A 585 MET cc_start: 0.8986 (mpp) cc_final: 0.8303 (mmt) REVERT: A 639 MET cc_start: 0.0072 (mmt) cc_final: -0.0820 (mmt) REVERT: A 641 MET cc_start: 0.5850 (ptt) cc_final: 0.5527 (ptt) REVERT: B 98 MET cc_start: 0.9354 (mmp) cc_final: 0.9081 (mmp) REVERT: B 198 MET cc_start: 0.8093 (ptt) cc_final: 0.7659 (tpt) REVERT: B 307 MET cc_start: -0.2864 (ptm) cc_final: -0.4375 (tpt) REVERT: B 386 PHE cc_start: 0.9146 (t80) cc_final: 0.8665 (t80) REVERT: B 445 VAL cc_start: 0.9148 (t) cc_final: 0.8780 (p) REVERT: C 68 LYS cc_start: 0.9200 (pttp) cc_final: 0.8909 (pptt) REVERT: C 123 LYS cc_start: 0.8717 (mttt) cc_final: 0.8095 (mtpt) REVERT: C 307 MET cc_start: 0.9220 (ptt) cc_final: 0.9006 (ppp) REVERT: C 747 VAL cc_start: 0.9160 (t) cc_final: 0.8951 (p) REVERT: C 834 GLU cc_start: 0.8793 (tp30) cc_final: 0.8038 (tp30) REVERT: D 182 MET cc_start: 0.9250 (ppp) cc_final: 0.9027 (ppp) REVERT: D 262 VAL cc_start: 0.9851 (t) cc_final: 0.9585 (p) REVERT: D 266 PHE cc_start: 0.9452 (m-80) cc_final: 0.9234 (m-80) REVERT: D 452 MET cc_start: 0.6998 (tpp) cc_final: 0.6759 (tpt) REVERT: D 618 LYS cc_start: 0.4959 (tttt) cc_final: 0.4701 (tttt) REVERT: E 182 MET cc_start: 0.7269 (ppp) cc_final: 0.6715 (ppp) REVERT: E 307 MET cc_start: 0.8020 (ppp) cc_final: 0.7754 (ppp) REVERT: E 360 MET cc_start: 0.9795 (mmm) cc_final: 0.9505 (mmm) REVERT: E 390 LEU cc_start: 0.7458 (mm) cc_final: 0.7169 (mm) REVERT: E 452 MET cc_start: 0.6555 (tpt) cc_final: 0.6342 (tpp) REVERT: E 613 ASP cc_start: 0.7983 (m-30) cc_final: 0.7532 (m-30) REVERT: F 182 MET cc_start: 0.9315 (ttt) cc_final: 0.8640 (ppp) REVERT: F 236 MET cc_start: 0.9374 (mmp) cc_final: 0.9128 (mmm) REVERT: F 307 MET cc_start: 0.8975 (ppp) cc_final: 0.8521 (ppp) REVERT: F 342 LEU cc_start: 0.9224 (tp) cc_final: 0.8870 (tp) REVERT: F 573 MET cc_start: 0.6095 (mtm) cc_final: 0.3748 (tmm) REVERT: F 585 MET cc_start: 0.5324 (tpt) cc_final: 0.3706 (tpt) REVERT: F 623 ASP cc_start: 0.8537 (p0) cc_final: 0.8319 (p0) REVERT: F 630 MET cc_start: 0.8825 (tpt) cc_final: 0.8604 (mmt) REVERT: F 717 PHE cc_start: 0.7626 (t80) cc_final: 0.7336 (t80) REVERT: G 636 ASN cc_start: 0.7949 (p0) cc_final: 0.7735 (p0) REVERT: G 704 ASN cc_start: 0.9449 (m110) cc_final: 0.9205 (t0) REVERT: H 78 ASN cc_start: 0.9261 (m-40) cc_final: 0.8928 (t0) REVERT: H 80 TYR cc_start: 0.9377 (m-10) cc_final: 0.8883 (m-80) REVERT: H 307 MET cc_start: 0.3037 (ptm) cc_final: 0.2740 (ppp) REVERT: H 360 MET cc_start: 0.0624 (mtt) cc_final: 0.0370 (mtt) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.5614 time to fit residues: 435.7387 Evaluate side-chains 370 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 526 optimal weight: 5.9990 chunk 554 optimal weight: 1.9990 chunk 506 optimal weight: 0.9990 chunk 539 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 423 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 487 optimal weight: 8.9990 chunk 510 optimal weight: 5.9990 chunk 537 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 132 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN D 30 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46850 Z= 0.188 Angle : 0.682 12.150 63536 Z= 0.342 Chirality : 0.045 0.258 7315 Planarity : 0.004 0.075 8252 Dihedral : 4.833 27.457 6439 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 6053 helix: 0.37 (0.10), residues: 2869 sheet: -0.78 (0.17), residues: 970 loop : -1.92 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 454 HIS 0.010 0.001 HIS E 70 PHE 0.030 0.001 PHE A 345 TYR 0.014 0.001 TYR B 580 ARG 0.016 0.001 ARG G 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 5.380 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: 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 52 MET cc_start: 0.8495 (ptm) cc_final: 0.8018 (tmm) REVERT: A 69 ASN cc_start: 0.9479 (m-40) cc_final: 0.9255 (m-40) REVERT: A 307 MET cc_start: 0.8259 (ppp) cc_final: 0.8037 (ppp) REVERT: A 396 LEU cc_start: 0.9111 (mm) cc_final: 0.8736 (tp) REVERT: A 507 MET cc_start: 0.2712 (mtp) cc_final: 0.2028 (ttt) REVERT: A 557 MET cc_start: 0.7128 (mmp) cc_final: 0.6823 (tpp) REVERT: A 585 MET cc_start: 0.8992 (mpp) cc_final: 0.8130 (mmp) REVERT: A 639 MET cc_start: 0.0214 (mmt) cc_final: -0.0692 (mmt) REVERT: B 98 MET cc_start: 0.9362 (mmp) cc_final: 0.9106 (mmp) REVERT: B 198 MET cc_start: 0.8107 (ptt) cc_final: 0.7675 (tpt) REVERT: B 307 MET cc_start: -0.2803 (ptm) cc_final: -0.4372 (tpt) REVERT: B 386 PHE cc_start: 0.9140 (t80) cc_final: 0.8650 (t80) REVERT: B 445 VAL cc_start: 0.9189 (t) cc_final: 0.8860 (p) REVERT: B 452 MET cc_start: 0.6648 (tpp) cc_final: 0.6350 (tpt) REVERT: C 65 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8570 (mttm) REVERT: C 68 LYS cc_start: 0.9193 (pttp) cc_final: 0.8917 (pptt) REVERT: C 123 LYS cc_start: 0.8690 (mttt) cc_final: 0.8082 (mtpt) REVERT: C 182 MET cc_start: 0.9018 (ptt) cc_final: 0.8440 (ppp) REVERT: C 266 PHE cc_start: 0.8379 (m-80) cc_final: 0.8045 (m-80) REVERT: C 307 MET cc_start: 0.9227 (ptt) cc_final: 0.9010 (ppp) REVERT: C 554 MET cc_start: 0.9288 (mmm) cc_final: 0.8349 (mmm) REVERT: C 747 VAL cc_start: 0.9158 (t) cc_final: 0.8943 (p) REVERT: C 834 GLU cc_start: 0.8810 (tp30) cc_final: 0.8049 (tp30) REVERT: D 182 MET cc_start: 0.9265 (ppp) cc_final: 0.9047 (ppp) REVERT: D 262 VAL cc_start: 0.9836 (t) cc_final: 0.9600 (t) REVERT: D 452 MET cc_start: 0.7296 (tpp) cc_final: 0.7018 (tpt) REVERT: D 618 LYS cc_start: 0.4893 (tttt) cc_final: 0.4583 (tttt) REVERT: E 70 HIS cc_start: 0.9232 (t-170) cc_final: 0.9029 (t70) REVERT: E 182 MET cc_start: 0.7420 (ppp) cc_final: 0.6649 (ppp) REVERT: E 198 MET cc_start: 0.9697 (tpt) cc_final: 0.9107 (ptt) REVERT: E 307 MET cc_start: 0.8011 (ppp) cc_final: 0.7747 (ppp) REVERT: E 360 MET cc_start: 0.9795 (mmm) cc_final: 0.9443 (mmm) REVERT: E 390 LEU cc_start: 0.7506 (mm) cc_final: 0.7234 (mm) REVERT: E 452 MET cc_start: 0.6638 (tpt) cc_final: 0.6372 (tpp) REVERT: E 554 MET cc_start: 0.9057 (ptm) cc_final: 0.8768 (ptm) REVERT: E 613 ASP cc_start: 0.8010 (m-30) cc_final: 0.7630 (m-30) REVERT: F 182 MET cc_start: 0.9316 (ttt) cc_final: 0.8633 (ppp) REVERT: F 236 MET cc_start: 0.9370 (mmp) cc_final: 0.9159 (mmp) REVERT: F 307 MET cc_start: 0.8993 (ppp) cc_final: 0.8571 (ppp) REVERT: F 342 LEU cc_start: 0.9169 (tp) cc_final: 0.8869 (tp) REVERT: F 552 LYS cc_start: 0.9215 (mttt) cc_final: 0.8980 (mtpt) REVERT: F 573 MET cc_start: 0.5775 (mtm) cc_final: 0.3007 (tmm) REVERT: F 585 MET cc_start: 0.5174 (tpt) cc_final: 0.3310 (tpt) REVERT: F 591 LEU cc_start: 0.9041 (tp) cc_final: 0.8666 (tp) REVERT: F 623 ASP cc_start: 0.8512 (p0) cc_final: 0.8281 (p0) REVERT: F 717 PHE cc_start: 0.7539 (t80) cc_final: 0.7282 (t80) REVERT: F 724 MET cc_start: 0.9267 (tpp) cc_final: 0.8858 (tpp) REVERT: G 636 ASN cc_start: 0.7998 (p0) cc_final: 0.7788 (p0) REVERT: H 36 ARG cc_start: 0.8927 (mtm180) cc_final: 0.8497 (mmt180) REVERT: H 78 ASN cc_start: 0.9272 (m-40) cc_final: 0.8964 (t0) REVERT: H 307 MET cc_start: 0.3054 (ptm) cc_final: 0.2768 (ppp) REVERT: H 360 MET cc_start: 0.0622 (mtt) cc_final: 0.0385 (mtt) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.5674 time to fit residues: 443.3948 Evaluate side-chains 373 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 354 optimal weight: 10.0000 chunk 570 optimal weight: 30.0000 chunk 348 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 396 optimal weight: 6.9990 chunk 598 optimal weight: 0.8980 chunk 551 optimal weight: 6.9990 chunk 476 optimal weight: 0.0070 chunk 49 optimal weight: 5.9990 chunk 368 optimal weight: 40.0000 chunk 292 optimal weight: 9.9990 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 43 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 69 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46850 Z= 0.181 Angle : 0.678 12.242 63536 Z= 0.338 Chirality : 0.045 0.256 7315 Planarity : 0.004 0.076 8252 Dihedral : 4.745 24.866 6439 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.11), residues: 6053 helix: 0.43 (0.10), residues: 2883 sheet: -0.70 (0.17), residues: 969 loop : -1.90 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 555 HIS 0.008 0.001 HIS E 564 PHE 0.029 0.001 PHE E 463 TYR 0.014 0.001 TYR D 580 ARG 0.008 0.001 ARG G 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12106 Ramachandran restraints generated. 6053 Oldfield, 0 Emsley, 6053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 5.420 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: 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 52 MET cc_start: 0.8445 (ptm) cc_final: 0.7978 (tmm) REVERT: A 69 ASN cc_start: 0.9478 (m-40) cc_final: 0.9259 (m-40) REVERT: A 396 LEU cc_start: 0.9121 (mm) cc_final: 0.8869 (tp) REVERT: A 507 MET cc_start: 0.2802 (mtp) cc_final: 0.2131 (ttt) REVERT: A 557 MET cc_start: 0.7049 (mmp) cc_final: 0.6740 (tpp) REVERT: A 585 MET cc_start: 0.8988 (mpp) cc_final: 0.8724 (mpp) REVERT: A 641 MET cc_start: 0.6685 (ptt) cc_final: 0.5148 (pmm) REVERT: B 198 MET cc_start: 0.8144 (ptt) cc_final: 0.7732 (tpt) REVERT: B 307 MET cc_start: -0.2693 (ptm) cc_final: -0.4249 (tpt) REVERT: B 386 PHE cc_start: 0.9136 (t80) cc_final: 0.8649 (t80) REVERT: B 452 MET cc_start: 0.6588 (tpp) cc_final: 0.6086 (tpt) REVERT: B 454 TRP cc_start: 0.6263 (m100) cc_final: 0.5469 (m100) REVERT: C 65 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8554 (mttm) REVERT: C 68 LYS cc_start: 0.9186 (pttp) cc_final: 0.8913 (pptt) REVERT: C 123 LYS cc_start: 0.8692 (mttt) cc_final: 0.8090 (mtpt) REVERT: C 266 PHE cc_start: 0.8371 (m-80) cc_final: 0.8023 (m-80) REVERT: C 307 MET cc_start: 0.9235 (ptt) cc_final: 0.9017 (ppp) REVERT: C 554 MET cc_start: 0.9162 (mmm) cc_final: 0.8423 (mmm) REVERT: C 747 VAL cc_start: 0.9159 (t) cc_final: 0.8934 (p) REVERT: C 834 GLU cc_start: 0.8740 (tp30) cc_final: 0.8002 (tp30) REVERT: D 182 MET cc_start: 0.9264 (ppp) cc_final: 0.9040 (ppp) REVERT: D 262 VAL cc_start: 0.9825 (t) cc_final: 0.9537 (p) REVERT: D 452 MET cc_start: 0.7315 (tpp) cc_final: 0.7106 (tpt) REVERT: D 618 LYS cc_start: 0.4632 (tttt) cc_final: 0.4399 (tttt) REVERT: D 659 GLU cc_start: 0.7938 (pp20) cc_final: 0.7249 (pp20) REVERT: D 681 LEU cc_start: 0.9063 (mt) cc_final: 0.8759 (pp) REVERT: E 182 MET cc_start: 0.7410 (ppp) cc_final: 0.6640 (ppp) REVERT: E 198 MET cc_start: 0.9691 (tpt) cc_final: 0.9138 (ptt) REVERT: E 266 PHE cc_start: 0.9653 (m-80) cc_final: 0.9362 (m-10) REVERT: E 307 MET cc_start: 0.8015 (ppp) cc_final: 0.7743 (ppp) REVERT: E 360 MET cc_start: 0.9797 (mmm) cc_final: 0.9461 (mmm) REVERT: E 390 LEU cc_start: 0.7614 (mm) cc_final: 0.7320 (mm) REVERT: E 452 MET cc_start: 0.6735 (tpt) cc_final: 0.6477 (tpp) REVERT: E 478 LYS cc_start: 0.7412 (ptpp) cc_final: 0.6971 (ptpp) REVERT: E 554 MET cc_start: 0.9097 (ptm) cc_final: 0.8846 (ptm) REVERT: E 613 ASP cc_start: 0.8013 (m-30) cc_final: 0.7646 (m-30) REVERT: F 182 MET cc_start: 0.9317 (ttt) cc_final: 0.8384 (tmm) REVERT: F 236 MET cc_start: 0.9395 (mmp) cc_final: 0.9188 (mmp) REVERT: F 307 MET cc_start: 0.9039 (ppp) cc_final: 0.8622 (ppp) REVERT: F 342 LEU cc_start: 0.9155 (tp) cc_final: 0.8856 (tp) REVERT: F 552 LYS cc_start: 0.9233 (mttt) cc_final: 0.8979 (mtpt) REVERT: F 573 MET cc_start: 0.5502 (mtm) cc_final: 0.2889 (tmm) REVERT: F 585 MET cc_start: 0.5000 (tpt) cc_final: 0.3407 (tpt) REVERT: F 623 ASP cc_start: 0.8482 (p0) cc_final: 0.8231 (p0) REVERT: F 717 PHE cc_start: 0.7412 (t80) cc_final: 0.7176 (t80) REVERT: F 724 MET cc_start: 0.9334 (tpp) cc_final: 0.8823 (tpp) REVERT: H 36 ARG cc_start: 0.8936 (mtm180) cc_final: 0.8495 (mmt180) REVERT: H 307 MET cc_start: 0.2916 (ptm) cc_final: 0.2611 (ppp) REVERT: H 360 MET cc_start: 0.0955 (mtt) cc_final: 0.0723 (mtt) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.5980 time to fit residues: 468.6367 Evaluate side-chains 373 residues out of total 4809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 5.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 378 optimal weight: 10.0000 chunk 507 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 439 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 490 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 HIS D 491 ASN D 751 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 759 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN F 455 HIS ** F 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.074510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.058406 restraints weight = 499371.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.059483 restraints weight = 315924.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.060002 restraints weight = 225593.001| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 46850 Z= 0.303 Angle : 0.755 12.168 63536 Z= 0.388 Chirality : 0.046 0.276 7315 Planarity : 0.005 0.120 8252 Dihedral : 5.097 25.782 6439 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.72 % 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: -1.23 (0.11), residues: 6053 helix: 0.14 (0.10), residues: 2881 sheet: -0.79 (0.17), residues: 951 loop : -2.03 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 454 HIS 0.008 0.002 HIS B 780 PHE 0.039 0.002 PHE E 463 TYR 0.024 0.002 TYR C 373 ARG 0.025 0.001 ARG H 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10578.98 seconds wall clock time: 193 minutes 47.65 seconds (11627.65 seconds total)