Starting phenix.real_space_refine on Tue Apr 16 01:09:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcm_28983/04_2024/8fcm_28983_updated.pdb" } resolution = 3.27 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= 0.003 sd= 0.058 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 188 5.16 5 C 23110 2.51 5 N 6466 2.21 5 O 7041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 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 "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 110": "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 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 52": "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 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D PHE 267": "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 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 PHE 52": "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 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 506": "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 "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 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "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 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 "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 PHE 223": "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" 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 TYR 244": "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" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36829 Number of models: 1 Model: "" Number of chains: 13 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: "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: 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: "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: "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: "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: "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: "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: 18.57, per 1000 atoms: 0.50 Number of scatterers: 36829 At special positions: 0 Unit cell: (183.48, 195.156, 114.258, 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 188 16.00 P 24 15.00 O 7041 8.00 N 6466 7.00 C 23110 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: 13.89 Conformation dependent library (CDL) restraints added in 6.4 seconds 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 234 helices and 33 sheets defined 43.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.03 Creating SS restraints... 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: 4.396A 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: 3.504A 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: 3.584A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.849A 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 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 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 removed outlier: 3.556A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 581 through 585 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 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.797A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.895A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.557A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 92 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 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' 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: 4.722A 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 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' 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: 3.608A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.906A 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 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 427 removed outlier: 3.641A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) 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 581 through 585 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: 5.019A 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: 3.655A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.162A 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 92 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: 4.642A 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: 3.585A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.867A 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 430 removed outlier: 3.691A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.843A 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 removed outlier: 3.509A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 581 through 585 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 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.688A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.771A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.109A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 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: 4.839A 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 232 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: 3.516A 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: 3.611A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.615A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.587A 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 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.508A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 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 663 removed outlier: 5.084A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.669A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.827A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 92 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: 4.815A 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: 3.618A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.764A 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 425 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' 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 586 removed outlier: 3.812A 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: 5.054A 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: 3.798A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.751A 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 'G' and resid 50 through 67 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.758A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 168 through 187 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: 4.114A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 4.813A 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: 3.610A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 5.198A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 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: 4.733A 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 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 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: 3.628A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.902A 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: 4.416A 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: 3.767A 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 663 removed outlier: 4.961A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) 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: 3.684A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing sheet with id= A, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.886A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.756A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.912A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 641 through 644 removed outlier: 4.035A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.928A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.836A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.796A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 368 removed outlier: 9.175A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.634A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 81 through 83 removed outlier: 7.466A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 55 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.919A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.744A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 641 through 644 removed outlier: 4.051A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.429A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.851A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.780A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.505A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.153A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.985A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.825A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.739A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 641 through 644 removed outlier: 4.114A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 122 through 124 Processing sheet with id= AA, first strand: chain 'G' and resid 196 through 198 Processing sheet with id= AB, first strand: chain 'G' and resid 275 through 278 Processing sheet with id= AC, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.408A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.054A 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: 6.773A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.227A 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: 4.226A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.862A 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: 8.750A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3642 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: 16.05 Time building geometry restraints manager: 14.93 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: 7567 1.33 - 1.45: 7838 1.45 - 1.57: 21708 1.57 - 1.69: 36 1.69 - 1.81: 299 Bond restraints: 37448 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 37443 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.84: 1522 107.84 - 114.87: 22397 114.87 - 121.90: 19137 121.90 - 128.93: 7415 128.93 - 135.96: 169 Bond angle restraints: 50640 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.97 -10.69 1.22e+00 6.72e-01 7.68e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.88 122.46 -9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.42 -6.60 1.16e+00 7.43e-01 3.24e+01 angle pdb=" C HIS F 226 " pdb=" N PRO F 227 " pdb=" CA PRO F 227 " ideal model delta sigma weight residual 119.28 124.46 -5.18 1.10e+00 8.26e-01 2.22e+01 angle pdb=" C GLN G 136 " pdb=" N ARG G 137 " pdb=" CA ARG G 137 " ideal model delta sigma weight residual 120.44 126.56 -6.12 1.30e+00 5.92e-01 2.22e+01 ... (remaining 50635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 22878 35.56 - 71.12: 251 71.12 - 106.69: 39 106.69 - 142.25: 8 142.25 - 177.81: 9 Dihedral angle restraints: 23185 sinusoidal: 9753 harmonic: 13432 Sorted by residual: dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual 300.00 122.19 177.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 127.80 172.19 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 111.81 -171.82 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 23182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4087 0.048 - 0.097: 988 0.097 - 0.145: 477 0.145 - 0.193: 150 0.193 - 0.242: 12 Chirality restraints: 5714 Sorted by residual: 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 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+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 1.42e+00 ... (remaining 5711 not shown) Planarity restraints: 6636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+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 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C GLU F 534 " -0.039 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 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 360 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C PHE F 360 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE F 360 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY F 361 " -0.013 2.00e-02 2.50e+03 ... (remaining 6633 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 13476 2.88 - 3.39: 35646 3.39 - 3.89: 63411 3.89 - 4.40: 72640 4.40 - 4.90: 117404 Nonbonded interactions: 302577 Sorted by model distance: nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.381 2.520 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.387 2.520 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.410 2.520 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.432 2.520 nonbonded pdb=" OD2 ASP G 176 " pdb=" NZ LYS G 180 " model vdw 2.432 2.520 ... (remaining 302572 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' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.050 Extract box with map and model: 14.790 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 96.640 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.190 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 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 37448 Z= 0.707 Angle : 0.852 12.442 50640 Z= 0.524 Chirality : 0.058 0.242 5714 Planarity : 0.004 0.036 6636 Dihedral : 12.277 177.812 14471 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.77 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.39 (0.11), residues: 4628 helix: -0.23 (0.10), residues: 2040 sheet: 0.71 (0.17), residues: 802 loop : 0.98 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 476 HIS 0.001 0.000 HIS A 115 PHE 0.002 0.000 PHE D 539 TYR 0.001 0.000 TYR D 143 ARG 0.001 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1287 time to evaluate : 4.161 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: B 499 HIS cc_start: 0.6731 (m-70) cc_final: 0.6439 (m170) REVERT: E 244 TYR cc_start: 0.6790 (p90) cc_final: 0.6449 (p90) REVERT: D 442 MET cc_start: 0.8427 (mmm) cc_final: 0.8109 (mmt) REVERT: D 524 LYS cc_start: 0.7264 (mttt) cc_final: 0.6916 (mtmm) REVERT: C 324 ILE cc_start: 0.8692 (tp) cc_final: 0.8417 (mt) REVERT: A 243 LEU cc_start: 0.8201 (mt) cc_final: 0.7393 (mp) REVERT: G 312 GLU cc_start: 0.7215 (tp30) cc_final: 0.6682 (mm-30) REVERT: G 389 GLU cc_start: 0.5080 (tt0) cc_final: 0.4425 (pt0) outliers start: 0 outliers final: 0 residues processed: 1287 average time/residue: 0.6082 time to fit residues: 1185.0483 Evaluate side-chains 645 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 237 optimal weight: 0.1980 chunk 188 optimal weight: 0.8980 chunk 364 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 422 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 296 ASN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN E 296 ASN E 421 GLN E 490 GLN E 660 ASN D 90 ASN D 91 ASN D 401 ASN D 421 GLN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** D 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 317 HIS C 660 ASN A 90 ASN A 285 ASN A 494 GLN A 602 ASN A 660 ASN F 103 GLN F 296 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN F 680 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37448 Z= 0.225 Angle : 0.648 11.791 50640 Z= 0.316 Chirality : 0.045 0.187 5714 Planarity : 0.004 0.039 6636 Dihedral : 9.639 176.245 5181 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.30 % Allowed : 9.11 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 4628 helix: 0.98 (0.11), residues: 2010 sheet: 0.78 (0.17), residues: 795 loop : 1.38 (0.16), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 476 HIS 0.011 0.001 HIS B 115 PHE 0.018 0.002 PHE G 408 TYR 0.024 0.002 TYR G 354 ARG 0.006 0.001 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 720 time to evaluate : 4.270 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: E 120 ASP cc_start: 0.5784 (p0) cc_final: 0.5568 (m-30) REVERT: D 140 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6860 (tt) REVERT: C 324 ILE cc_start: 0.8545 (tp) cc_final: 0.8278 (mt) REVERT: G 278 GLN cc_start: 0.6197 (tp40) cc_final: 0.5986 (tt0) REVERT: G 304 GLN cc_start: 0.7870 (tp40) cc_final: 0.7635 (tm-30) REVERT: G 320 LYS cc_start: 0.7629 (ptmm) cc_final: 0.7413 (ttmt) REVERT: G 325 LYS cc_start: 0.7347 (ptmm) cc_final: 0.7082 (ptmm) REVERT: F 536 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6471 (tp40) REVERT: F 678 MET cc_start: 0.5931 (mmm) cc_final: 0.5537 (mmt) outliers start: 91 outliers final: 55 residues processed: 779 average time/residue: 0.5189 time to fit residues: 645.9873 Evaluate side-chains 643 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 586 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 536 GLN Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 351 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 423 optimal weight: 6.9990 chunk 456 optimal weight: 2.9990 chunk 376 optimal weight: 30.0000 chunk 419 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 GLN B 490 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS D 91 ASN D 384 HIS ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN D 660 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN A 327 GLN A 494 GLN A 735 HIS F 226 HIS F 337 GLN F 384 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37448 Z= 0.300 Angle : 0.663 11.461 50640 Z= 0.320 Chirality : 0.047 0.354 5714 Planarity : 0.005 0.065 6636 Dihedral : 9.034 177.585 5181 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.26 % Allowed : 10.50 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.31 (0.12), residues: 4628 helix: 0.85 (0.11), residues: 2064 sheet: 0.76 (0.18), residues: 786 loop : 1.26 (0.16), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 476 HIS 0.007 0.001 HIS A 735 PHE 0.031 0.002 PHE F 52 TYR 0.026 0.002 TYR D 203 ARG 0.009 0.001 ARG G 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 620 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 292 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5947 (mm-30) REVERT: C 322 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7060 (mmm160) REVERT: C 324 ILE cc_start: 0.8723 (tp) cc_final: 0.8497 (tt) REVERT: C 444 SER cc_start: 0.7814 (p) cc_final: 0.7503 (t) REVERT: G 54 MET cc_start: 0.2483 (tpt) cc_final: 0.2070 (tpt) REVERT: G 277 PHE cc_start: 0.7249 (m-80) cc_final: 0.6070 (m-80) REVERT: G 325 LYS cc_start: 0.6996 (ptmm) cc_final: 0.6377 (ptmm) REVERT: G 350 GLN cc_start: 0.7587 (tt0) cc_final: 0.7385 (tp40) REVERT: F 57 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7430 (m) REVERT: F 80 GLU cc_start: 0.7132 (tp30) cc_final: 0.6912 (tp30) outliers start: 129 outliers final: 85 residues processed: 703 average time/residue: 0.5075 time to fit residues: 572.7539 Evaluate side-chains 609 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 523 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 385 GLN Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 536 GLN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 686 ASP Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 284 optimal weight: 0.1980 chunk 424 optimal weight: 0.6980 chunk 449 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 402 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 660 ASN D 285 ASN D 443 ASN D 460 ASN D 568 GLN C 327 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN C 660 ASN A 490 GLN A 735 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN F 602 ASN F 660 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37448 Z= 0.188 Angle : 0.595 10.408 50640 Z= 0.283 Chirality : 0.044 0.228 5714 Planarity : 0.004 0.049 6636 Dihedral : 8.511 172.593 5181 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 12.52 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.53 (0.12), residues: 4628 helix: 1.11 (0.11), residues: 2017 sheet: 0.80 (0.18), residues: 783 loop : 1.28 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 476 HIS 0.005 0.001 HIS A 735 PHE 0.025 0.001 PHE G 377 TYR 0.025 0.001 TYR E 244 ARG 0.008 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 584 time to evaluate : 4.348 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: B 348 ASN cc_start: 0.7677 (m-40) cc_final: 0.7422 (m-40) REVERT: B 657 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5922 (mm) REVERT: D 442 MET cc_start: 0.8686 (mmm) cc_final: 0.8405 (mmt) REVERT: D 464 LEU cc_start: 0.8696 (tp) cc_final: 0.8490 (mt) REVERT: C 244 TYR cc_start: 0.7264 (p90) cc_final: 0.6945 (p90) REVERT: C 444 SER cc_start: 0.7838 (p) cc_final: 0.7581 (t) REVERT: G 54 MET cc_start: 0.2306 (tpt) cc_final: 0.1944 (tpt) REVERT: G 320 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7184 (ttmt) REVERT: G 350 GLN cc_start: 0.7404 (tt0) cc_final: 0.7007 (tp40) outliers start: 95 outliers final: 63 residues processed: 645 average time/residue: 0.5030 time to fit residues: 527.8278 Evaluate side-chains 584 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 520 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 50.0000 chunk 255 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 334 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 383 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 ASN B 763 GLN E 398 GLN E 536 GLN D 226 HIS D 340 HIS D 460 ASN D 568 GLN C 91 ASN C 406 HIS C 443 ASN C 568 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN A 735 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37448 Z= 0.272 Angle : 0.628 10.895 50640 Z= 0.300 Chirality : 0.045 0.166 5714 Planarity : 0.005 0.054 6636 Dihedral : 8.174 173.599 5181 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.15 % Allowed : 13.05 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.36 (0.12), residues: 4628 helix: 1.04 (0.11), residues: 2033 sheet: 0.78 (0.18), residues: 759 loop : 1.08 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 476 HIS 0.007 0.001 HIS C 499 PHE 0.027 0.002 PHE G 377 TYR 0.029 0.002 TYR B 644 ARG 0.007 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 561 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 ASN cc_start: 0.7733 (m-40) cc_final: 0.7498 (m-40) REVERT: B 577 ASP cc_start: 0.7372 (t0) cc_final: 0.7162 (t0) REVERT: B 657 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6061 (mm) REVERT: D 60 LYS cc_start: 0.7855 (mttm) cc_final: 0.7598 (mttp) REVERT: D 100 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7371 (pp) REVERT: C 444 SER cc_start: 0.8048 (p) cc_final: 0.7803 (t) REVERT: G 54 MET cc_start: 0.2226 (tpt) cc_final: 0.1862 (tpt) REVERT: F 150 ASP cc_start: 0.6344 (m-30) cc_final: 0.6015 (m-30) REVERT: F 270 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6785 (p0) REVERT: F 678 MET cc_start: 0.5870 (mmm) cc_final: 0.5611 (mmt) outliers start: 125 outliers final: 85 residues processed: 643 average time/residue: 0.5061 time to fit residues: 526.0616 Evaluate side-chains 596 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 508 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 536 GLN Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 0.9980 chunk 404 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 263 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 449 optimal weight: 3.9990 chunk 373 optimal weight: 50.0000 chunk 208 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS B 568 GLN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS D 602 ASN C 340 HIS C 568 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 750 ASN ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 37448 Z= 0.352 Angle : 0.668 8.606 50640 Z= 0.320 Chirality : 0.047 0.173 5714 Planarity : 0.005 0.059 6636 Dihedral : 7.803 176.981 5181 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.28 % Allowed : 14.53 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.05 (0.12), residues: 4628 helix: 0.83 (0.11), residues: 2054 sheet: 0.61 (0.19), residues: 735 loop : 0.84 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 476 HIS 0.006 0.001 HIS E 384 PHE 0.024 0.002 PHE G 377 TYR 0.028 0.002 TYR F 203 ARG 0.015 0.001 ARG E 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 556 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 ASN cc_start: 0.7755 (m-40) cc_final: 0.7542 (m-40) REVERT: B 427 MET cc_start: 0.4314 (tpp) cc_final: 0.3924 (tpt) REVERT: B 577 ASP cc_start: 0.7390 (t0) cc_final: 0.7169 (t0) REVERT: B 657 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5977 (mm) REVERT: D 358 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: G 54 MET cc_start: 0.2315 (tpt) cc_final: 0.1948 (tpt) REVERT: F 150 ASP cc_start: 0.6318 (m-30) cc_final: 0.6074 (m-30) REVERT: F 270 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6696 (p0) REVERT: F 442 MET cc_start: 0.8202 (mmt) cc_final: 0.7615 (mmt) outliers start: 130 outliers final: 102 residues processed: 630 average time/residue: 0.5141 time to fit residues: 525.8447 Evaluate side-chains 622 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 518 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 536 GLN Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 328 optimal weight: 0.0470 chunk 254 optimal weight: 0.3980 chunk 378 optimal weight: 0.8980 chunk 251 optimal weight: 0.6980 chunk 448 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 568 GLN E 285 ASN E 404 HIS C 183 HIS C 421 GLN C 602 ASN C 660 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37448 Z= 0.175 Angle : 0.600 10.779 50640 Z= 0.283 Chirality : 0.044 0.216 5714 Planarity : 0.004 0.063 6636 Dihedral : 7.341 179.955 5181 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.42 % Allowed : 15.82 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.27 (0.13), residues: 4628 helix: 1.02 (0.12), residues: 2057 sheet: 0.59 (0.18), residues: 776 loop : 1.03 (0.16), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP B 476 HIS 0.006 0.001 HIS C 499 PHE 0.026 0.001 PHE G 377 TYR 0.025 0.001 TYR C 203 ARG 0.010 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 566 time to evaluate : 4.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 ASN cc_start: 0.7575 (m-40) cc_final: 0.7343 (m-40) REVERT: B 425 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7251 (ttmm) REVERT: B 657 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5820 (mm) REVERT: E 508 MET cc_start: 0.7633 (tpt) cc_final: 0.7326 (tpt) REVERT: D 100 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7457 (pp) REVERT: C 187 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 322 ARG cc_start: 0.6402 (mtt90) cc_final: 0.6044 (mtt90) REVERT: G 54 MET cc_start: 0.2224 (tpt) cc_final: 0.1943 (tpt) REVERT: F 80 GLU cc_start: 0.6562 (tp30) cc_final: 0.6232 (tp30) REVERT: F 150 ASP cc_start: 0.6294 (m-30) cc_final: 0.6045 (m-30) REVERT: F 270 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6623 (p0) outliers start: 96 outliers final: 77 residues processed: 621 average time/residue: 0.5081 time to fit residues: 513.6285 Evaluate side-chains 606 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 525 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 284 optimal weight: 0.9990 chunk 305 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 352 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 GLN C 568 GLN C 660 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 735 HIS F 36 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37448 Z= 0.235 Angle : 0.619 10.214 50640 Z= 0.292 Chirality : 0.045 0.244 5714 Planarity : 0.004 0.069 6636 Dihedral : 7.151 176.775 5181 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.62 % Allowed : 15.92 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.24 (0.13), residues: 4628 helix: 1.04 (0.12), residues: 2056 sheet: 0.51 (0.18), residues: 778 loop : 0.97 (0.16), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 551 HIS 0.008 0.001 HIS C 499 PHE 0.033 0.001 PHE B 131 TYR 0.027 0.002 TYR C 203 ARG 0.006 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 543 time to evaluate : 4.121 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: B 348 ASN cc_start: 0.7603 (m-40) cc_final: 0.7371 (m-40) REVERT: B 425 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7276 (ttmm) REVERT: E 508 MET cc_start: 0.7642 (tpt) cc_final: 0.7355 (tpt) REVERT: E 733 ARG cc_start: 0.5148 (ttt-90) cc_final: 0.4944 (mmm160) REVERT: D 100 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7387 (pp) REVERT: C 187 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 322 ARG cc_start: 0.6501 (mtt90) cc_final: 0.6220 (mtt90) REVERT: G 54 MET cc_start: 0.2177 (tpt) cc_final: 0.1895 (tpt) REVERT: F 80 GLU cc_start: 0.6736 (tp30) cc_final: 0.6429 (tp30) REVERT: F 150 ASP cc_start: 0.6347 (m-30) cc_final: 0.6113 (m-30) REVERT: F 270 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6665 (p0) REVERT: F 442 MET cc_start: 0.8206 (mmt) cc_final: 0.7826 (mmt) outliers start: 104 outliers final: 85 residues processed: 599 average time/residue: 0.4993 time to fit residues: 487.2639 Evaluate side-chains 603 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 515 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 0.9990 chunk 429 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 417 optimal weight: 2.9990 chunk 251 optimal weight: 0.0040 chunk 181 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 416 optimal weight: 0.8980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 568 GLN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37448 Z= 0.206 Angle : 0.606 9.676 50640 Z= 0.286 Chirality : 0.044 0.236 5714 Planarity : 0.004 0.073 6636 Dihedral : 6.758 169.329 5181 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.40 % Allowed : 16.43 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.26 (0.13), residues: 4628 helix: 1.05 (0.12), residues: 2071 sheet: 0.54 (0.19), residues: 739 loop : 0.97 (0.16), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 551 HIS 0.020 0.001 HIS A 735 PHE 0.032 0.001 PHE B 131 TYR 0.027 0.002 TYR C 517 ARG 0.006 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 539 time to evaluate : 4.304 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: B 348 ASN cc_start: 0.7554 (m-40) cc_final: 0.7281 (m-40) REVERT: E 508 MET cc_start: 0.7633 (tpt) cc_final: 0.7368 (tpt) REVERT: E 733 ARG cc_start: 0.5154 (ttt-90) cc_final: 0.4878 (mmm160) REVERT: D 100 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7476 (pp) REVERT: A 322 ARG cc_start: 0.6480 (mtt90) cc_final: 0.6245 (mtt90) REVERT: G 54 MET cc_start: 0.2197 (tpt) cc_final: 0.1934 (tpt) REVERT: F 80 GLU cc_start: 0.6825 (tp30) cc_final: 0.6499 (tp30) REVERT: F 150 ASP cc_start: 0.6291 (m-30) cc_final: 0.6063 (m-30) REVERT: F 270 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6632 (p0) REVERT: F 442 MET cc_start: 0.8168 (mmt) cc_final: 0.7787 (mmt) REVERT: F 678 MET cc_start: 0.5889 (mmm) cc_final: 0.5595 (mmt) outliers start: 95 outliers final: 85 residues processed: 591 average time/residue: 0.5058 time to fit residues: 483.9106 Evaluate side-chains 599 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 512 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 0.6980 chunk 441 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 463 optimal weight: 5.9990 chunk 426 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS F 36 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37448 Z= 0.216 Angle : 0.617 10.939 50640 Z= 0.291 Chirality : 0.044 0.220 5714 Planarity : 0.004 0.076 6636 Dihedral : 6.497 157.526 5181 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.30 % Allowed : 16.81 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.25 (0.13), residues: 4628 helix: 1.08 (0.12), residues: 2071 sheet: 0.52 (0.19), residues: 744 loop : 0.93 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 551 HIS 0.007 0.001 HIS C 499 PHE 0.029 0.001 PHE B 131 TYR 0.023 0.002 TYR C 203 ARG 0.005 0.000 ARG A 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 523 time to evaluate : 4.043 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 348 ASN cc_start: 0.7514 (m-40) cc_final: 0.7228 (m-40) REVERT: E 508 MET cc_start: 0.7652 (tpt) cc_final: 0.7381 (tpt) REVERT: E 733 ARG cc_start: 0.5181 (ttt-90) cc_final: 0.4859 (mmm160) REVERT: D 100 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7417 (pp) REVERT: C 51 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.3526 (pp) REVERT: A 322 ARG cc_start: 0.6464 (mtt90) cc_final: 0.6211 (mtt90) REVERT: G 54 MET cc_start: 0.2143 (tpt) cc_final: 0.1890 (tpt) REVERT: F 80 GLU cc_start: 0.6839 (tp30) cc_final: 0.6546 (tp30) REVERT: F 270 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6612 (p0) REVERT: F 442 MET cc_start: 0.8174 (mmt) cc_final: 0.7788 (mmt) REVERT: F 678 MET cc_start: 0.5886 (mmm) cc_final: 0.5606 (mmt) outliers start: 91 outliers final: 83 residues processed: 576 average time/residue: 0.5117 time to fit residues: 479.9672 Evaluate side-chains 596 residues out of total 3963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 510 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain G residue 324 GLU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 9.9990 chunk 392 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 369 optimal weight: 40.0000 chunk 154 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 533 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN F 36 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133131 restraints weight = 51391.494| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.10 r_work: 0.3391 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6165 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: