Starting phenix.real_space_refine on Sun Mar 24 02:31:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcp_28989/03_2024/8fcp_28989_updated.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 196 5.16 5 C 24794 2.51 5 N 6932 2.21 5 O 7548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 357": "OE1" <-> "OE2" Residue "H TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39494 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "H" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "G" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.43, per 1000 atoms: 0.52 Number of scatterers: 39494 At special positions: 0 Unit cell: (195.99, 181.812, 118.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 196 16.00 P 24 15.00 O 7548 8.00 N 6932 7.00 C 24794 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: 14.57 Conformation dependent library (CDL) restraints added in 7.0 seconds 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 248 helices and 36 sheets defined 43.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.23 Creating SS restraints... Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.485A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 319 through 336 removed outlier: 3.550A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 426 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 585 removed outlier: 4.062A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 663 removed outlier: 4.889A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.703A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.769A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 3.504A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.812A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 319 through 336 removed outlier: 3.607A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 429 removed outlier: 4.104A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.916A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 663 removed outlier: 5.142A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.927A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.754A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.018A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.726A pdb=" N LYS C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.509A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 319 through 336 removed outlier: 3.564A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 387 removed outlier: 5.140A pdb=" N ASN C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 4.456A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.549A pdb=" N PHE C 563 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.807A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.730A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 Processing helix chain 'H' and resid 50 through 67 Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.776A pdb=" N PHE H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 Processing helix chain 'H' and resid 168 through 187 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 202 through 207 Processing helix chain 'H' and resid 214 through 220 Processing helix chain 'H' and resid 244 through 247 No H-bonds generated for 'chain 'H' and resid 244 through 247' Processing helix chain 'H' and resid 250 through 261 Processing helix chain 'H' and resid 281 through 284 Processing helix chain 'H' and resid 297 through 315 Processing helix chain 'H' and resid 320 through 330 removed outlier: 4.067A pdb=" N ARG H 329 " --> pdb=" O LYS H 325 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY H 330 " --> pdb=" O GLU H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 Processing helix chain 'H' and resid 395 through 398 No H-bonds generated for 'chain 'H' and resid 395 through 398' Processing helix chain 'H' and resid 412 through 420 removed outlier: 3.552A pdb=" N ASP H 417 " --> pdb=" O ALA H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 436 removed outlier: 5.136A pdb=" N ALA H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.605A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.506A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.559A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 585 removed outlier: 4.036A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 663 removed outlier: 4.939A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.806A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.786A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.525A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.785A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.560A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 429 removed outlier: 3.989A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.960A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 663 removed outlier: 5.146A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.931A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.705A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 5.056A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.840A pdb=" N LYS F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.511A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 319 through 336 removed outlier: 3.568A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 430 removed outlier: 4.351A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.866A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.717A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing helix chain 'G' and resid 50 through 67 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.779A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 Processing helix chain 'G' and resid 168 through 187 removed outlier: 3.523A pdb=" N ILE G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 202 through 207 Processing helix chain 'G' and resid 214 through 220 Processing helix chain 'G' and resid 244 through 247 No H-bonds generated for 'chain 'G' and resid 244 through 247' Processing helix chain 'G' and resid 251 through 261 Processing helix chain 'G' and resid 281 through 284 Processing helix chain 'G' and resid 297 through 315 Processing helix chain 'G' and resid 320 through 330 removed outlier: 4.073A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 369 Processing helix chain 'G' and resid 395 through 398 No H-bonds generated for 'chain 'G' and resid 395 through 398' Processing helix chain 'G' and resid 412 through 420 removed outlier: 3.531A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 5.155A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.881A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.879A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.946A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 641 through 644 removed outlier: 3.640A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.268A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.951A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.770A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.721A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 641 through 644 removed outlier: 4.065A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.281A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.777A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.818A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.797A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.510A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 122 through 124 Processing sheet with id= Q, first strand: chain 'H' and resid 196 through 198 Processing sheet with id= R, first strand: chain 'H' and resid 275 through 277 Processing sheet with id= S, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.834A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.904A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= V, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.958A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.612A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.277A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.960A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.768A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.690A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 641 through 644 removed outlier: 4.070A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.467A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.795A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AF, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.794A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 641 through 644 removed outlier: 8.593A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 122 through 124 Processing sheet with id= AI, first strand: chain 'G' and resid 196 through 198 Processing sheet with id= AJ, first strand: chain 'G' and resid 275 through 277 1426 hydrogen bonds defined for protein. 3981 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: 15.56 Time building geometry restraints manager: 15.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8161 1.33 - 1.45: 8377 1.45 - 1.57: 23272 1.57 - 1.69: 36 1.69 - 1.81: 310 Bond restraints: 40156 Sorted by residual: bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 40151 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.83: 1606 107.83 - 114.85: 23888 114.85 - 121.86: 20469 121.86 - 128.88: 8147 128.88 - 135.90: 184 Bond angle restraints: 54294 Sorted by residual: angle pdb=" N LEU H 331 " pdb=" CA LEU H 331 " pdb=" C LEU H 331 " ideal model delta sigma weight residual 113.28 124.02 -10.74 1.22e+00 6.72e-01 7.75e+01 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.94 -10.66 1.22e+00 6.72e-01 7.64e+01 angle pdb=" N ARG H 332 " pdb=" CA ARG H 332 " pdb=" C ARG H 332 " ideal model delta sigma weight residual 112.88 122.46 -9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.88 122.44 -9.56 1.29e+00 6.01e-01 5.49e+01 angle pdb=" CA ASP C 592 " pdb=" C ASP C 592 " pdb=" O ASP C 592 " ideal model delta sigma weight residual 117.94 121.75 -3.81 5.80e-01 2.97e+00 4.31e+01 ... (remaining 54289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 24523 34.01 - 68.01: 284 68.01 - 102.02: 37 102.02 - 136.02: 12 136.02 - 170.03: 10 Dihedral angle restraints: 24866 sinusoidal: 10458 harmonic: 14408 Sorted by residual: dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 129.97 170.03 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual 300.00 132.03 167.97 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 143.74 156.26 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 24863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4352 0.047 - 0.094: 1069 0.094 - 0.141: 480 0.141 - 0.189: 211 0.189 - 0.236: 12 Chirality restraints: 6124 Sorted by residual: chirality pdb=" CA ILE B 590 " pdb=" N ILE B 590 " pdb=" C ILE B 590 " pdb=" CB ILE B 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 590 " pdb=" N ILE A 590 " pdb=" C ILE A 590 " pdb=" CB ILE A 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE F 590 " pdb=" N ILE F 590 " pdb=" C ILE F 590 " pdb=" CB ILE F 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 6121 not shown) Planarity restraints: 7116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 254 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C GLU H 254 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU H 254 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG H 255 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C GLU G 254 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU G 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C GLU F 534 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU F 534 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " 0.013 2.00e-02 2.50e+03 ... (remaining 7113 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 14606 2.89 - 3.39: 38411 3.39 - 3.90: 67658 3.90 - 4.40: 77816 4.40 - 4.90: 125091 Nonbonded interactions: 323582 Sorted by model distance: nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.390 2.520 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.391 2.520 nonbonded pdb=" NZ LYS C 211 " pdb=" O ALA C 570 " model vdw 2.416 2.520 nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.434 2.520 nonbonded pdb=" OD2 ASP H 176 " pdb=" NZ LYS H 180 " model vdw 2.438 2.520 ... (remaining 323577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.570 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 103.020 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 : 0.011 0.111 40156 Z= 0.714 Angle : 0.891 12.445 54294 Z= 0.563 Chirality : 0.058 0.236 6124 Planarity : 0.004 0.032 7116 Dihedral : 12.106 170.027 15514 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.76 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 4954 helix: 0.03 (0.10), residues: 2180 sheet: 0.60 (0.16), residues: 858 loop : 0.97 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 454 HIS 0.001 0.000 HIS D 340 PHE 0.002 0.000 PHE A 266 TYR 0.001 0.000 TYR G 363 ARG 0.001 0.000 ARG F 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1400 time to evaluate : 4.142 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: D 26 LEU cc_start: 0.5774 (mt) cc_final: 0.5477 (mt) REVERT: D 441 VAL cc_start: 0.7972 (t) cc_final: 0.7676 (p) REVERT: C 102 ILE cc_start: 0.8732 (mp) cc_final: 0.8186 (mt) REVERT: C 332 MET cc_start: 0.7129 (mmm) cc_final: 0.6896 (mmm) REVERT: B 138 TYR cc_start: 0.7031 (t80) cc_final: 0.6822 (t80) REVERT: B 449 MET cc_start: 0.7805 (tpt) cc_final: 0.7580 (tpp) REVERT: A 26 LEU cc_start: 0.5629 (mt) cc_final: 0.5311 (mt) REVERT: A 182 ILE cc_start: 0.7834 (mt) cc_final: 0.7620 (mt) REVERT: A 420 LEU cc_start: 0.7519 (tp) cc_final: 0.7309 (tp) REVERT: A 441 VAL cc_start: 0.8280 (t) cc_final: 0.6758 (t) REVERT: F 102 ILE cc_start: 0.8919 (mt) cc_final: 0.8521 (mt) outliers start: 0 outliers final: 0 residues processed: 1400 average time/residue: 0.5823 time to fit residues: 1250.2061 Evaluate side-chains 687 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 3.9990 chunk 377 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 390 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 452 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN D 348 ASN D 568 GLN D 641 GLN D 660 ASN D 680 ASN C 115 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN C 680 ASN B 90 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 499 HIS B 660 ASN A 348 ASN A 641 GLN A 660 ASN F 115 HIS ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN G 278 GLN G 294 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40156 Z= 0.291 Angle : 0.694 11.555 54294 Z= 0.340 Chirality : 0.046 0.234 6124 Planarity : 0.005 0.065 7116 Dihedral : 9.801 163.119 5544 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.17 % Favored : 98.75 % Rotamer: Outliers : 2.59 % Allowed : 9.86 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4954 helix: 1.09 (0.11), residues: 2188 sheet: 0.63 (0.17), residues: 852 loop : 1.24 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 551 HIS 0.008 0.001 HIS F 384 PHE 0.021 0.002 PHE D 131 TYR 0.022 0.002 TYR B 134 ARG 0.016 0.001 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 672 time to evaluate : 4.608 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: E 158 MET cc_start: 0.6877 (mmm) cc_final: 0.6622 (mmt) REVERT: E 467 THR cc_start: 0.7861 (m) cc_final: 0.7626 (m) REVERT: D 72 LEU cc_start: 0.8403 (tp) cc_final: 0.8038 (tt) REVERT: C 546 GLU cc_start: 0.5727 (tp30) cc_final: 0.5495 (tm-30) REVERT: H 354 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3981 (t80) REVERT: B 203 TYR cc_start: 0.8497 (m-10) cc_final: 0.8252 (m-80) REVERT: B 742 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.5224 (t80) REVERT: A 72 LEU cc_start: 0.8396 (tp) cc_final: 0.7992 (tt) REVERT: F 332 MET cc_start: 0.7573 (mmm) cc_final: 0.7332 (mmm) outliers start: 110 outliers final: 61 residues processed: 739 average time/residue: 0.5004 time to fit residues: 602.6846 Evaluate side-chains 589 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 526 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 354 TYR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 453 optimal weight: 0.0040 chunk 489 optimal weight: 9.9990 chunk 403 optimal weight: 6.9990 chunk 449 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 363 optimal weight: 7.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40156 Z= 0.280 Angle : 0.646 12.383 54294 Z= 0.314 Chirality : 0.045 0.169 6124 Planarity : 0.004 0.058 7116 Dihedral : 9.418 171.811 5544 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.41 % Rotamer: Outliers : 2.87 % Allowed : 11.18 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.12), residues: 4954 helix: 1.21 (0.11), residues: 2212 sheet: 0.65 (0.17), residues: 844 loop : 1.09 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 374 HIS 0.006 0.001 HIS E 183 PHE 0.022 0.002 PHE G 377 TYR 0.026 0.002 TYR F 644 ARG 0.008 0.000 ARG H 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 581 time to evaluate : 4.671 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: D 146 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7159 (pt) REVERT: C 217 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (mtmm) REVERT: B 671 ASP cc_start: 0.5487 (t0) cc_final: 0.5002 (p0) REVERT: B 742 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.5256 (t80) REVERT: A 146 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7138 (pt) REVERT: G 428 ILE cc_start: 0.6476 (mm) cc_final: 0.6203 (mm) outliers start: 122 outliers final: 81 residues processed: 667 average time/residue: 0.4954 time to fit residues: 544.2588 Evaluate side-chains 583 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 498 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 6.9990 chunk 340 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 454 optimal weight: 2.9990 chunk 481 optimal weight: 0.0010 chunk 237 optimal weight: 3.9990 chunk 430 optimal weight: 0.0030 chunk 129 optimal weight: 5.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 404 HIS C 603 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 443 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN G 294 ASN G 371 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40156 Z= 0.231 Angle : 0.612 11.342 54294 Z= 0.293 Chirality : 0.044 0.208 6124 Planarity : 0.004 0.054 7116 Dihedral : 8.973 148.680 5544 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.08 % Allowed : 12.88 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.12), residues: 4954 helix: 1.37 (0.11), residues: 2194 sheet: 0.58 (0.17), residues: 836 loop : 0.93 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 374 HIS 0.005 0.001 HIS E 183 PHE 0.025 0.001 PHE G 377 TYR 0.028 0.002 TYR A 203 ARG 0.009 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 557 time to evaluate : 4.909 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: D 450 ASP cc_start: 0.6948 (t70) cc_final: 0.6730 (t0) REVERT: B 671 ASP cc_start: 0.5487 (t0) cc_final: 0.5188 (p0) REVERT: B 742 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.5211 (t80) REVERT: A 229 LEU cc_start: 0.6946 (mm) cc_final: 0.6628 (mm) REVERT: G 386 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7905 (tttp) outliers start: 131 outliers final: 94 residues processed: 641 average time/residue: 0.4819 time to fit residues: 513.0725 Evaluate side-chains 579 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 484 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 410 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 432 optimal weight: 0.8980 chunk 121 optimal weight: 0.0570 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN D 680 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 327 GLN C 404 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN F 183 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40156 Z= 0.189 Angle : 0.591 10.502 54294 Z= 0.282 Chirality : 0.044 0.211 6124 Planarity : 0.004 0.082 7116 Dihedral : 8.532 142.236 5544 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.78 % Allowed : 13.77 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.12), residues: 4954 helix: 1.48 (0.11), residues: 2172 sheet: 0.57 (0.17), residues: 830 loop : 0.82 (0.15), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 374 HIS 0.005 0.001 HIS E 183 PHE 0.026 0.001 PHE A 152 TYR 0.024 0.002 TYR C 644 ARG 0.006 0.000 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 543 time to evaluate : 4.768 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: B 508 MET cc_start: 0.6749 (tpp) cc_final: 0.6445 (tpp) REVERT: B 550 MET cc_start: 0.4184 (OUTLIER) cc_final: 0.3974 (ptp) REVERT: B 742 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.5159 (t80) REVERT: A 229 LEU cc_start: 0.6937 (mm) cc_final: 0.6663 (mm) REVERT: A 492 LEU cc_start: 0.8057 (mm) cc_final: 0.7777 (mt) outliers start: 118 outliers final: 83 residues processed: 612 average time/residue: 0.4815 time to fit residues: 487.6736 Evaluate side-chains 566 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 481 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.0980 chunk 433 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 481 optimal weight: 2.9990 chunk 399 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 252 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 603 GLN H 371 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN G 371 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40156 Z= 0.177 Angle : 0.586 10.035 54294 Z= 0.278 Chirality : 0.043 0.205 6124 Planarity : 0.004 0.068 7116 Dihedral : 8.090 133.379 5544 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.87 % Allowed : 14.48 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 4954 helix: 1.61 (0.11), residues: 2126 sheet: 0.55 (0.17), residues: 826 loop : 0.78 (0.15), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 374 HIS 0.008 0.001 HIS D 183 PHE 0.027 0.001 PHE G 377 TYR 0.037 0.002 TYR B 495 ARG 0.011 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 523 time to evaluate : 4.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 427 MET cc_start: 0.3609 (tpt) cc_final: 0.3379 (tpt) REVERT: E 671 ASP cc_start: 0.5575 (t0) cc_final: 0.4981 (p0) REVERT: H 327 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: B 427 MET cc_start: 0.3843 (tpt) cc_final: 0.3607 (tpt) REVERT: B 508 MET cc_start: 0.6859 (tpp) cc_final: 0.6420 (tpp) REVERT: B 742 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.5117 (t80) REVERT: A 229 LEU cc_start: 0.6945 (mm) cc_final: 0.6578 (mm) REVERT: A 492 LEU cc_start: 0.8081 (mm) cc_final: 0.7794 (mt) REVERT: F 140 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7188 (tt) REVERT: G 327 GLU cc_start: 0.7359 (mp0) cc_final: 0.7122 (mt-10) outliers start: 122 outliers final: 89 residues processed: 603 average time/residue: 0.4896 time to fit residues: 487.6973 Evaluate side-chains 582 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 490 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 269 optimal weight: 0.0770 chunk 479 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 421 GLN C 603 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 40156 Z= 0.176 Angle : 0.585 9.687 54294 Z= 0.277 Chirality : 0.043 0.199 6124 Planarity : 0.004 0.064 7116 Dihedral : 7.864 128.932 5544 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.90 % Allowed : 14.57 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 4954 helix: 1.59 (0.11), residues: 2128 sheet: 0.58 (0.18), residues: 822 loop : 0.79 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 551 HIS 0.006 0.001 HIS E 183 PHE 0.022 0.001 PHE G 377 TYR 0.028 0.002 TYR B 495 ARG 0.007 0.000 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 524 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 427 MET cc_start: 0.3744 (tpt) cc_final: 0.3470 (tpt) REVERT: D 427 MET cc_start: 0.7598 (tmm) cc_final: 0.6736 (ttp) REVERT: D 492 LEU cc_start: 0.7979 (mm) cc_final: 0.7717 (mt) REVERT: H 327 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: B 427 MET cc_start: 0.3923 (tpt) cc_final: 0.3579 (tpt) REVERT: B 508 MET cc_start: 0.6915 (tpp) cc_final: 0.6452 (tpp) REVERT: B 742 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.5182 (t80) REVERT: A 229 LEU cc_start: 0.6914 (mm) cc_final: 0.6582 (mm) REVERT: F 140 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7289 (tt) REVERT: F 465 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7054 (mpp80) REVERT: G 327 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7160 (mt-10) outliers start: 123 outliers final: 93 residues processed: 605 average time/residue: 0.4968 time to fit residues: 497.0252 Evaluate side-chains 584 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 486 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 568 GLN Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 754 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 465 ARG Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 286 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 94 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 327 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 377 optimal weight: 8.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS C 421 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 40156 Z= 0.247 Angle : 0.617 10.179 54294 Z= 0.295 Chirality : 0.044 0.204 6124 Planarity : 0.004 0.063 7116 Dihedral : 7.732 123.487 5544 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.94 % Allowed : 15.16 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.12), residues: 4954 helix: 1.49 (0.11), residues: 2148 sheet: 0.53 (0.18), residues: 832 loop : 0.77 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 374 HIS 0.004 0.001 HIS E 183 PHE 0.026 0.001 PHE G 377 TYR 0.033 0.002 TYR A 203 ARG 0.009 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 497 time to evaluate : 4.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 427 MET cc_start: 0.7614 (tmm) cc_final: 0.6844 (ttp) REVERT: D 492 LEU cc_start: 0.7921 (mm) cc_final: 0.7648 (mt) REVERT: D 543 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7340 (mtpt) REVERT: H 327 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: B 508 MET cc_start: 0.6958 (tpp) cc_final: 0.6491 (tpp) REVERT: B 742 PHE cc_start: 0.5480 (OUTLIER) cc_final: 0.5172 (t80) REVERT: F 634 LEU cc_start: 0.7664 (mt) cc_final: 0.7386 (mt) outliers start: 125 outliers final: 100 residues processed: 579 average time/residue: 0.4835 time to fit residues: 464.3557 Evaluate side-chains 571 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 468 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 3.9990 chunk 459 optimal weight: 3.9990 chunk 419 optimal weight: 4.9990 chunk 447 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 404 optimal weight: 1.9990 chunk 423 optimal weight: 0.8980 chunk 445 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS B 183 HIS B 568 GLN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 40156 Z= 0.266 Angle : 0.630 10.364 54294 Z= 0.302 Chirality : 0.045 0.194 6124 Planarity : 0.004 0.063 7116 Dihedral : 7.607 121.741 5544 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.94 % Allowed : 15.18 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.12), residues: 4954 helix: 1.42 (0.11), residues: 2164 sheet: 0.62 (0.18), residues: 796 loop : 0.66 (0.15), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 374 HIS 0.008 0.001 HIS A 183 PHE 0.023 0.001 PHE G 377 TYR 0.036 0.002 TYR A 203 ARG 0.009 0.000 ARG F 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 487 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 427 MET cc_start: 0.4061 (tpt) cc_final: 0.3731 (tpt) REVERT: D 427 MET cc_start: 0.7575 (tmm) cc_final: 0.6878 (ttp) REVERT: D 543 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7283 (mtpt) REVERT: H 327 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 508 MET cc_start: 0.6978 (tpp) cc_final: 0.6474 (tpp) REVERT: B 608 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5637 (mtp) REVERT: B 742 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.5288 (t80) REVERT: F 140 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7359 (tt) outliers start: 125 outliers final: 104 residues processed: 563 average time/residue: 0.4825 time to fit residues: 453.6582 Evaluate side-chains 570 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 461 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 705 SER Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 4.9990 chunk 472 optimal weight: 0.0770 chunk 288 optimal weight: 2.9990 chunk 224 optimal weight: 0.3980 chunk 328 optimal weight: 0.9980 chunk 496 optimal weight: 0.0000 chunk 456 optimal weight: 0.9990 chunk 395 optimal weight: 4.9990 chunk 41 optimal weight: 0.0020 chunk 305 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS B 317 HIS B 568 GLN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 40156 Z= 0.159 Angle : 0.610 10.361 54294 Z= 0.289 Chirality : 0.044 0.220 6124 Planarity : 0.004 0.100 7116 Dihedral : 7.335 122.560 5544 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.81 % Allowed : 16.50 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.12), residues: 4954 helix: 1.46 (0.12), residues: 2138 sheet: 0.76 (0.18), residues: 784 loop : 0.65 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 454 HIS 0.008 0.001 HIS D 183 PHE 0.024 0.001 PHE G 377 TYR 0.028 0.002 TYR E 495 ARG 0.007 0.000 ARG B 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9908 Ramachandran restraints generated. 4954 Oldfield, 0 Emsley, 4954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 521 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 427 MET cc_start: 0.7588 (tmm) cc_final: 0.6924 (ttp) REVERT: C 140 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7198 (tt) REVERT: B 99 VAL cc_start: 0.8084 (p) cc_final: 0.7811 (m) REVERT: B 508 MET cc_start: 0.7014 (tpp) cc_final: 0.6512 (tpp) REVERT: B 742 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.5177 (t80) REVERT: A 492 LEU cc_start: 0.8005 (mm) cc_final: 0.7732 (mt) REVERT: F 140 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7210 (tt) outliers start: 77 outliers final: 65 residues processed: 563 average time/residue: 0.5032 time to fit residues: 468.7103 Evaluate side-chains 532 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 464 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 580 ASP Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 9.9990 chunk 420 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 364 optimal weight: 0.0010 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 395 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 406 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 GLN B 90 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.161332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123857 restraints weight = 75730.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123718 restraints weight = 47584.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125277 restraints weight = 34386.524| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 40156 Z= 0.185 Angle : 0.618 11.122 54294 Z= 0.293 Chirality : 0.044 0.289 6124 Planarity : 0.004 0.089 7116 Dihedral : 7.244 123.566 5544 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.91 % Allowed : 16.93 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4954 helix: 1.45 (0.12), residues: 2140 sheet: 0.79 (0.18), residues: 784 loop : 0.63 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 454 HIS 0.008 0.001 HIS D 183 PHE 0.023 0.001 PHE G 377 TYR 0.034 0.002 TYR D 495 ARG 0.007 0.000 ARG B 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9869.11 seconds wall clock time: 177 minutes 10.93 seconds (10630.93 seconds total)