Starting phenix.real_space_refine on Fri Feb 23 20:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fco_28988/02_2024/8fco_28988_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 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 197 5.16 5 C 24846 2.51 5 N 6943 2.21 5 O 7559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "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 GLU 546": "OE1" <-> "OE2" Residue "C PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "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 "B TYR 110": "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 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "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 "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 357": "OE1" <-> "OE2" Residue "H TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 758": "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 PHE 163": "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 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 TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 357": "OE1" <-> "OE2" Residue "G TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39569 Number of models: 1 Model: "" Number of chains: 14 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: "B" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "H" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 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: "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: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} Time building chain proxies: 19.33, per 1000 atoms: 0.49 Number of scatterers: 39569 At special positions: 0 Unit cell: (214.338, 193.488, 115.926, 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 197 16.00 P 24 15.00 O 7559 8.00 N 6943 7.00 C 24846 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: 15.40 Conformation dependent library (CDL) restraints added in 8.2 seconds 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 247 helices and 36 sheets defined 43.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.03 Creating SS restraints... Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.054A 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 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: 3.582A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.773A 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 429 removed outlier: 4.302A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.419A 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 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 579 through 585 removed outlier: 3.865A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) 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 661 removed outlier: 3.616A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.852A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.739A 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 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 92 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: 4.882A 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 231 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: 3.507A 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: 3.544A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 430 removed outlier: 4.362A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) 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 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.900A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.803A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 Processing helix chain 'H' and resid 50 through 67 Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.739A pdb=" N PHE H 149 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 168 through 187 removed outlier: 3.511A pdb=" N ILE H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 202 through 207 Processing helix chain 'H' and resid 214 through 220 Processing helix chain 'H' and resid 244 through 247 No H-bonds generated for 'chain 'H' and resid 244 through 247' Processing helix chain 'H' and resid 251 through 261 Processing helix chain 'H' and resid 281 through 284 Processing helix chain 'H' and resid 297 through 315 Processing helix chain 'H' and resid 320 through 330 removed outlier: 4.042A pdb=" N ARG H 329 " --> pdb=" O LYS H 325 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY H 330 " --> pdb=" O GLU H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 Processing helix chain 'H' and resid 412 through 420 removed outlier: 3.595A pdb=" N ASP H 417 " --> pdb=" O ALA H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 436 removed outlier: 5.138A pdb=" N ALA H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) 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: 4.641A 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: 3.665A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 429 removed outlier: 4.188A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.758A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (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: 5.096A 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: 3.915A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.732A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'F' and resid 43 through 48 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: 3.720A 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 removed outlier: 3.500A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 319 through 336 removed outlier: 3.725A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 4.853A 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: 4.565A 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 removed outlier: 3.616A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 removed outlier: 4.039A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) 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: 3.827A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.805A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.824A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 319 through 336 removed outlier: 3.562A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' 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 430 removed outlier: 4.833A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (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 removed outlier: 3.506A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) 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: 5.001A 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: 3.683A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.775A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.169A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.810A 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: 3.598A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.886A 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: 3.560A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.828A 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 457 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: 3.505A 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 removed outlier: 3.503A pdb=" N PHE D 563 " --> pdb=" O ARG D 560 " (cutoff:3.500A) 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 663 removed outlier: 5.102A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.698A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.784A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.281A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 67 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.803A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 Processing helix chain 'G' and resid 168 through 187 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 250 through 261 Processing helix chain 'G' and resid 281 through 284 removed outlier: 3.541A pdb=" N SER G 284 " --> pdb=" O PRO G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 281 through 284' Processing helix chain 'G' and resid 290 through 293 removed outlier: 4.346A pdb=" N PHE G 293 " --> pdb=" O GLY G 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 290 through 293' Processing helix chain 'G' and resid 297 through 315 Processing helix chain 'G' and resid 320 through 330 removed outlier: 3.908A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 369 removed outlier: 3.600A pdb=" N ALA G 369 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 420 removed outlier: 3.577A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 4.906A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.377A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.970A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.810A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.750A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 641 through 644 removed outlier: 4.121A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.453A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.785A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.917A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 8.601A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 122 through 124 Processing sheet with id= L, first strand: chain 'H' and resid 196 through 198 Processing sheet with id= M, first strand: chain 'H' and resid 438 through 440 Processing sheet with id= N, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.377A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 55 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.830A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.694A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.710A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 641 through 644 removed outlier: 4.003A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.681A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.729A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.791A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 365 through 368 removed outlier: 4.023A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 641 through 644 removed outlier: 8.775A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.970A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.507A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.806A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.692A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 641 through 644 removed outlier: 3.544A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.731A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 55 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.979A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= AF, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.585A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 641 through 644 removed outlier: 4.113A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 122 through 124 Processing sheet with id= AI, first strand: chain 'G' and resid 196 through 198 Processing sheet with id= AJ, first strand: chain 'G' and resid 275 through 277 1434 hydrogen bonds defined for protein. 3999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.61 Time building geometry restraints manager: 16.22 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: 8204 1.33 - 1.45: 8363 1.45 - 1.57: 23320 1.57 - 1.69: 36 1.69 - 1.81: 312 Bond restraints: 40235 Sorted by residual: 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 3.05e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 40230 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.48: 1220 105.48 - 113.08: 21755 113.08 - 120.68: 18129 120.68 - 128.28: 13097 128.28 - 135.88: 199 Bond angle restraints: 54400 Sorted by residual: angle pdb=" N LEU H 331 " pdb=" CA LEU H 331 " pdb=" C LEU H 331 " ideal model delta sigma weight residual 113.28 123.94 -10.66 1.22e+00 6.72e-01 7.63e+01 angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.50 123.95 -10.45 1.23e+00 6.61e-01 7.21e+01 angle pdb=" N ARG H 332 " pdb=" CA ARG H 332 " pdb=" C ARG H 332 " ideal model delta sigma weight residual 112.41 122.50 -10.09 1.30e+00 5.92e-01 6.02e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 113.17 122.40 -9.23 1.26e+00 6.30e-01 5.36e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.40 -6.58 1.16e+00 7.43e-01 3.22e+01 ... (remaining 54395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 24600 35.89 - 71.77: 258 71.77 - 107.66: 40 107.66 - 143.55: 9 143.55 - 179.43: 7 Dihedral angle restraints: 24914 sinusoidal: 10480 harmonic: 14434 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 119.43 -179.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 118.43 -178.43 1 2.00e+01 2.50e-03 4.80e+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 -60.00 116.88 -176.88 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 24911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4378 0.048 - 0.096: 1065 0.096 - 0.144: 493 0.144 - 0.192: 185 0.192 - 0.240: 12 Chirality restraints: 6133 Sorted by residual: chirality pdb=" CA ILE B 590 " pdb=" N ILE B 590 " pdb=" C ILE B 590 " pdb=" CB ILE B 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE A 590 " pdb=" N ILE A 590 " pdb=" C ILE A 590 " pdb=" CB ILE A 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6130 not shown) Planarity restraints: 7130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C GLU F 534 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU F 534 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+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 H 254 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C GLU H 254 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU H 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG H 255 " -0.013 2.00e-02 2.50e+03 ... (remaining 7127 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13590 2.87 - 3.37: 37915 3.37 - 3.88: 67427 3.88 - 4.39: 78454 4.39 - 4.90: 127178 Nonbonded interactions: 324564 Sorted by model distance: nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.358 2.520 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.399 2.520 nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.399 2.520 nonbonded pdb=" NZ LYS B 512 " pdb=" O GLY B 637 " model vdw 2.414 2.520 nonbonded pdb=" OD2 ASP G 176 " pdb=" NZ LYS G 180 " model vdw 2.419 2.520 ... (remaining 324559 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' 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' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.540 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: 0.040 Extract box with map and model: 15.430 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 101.720 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 0.110 40235 Z= 0.716 Angle : 0.890 12.403 54400 Z= 0.561 Chirality : 0.058 0.240 6133 Planarity : 0.004 0.035 7130 Dihedral : 12.140 179.435 15546 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 0.37 (0.11), residues: 4965 helix: -0.18 (0.10), residues: 2216 sheet: 0.64 (0.16), residues: 881 loop : 0.93 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 476 HIS 0.001 0.000 HIS H 256 PHE 0.001 0.000 PHE C 363 TYR 0.001 0.000 TYR H 334 ARG 0.001 0.000 ARG B 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1473 time to evaluate : 4.052 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: C 506 PHE cc_start: 0.5812 (m-80) cc_final: 0.5561 (m-10) REVERT: C 509 THR cc_start: 0.7074 (m) cc_final: 0.6727 (p) REVERT: H 408 PHE cc_start: 0.6370 (t80) cc_final: 0.5951 (t80) REVERT: A 219 MET cc_start: 0.8052 (mtm) cc_final: 0.7756 (mtp) REVERT: A 427 MET cc_start: 0.4983 (mtp) cc_final: 0.3988 (mtp) REVERT: D 432 LEU cc_start: 0.4168 (tt) cc_final: 0.3861 (tt) REVERT: D 630 ASP cc_start: 0.5562 (t0) cc_final: 0.5301 (t70) outliers start: 0 outliers final: 0 residues processed: 1473 average time/residue: 0.6030 time to fit residues: 1359.9078 Evaluate side-chains 686 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 421 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 391 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 453 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 327 GLN C 348 ASN C 490 GLN C 603 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 443 ASN B 490 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 ASN A 183 HIS A 215 GLN A 404 HIS A 406 HIS A 602 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 115 HIS F 443 ASN F 460 ASN F 494 GLN F 603 GLN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 GLN D 199 ASN D 421 GLN D 460 ASN D 603 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40235 Z= 0.265 Angle : 0.682 10.098 54400 Z= 0.334 Chirality : 0.046 0.183 6133 Planarity : 0.005 0.057 7130 Dihedral : 9.800 175.916 5554 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.31 % Favored : 98.61 % Rotamer: Outliers : 2.98 % Allowed : 9.77 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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 (0.12), residues: 4965 helix: 0.89 (0.11), residues: 2222 sheet: 0.58 (0.16), residues: 892 loop : 1.18 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 551 HIS 0.009 0.001 HIS A 499 PHE 0.022 0.002 PHE D 516 TYR 0.023 0.002 TYR C 244 ARG 0.010 0.001 ARG H 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 723 time to evaluate : 4.610 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: C 309 ILE cc_start: 0.8178 (tt) cc_final: 0.7964 (tt) REVERT: B 75 ASP cc_start: 0.5248 (t0) cc_final: 0.4956 (t0) REVERT: B 150 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: B 221 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6125 (tt0) REVERT: A 150 ASP cc_start: 0.6859 (t0) cc_final: 0.6658 (t0) REVERT: A 574 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7742 (tp) REVERT: E 84 MET cc_start: 0.7158 (ptp) cc_final: 0.6886 (ptp) REVERT: D 738 GLU cc_start: 0.3983 (tp30) cc_final: 0.3783 (tp30) REVERT: G 342 ARG cc_start: 0.7109 (tpp80) cc_final: 0.6286 (tpp-160) outliers start: 127 outliers final: 81 residues processed: 813 average time/residue: 0.5367 time to fit residues: 709.2117 Evaluate side-chains 632 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 548 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 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 366 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 560 ARG Chi-restraints excluded: chain D residue 603 GLN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 251 optimal weight: 0.0980 chunk 140 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 453 optimal weight: 0.5980 chunk 490 optimal weight: 1.9990 chunk 404 optimal weight: 5.9990 chunk 450 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 364 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 327 GLN C 351 ASN C 460 ASN C 616 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 443 ASN B 460 ASN B 603 GLN B 616 ASN B 680 ASN H 294 ASN A 90 ASN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 340 HIS E 660 ASN D 33 ASN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 602 ASN D 660 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40235 Z= 0.170 Angle : 0.613 11.366 54400 Z= 0.292 Chirality : 0.044 0.289 6133 Planarity : 0.004 0.075 7130 Dihedral : 9.280 172.072 5554 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.87 % Allowed : 11.49 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4965 helix: 1.14 (0.11), residues: 2211 sheet: 0.62 (0.17), residues: 877 loop : 1.19 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 476 HIS 0.011 0.001 HIS A 499 PHE 0.021 0.001 PHE C 131 TYR 0.026 0.002 TYR C 244 ARG 0.006 0.000 ARG C 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 610 time to evaluate : 4.462 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: C 309 ILE cc_start: 0.8210 (tt) cc_final: 0.8001 (tt) REVERT: B 75 ASP cc_start: 0.5297 (t0) cc_final: 0.5030 (t0) REVERT: B 150 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: B 221 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6036 (tt0) REVERT: B 427 MET cc_start: 0.4369 (tpt) cc_final: 0.2290 (tmm) REVERT: H 159 MET cc_start: 0.1439 (mmm) cc_final: -0.0512 (tpt) REVERT: A 278 LEU cc_start: 0.6861 (pp) cc_final: 0.6560 (mp) REVERT: A 427 MET cc_start: 0.4971 (mtp) cc_final: 0.4468 (mtp) REVERT: A 574 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7745 (tp) REVERT: F 73 SER cc_start: 0.7957 (p) cc_final: 0.7739 (p) REVERT: F 76 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7832 (m) REVERT: D 738 GLU cc_start: 0.3939 (tp30) cc_final: 0.3720 (tp30) REVERT: G 342 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6234 (tpp-160) outliers start: 122 outliers final: 82 residues processed: 693 average time/residue: 0.5162 time to fit residues: 592.1346 Evaluate side-chains 598 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 512 time to evaluate : 5.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 448 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 455 optimal weight: 0.6980 chunk 482 optimal weight: 8.9990 chunk 238 optimal weight: 1.9990 chunk 431 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 494 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN H 294 ASN F 317 HIS ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 499 HIS D 199 ASN D 327 GLN D 460 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 40235 Z= 0.376 Angle : 0.690 10.725 54400 Z= 0.334 Chirality : 0.047 0.306 6133 Planarity : 0.005 0.074 7130 Dihedral : 9.102 178.541 5554 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.43 % Allowed : 12.90 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.18 (0.12), residues: 4965 helix: 1.02 (0.11), residues: 2230 sheet: 0.50 (0.17), residues: 858 loop : 0.90 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 476 HIS 0.010 0.001 HIS C 499 PHE 0.019 0.002 PHE D 674 TYR 0.024 0.002 TYR C 244 ARG 0.016 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 565 time to evaluate : 4.513 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: C 309 ILE cc_start: 0.8392 (tt) cc_final: 0.8139 (tt) REVERT: B 75 ASP cc_start: 0.5522 (t0) cc_final: 0.5172 (t0) REVERT: B 150 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: H 354 TYR cc_start: 0.6640 (m-80) cc_final: 0.6258 (m-80) REVERT: E 230 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7515 (t80) outliers start: 146 outliers final: 109 residues processed: 668 average time/residue: 0.5025 time to fit residues: 551.5634 Evaluate side-chains 600 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 489 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 401 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 411 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 432 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN C 460 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN H 294 ASN A 90 ASN ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 406 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 285 ASN D 460 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 40235 Z= 0.231 Angle : 0.619 11.100 54400 Z= 0.295 Chirality : 0.044 0.229 6133 Planarity : 0.004 0.076 7130 Dihedral : 8.634 162.228 5554 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.12 % Allowed : 13.82 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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 (0.12), residues: 4965 helix: 1.13 (0.11), residues: 2226 sheet: 0.54 (0.17), residues: 862 loop : 0.88 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 476 HIS 0.006 0.001 HIS E 340 PHE 0.019 0.001 PHE D 682 TYR 0.025 0.002 TYR C 244 ARG 0.011 0.000 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 551 time to evaluate : 4.482 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: C 309 ILE cc_start: 0.8389 (tt) cc_final: 0.8145 (tt) REVERT: B 75 ASP cc_start: 0.5535 (t0) cc_final: 0.5216 (t0) REVERT: B 150 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: H 354 TYR cc_start: 0.6644 (m-80) cc_final: 0.6262 (m-80) REVERT: H 363 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6614 (t80) REVERT: F 141 GLU cc_start: 0.7338 (pp20) cc_final: 0.7073 (pp20) REVERT: E 230 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7819 (t80) REVERT: D 319 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6443 (mm-30) REVERT: D 738 GLU cc_start: 0.4027 (tp30) cc_final: 0.3779 (tp30) REVERT: G 401 VAL cc_start: 0.8793 (t) cc_final: 0.8563 (p) outliers start: 133 outliers final: 96 residues processed: 642 average time/residue: 0.4932 time to fit residues: 524.8679 Evaluate side-chains 601 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 502 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 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 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 162 optimal weight: 0.9990 chunk 434 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 482 optimal weight: 5.9990 chunk 400 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40235 Z= 0.291 Angle : 0.644 13.745 54400 Z= 0.307 Chirality : 0.045 0.258 6133 Planarity : 0.005 0.077 7130 Dihedral : 8.325 158.985 5554 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.78 % Allowed : 13.67 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.16 (0.12), residues: 4965 helix: 1.12 (0.11), residues: 2210 sheet: 0.48 (0.17), residues: 844 loop : 0.72 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 476 HIS 0.006 0.001 HIS E 340 PHE 0.018 0.002 PHE H 408 TYR 0.024 0.002 TYR C 244 ARG 0.006 0.000 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 552 time to evaluate : 4.674 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: C 309 ILE cc_start: 0.8426 (tt) cc_final: 0.8142 (tt) REVERT: B 75 ASP cc_start: 0.5527 (t0) cc_final: 0.5288 (t0) REVERT: B 150 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: B 221 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: H 354 TYR cc_start: 0.6704 (m-80) cc_final: 0.6289 (m-80) REVERT: H 363 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6724 (t80) REVERT: F 141 GLU cc_start: 0.7342 (pp20) cc_final: 0.7122 (pp20) REVERT: E 230 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7716 (t80) outliers start: 161 outliers final: 121 residues processed: 656 average time/residue: 0.5182 time to fit residues: 557.6086 Evaluate side-chains 629 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 504 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 352 SER Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain H residue 363 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 465 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 406 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 480 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 750 ASN ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN D 460 ASN G 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40235 Z= 0.292 Angle : 0.656 13.432 54400 Z= 0.313 Chirality : 0.045 0.287 6133 Planarity : 0.005 0.080 7130 Dihedral : 7.947 155.946 5554 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.71 % Allowed : 14.31 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.07 (0.12), residues: 4965 helix: 1.05 (0.11), residues: 2219 sheet: 0.45 (0.18), residues: 827 loop : 0.66 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 476 HIS 0.007 0.001 HIS E 340 PHE 0.017 0.002 PHE F 363 TYR 0.025 0.002 TYR C 244 ARG 0.017 0.001 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 541 time to evaluate : 4.628 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: C 309 ILE cc_start: 0.8411 (tt) cc_final: 0.8107 (tt) REVERT: B 75 ASP cc_start: 0.5645 (t0) cc_final: 0.5384 (t0) REVERT: B 221 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6334 (tt0) REVERT: H 354 TYR cc_start: 0.6709 (m-80) cc_final: 0.6276 (m-80) REVERT: E 230 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7811 (t80) REVERT: D 221 GLU cc_start: 0.7448 (pp20) cc_final: 0.7083 (pp20) REVERT: G 401 VAL cc_start: 0.8746 (t) cc_final: 0.8511 (p) outliers start: 158 outliers final: 126 residues processed: 646 average time/residue: 0.5146 time to fit residues: 543.1704 Evaluate side-chains 632 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 504 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 352 SER Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 322 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 297 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 94 optimal weight: 0.0670 chunk 93 optimal weight: 0.0670 chunk 305 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS F 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN F 750 ASN ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 460 ASN D 602 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 40235 Z= 0.165 Angle : 0.615 12.113 54400 Z= 0.292 Chirality : 0.043 0.254 6133 Planarity : 0.004 0.091 7130 Dihedral : 7.561 151.415 5554 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 15.62 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.22 (0.12), residues: 4965 helix: 1.14 (0.11), residues: 2231 sheet: 0.48 (0.18), residues: 842 loop : 0.82 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 476 HIS 0.006 0.001 HIS E 340 PHE 0.018 0.001 PHE D 742 TYR 0.038 0.002 TYR H 336 ARG 0.012 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 558 time to evaluate : 4.867 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: C 309 ILE cc_start: 0.8362 (tt) cc_final: 0.8117 (tt) REVERT: B 75 ASP cc_start: 0.5626 (t0) cc_final: 0.5339 (t0) REVERT: H 354 TYR cc_start: 0.6655 (m-80) cc_final: 0.6216 (m-80) REVERT: H 408 PHE cc_start: 0.6304 (t80) cc_final: 0.6094 (t80) REVERT: A 221 GLU cc_start: 0.6979 (pm20) cc_final: 0.6698 (pm20) REVERT: A 574 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 668 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7383 (mttt) REVERT: E 230 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7901 (t80) REVERT: D 46 MET cc_start: 0.4714 (ppp) cc_final: 0.4483 (tmm) REVERT: D 322 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6503 (ttt-90) REVERT: G 401 VAL cc_start: 0.8701 (t) cc_final: 0.8458 (p) outliers start: 110 outliers final: 91 residues processed: 631 average time/residue: 0.5240 time to fit residues: 537.9351 Evaluate side-chains 609 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 515 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 437 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 420 optimal weight: 1.9990 chunk 448 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 351 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 405 optimal weight: 0.8980 chunk 423 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN F 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 750 ASN ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 460 ASN D 602 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 40235 Z= 0.176 Angle : 0.627 12.002 54400 Z= 0.294 Chirality : 0.044 0.268 6133 Planarity : 0.004 0.085 7130 Dihedral : 7.319 148.109 5554 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 15.67 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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 (0.12), residues: 4965 helix: 1.17 (0.11), residues: 2235 sheet: 0.49 (0.18), residues: 846 loop : 0.84 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 410 HIS 0.023 0.001 HIS A 183 PHE 0.024 0.001 PHE A 618 TYR 0.025 0.002 TYR E 517 ARG 0.009 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 531 time to evaluate : 4.607 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: C 309 ILE cc_start: 0.8322 (tt) cc_final: 0.8082 (tt) REVERT: C 550 MET cc_start: 0.2402 (tmm) cc_final: 0.2152 (ttp) REVERT: B 75 ASP cc_start: 0.5604 (t0) cc_final: 0.5313 (t0) REVERT: H 354 TYR cc_start: 0.6644 (m-80) cc_final: 0.6217 (m-80) REVERT: A 221 GLU cc_start: 0.7025 (pm20) cc_final: 0.6790 (pm20) REVERT: A 668 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7398 (mttt) REVERT: E 230 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7913 (t80) REVERT: D 46 MET cc_start: 0.4671 (ppp) cc_final: 0.4427 (tmm) REVERT: D 322 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6465 (ttt-90) outliers start: 116 outliers final: 101 residues processed: 608 average time/residue: 0.5218 time to fit residues: 517.0886 Evaluate side-chains 613 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 510 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 294 optimal weight: 8.9990 chunk 473 optimal weight: 40.0000 chunk 289 optimal weight: 0.0870 chunk 224 optimal weight: 8.9990 chunk 329 optimal weight: 0.9990 chunk 497 optimal weight: 5.9990 chunk 457 optimal weight: 9.9990 chunk 395 optimal weight: 0.0170 chunk 41 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 494 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 763 GLN D 460 ASN D 602 ASN D 660 ASN G 278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 40235 Z= 0.352 Angle : 0.704 11.954 54400 Z= 0.337 Chirality : 0.046 0.252 6133 Planarity : 0.005 0.107 7130 Dihedral : 7.334 149.268 5554 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.63 % Allowed : 15.93 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.04 (0.12), residues: 4965 helix: 1.08 (0.11), residues: 2210 sheet: 0.44 (0.18), residues: 797 loop : 0.56 (0.15), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 476 HIS 0.006 0.001 HIS E 340 PHE 0.017 0.002 PHE B 52 TYR 0.022 0.002 TYR C 244 ARG 0.009 0.001 ARG F 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 512 time to evaluate : 4.853 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: C 309 ILE cc_start: 0.8436 (tt) cc_final: 0.8161 (tt) REVERT: B 75 ASP cc_start: 0.5915 (t0) cc_final: 0.5612 (t0) REVERT: H 354 TYR cc_start: 0.6827 (m-80) cc_final: 0.6326 (m-80) REVERT: A 221 GLU cc_start: 0.7123 (pm20) cc_final: 0.6914 (pm20) REVERT: E 230 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7997 (t80) REVERT: D 221 GLU cc_start: 0.7407 (pp20) cc_final: 0.7139 (pp20) REVERT: G 402 PRO cc_start: 0.8258 (Cg_endo) cc_final: 0.8037 (Cg_exo) outliers start: 112 outliers final: 100 residues processed: 588 average time/residue: 0.5193 time to fit residues: 504.8883 Evaluate side-chains 594 residues out of total 4256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 493 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 173 TYR 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 366 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 734 ASP Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 757 MET Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 209 CYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 680 ASN Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain G residue 390 ASP Chi-restraints excluded: chain G residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 314 optimal weight: 6.9990 chunk 421 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 396 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 407 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 460 ASN D 602 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115794 restraints weight = 72346.916| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.10 r_work: 0.3340 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 40235 Z= 0.195 Angle : 0.647 11.780 54400 Z= 0.305 Chirality : 0.044 0.315 6133 Planarity : 0.004 0.084 7130 Dihedral : 6.966 145.207 5554 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.70 % Allowed : 16.35 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: 1.15 (0.12), residues: 4965 helix: 1.14 (0.11), residues: 2222 sheet: 0.45 (0.18), residues: 807 loop : 0.67 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 410 HIS 0.006 0.001 HIS E 340 PHE 0.028 0.001 PHE A 618 TYR 0.037 0.002 TYR E 517 ARG 0.009 0.000 ARG F 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11793.45 seconds wall clock time: 217 minutes 8.33 seconds (13028.33 seconds total)