Starting phenix.real_space_refine on Mon Mar 18 15:30:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uea_20752/03_2024/6uea_20752.pdb" } resolution = 3.0 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= -0.014 sd= 0.421 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13427 2.51 5 N 3672 2.21 5 O 4088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 423": "OD1" <-> "OD2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "K PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "H PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "I PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 389": "OE1" <-> "OE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "J GLU 403": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21299 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1686 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4118 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 507} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1581 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1543 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1570 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1556 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1536 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 98 Chain: "J" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1476 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 18, 'TRANS': 199} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 120 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.86, per 1000 atoms: 0.56 Number of scatterers: 21299 At special positions: 0 Unit cell: (190.516, 156.895, 174.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4088 8.00 N 3672 7.00 C 13427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.05 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.05 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS L 299 " distance=2.04 Simple disulfide: pdb=" SG CYS K 266 " - pdb=" SG CYS K 323 " distance=2.04 Simple disulfide: pdb=" SG CYS K 299 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 369 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 266 " - pdb=" SG CYS L 323 " distance=2.04 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS H 299 " distance=2.04 Simple disulfide: pdb=" SG CYS E 299 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.04 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.04 Simple disulfide: pdb=" SG CYS I 242 " - pdb=" SG CYS J 299 " distance=2.03 Simple disulfide: pdb=" SG CYS I 266 " - pdb=" SG CYS I 323 " distance=2.04 Simple disulfide: pdb=" SG CYS I 299 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 369 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 266 " - pdb=" SG CYS J 323 " distance=2.03 Simple disulfide: pdb=" SG CYS J 369 " - pdb=" SG CYS J 432 " distance=2.03 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG C 603 " - " ASN C 65 " " NAG C 606 " - " ASN C 403 " " NAG M 1 " - " ASN A 337 " " NAG N 1 " - " ASN B 337 " " NAG O 1 " - " ASN C 72 " " NAG P 1 " - " ASN C 451 " " NAG Q 1 " - " ASN D 49 " " NAG R 1 " - " ASN F 337 " " NAG S 1 " - " ASN G 337 " Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 3.9 seconds 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 66 sheets defined 9.7% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.933A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.935A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.861A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.805A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.762A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.713A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.688A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.841A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 removed outlier: 4.050A pdb=" N ASP C 520 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 521 " --> pdb=" O ARG C 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 517 through 521' Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.960A pdb=" N LEU F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 362' Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.801A pdb=" N GLY F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.878A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 311 through 318 removed outlier: 3.541A pdb=" N TRP K 315 " --> pdb=" O CYS K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 331 removed outlier: 3.549A pdb=" N LEU K 330 " --> pdb=" O HIS K 327 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS K 331 " --> pdb=" O PRO K 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 327 through 331' Processing helix chain 'K' and resid 356 through 362 removed outlier: 3.728A pdb=" N LEU K 361 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN K 362 " --> pdb=" O GLU K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 311 through 316 removed outlier: 4.147A pdb=" N TRP L 315 " --> pdb=" O CYS L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing helix chain 'L' and resid 391 through 393 No H-bonds generated for 'chain 'L' and resid 391 through 393' Processing helix chain 'L' and resid 421 through 427 removed outlier: 3.555A pdb=" N GLY L 427 " --> pdb=" O ASP L 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.535A pdb=" N TRP E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 256 Processing helix chain 'H' and resid 312 through 317 Processing helix chain 'H' and resid 421 through 427 removed outlier: 3.989A pdb=" N LYS H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 356 through 360 removed outlier: 3.930A pdb=" N LEU I 359 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 427 Processing helix chain 'J' and resid 252 through 257 removed outlier: 3.985A pdb=" N LEU J 256 " --> pdb=" O ALA J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 317 removed outlier: 4.206A pdb=" N HIS J 317 " --> pdb=" O PRO J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 360 removed outlier: 4.278A pdb=" N LEU J 359 " --> pdb=" O PRO J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 4.030A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.836A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.836A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR A 410 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.555A pdb=" N SER A 431 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 446 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 8.471A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR D 63 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 463 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS A 457 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL B 460 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET B 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 463 " --> pdb=" O MET B 464 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE K 458 " --> pdb=" O HIS L 457 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 463 " --> pdb=" O VAL L 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.873A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 249 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 266 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 270 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.632A pdb=" N ALA B 326 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 323 removed outlier: 3.584A pdb=" N PHE B 321 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.599A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.599A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.241A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS C 38 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.618A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 122 through 124 removed outlier: 7.001A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.883A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.991A pdb=" N LEU C 147 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.598A pdb=" N ASP C 176 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.534A pdb=" N CYS C 202 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.521A pdb=" N GLY C 308 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 249 " --> pdb=" O HIS C 310 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS C 250 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN C 266 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.666A pdb=" N VAL C 292 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS C 239 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 290 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 340 through 341 removed outlier: 6.534A pdb=" N LYS C 364 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP C 382 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.509A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 405 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU C 400 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 396 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 474 through 480 removed outlier: 3.772A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 474 through 480 removed outlier: 3.772A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 6 through 11 removed outlier: 3.513A pdb=" N ILE D 6 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 18 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP D 10 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 16 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 23 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 33 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 458 " --> pdb=" O ASN G 459 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER G 461 " --> pdb=" O ILE F 458 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 460 " --> pdb=" O SER G 461 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL G 463 " --> pdb=" O VAL F 460 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 462 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AD2, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AD3, first strand: chain 'F' and resid 246 through 249 removed outlier: 4.207A pdb=" N SER F 247 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR F 267 " --> pdb=" O SER F 247 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS F 249 " --> pdb=" O THR F 265 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 306 " --> pdb=" O CYS F 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 278 through 280 removed outlier: 4.183A pdb=" N THR F 278 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA F 326 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 324 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 320 through 321 Processing sheet with id=AD6, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.676A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.676A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 388 through 389 removed outlier: 3.551A pdb=" N MET F 433 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 245 through 246 removed outlier: 3.586A pdb=" N LEU G 268 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 304 " --> pdb=" O LEU G 268 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 278 through 281 removed outlier: 3.814A pdb=" N THR G 278 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 326 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AE3, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.062A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.062A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 388 through 389 removed outlier: 3.736A pdb=" N MET G 433 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 265 through 268 removed outlier: 3.540A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 265 through 268 removed outlier: 3.683A pdb=" N LEU K 298 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER K 303 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG K 296 " --> pdb=" O SER K 303 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 320 through 323 removed outlier: 3.692A pdb=" N ALA K 336 " --> pdb=" O CYS K 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 348 through 352 removed outlier: 3.823A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 419 " --> pdb=" O VAL K 365 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR K 411 " --> pdb=" O GLY K 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 348 through 352 removed outlier: 3.823A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 419 " --> pdb=" O VAL K 365 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR K 411 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.797A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE K 430 " --> pdb=" O ILE K 448 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 264 through 265 removed outlier: 3.711A pdb=" N LEU L 308 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.973A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.973A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.893A pdb=" N VAL L 434 " --> pdb=" O THR L 444 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR L 444 " --> pdb=" O VAL L 434 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.561A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 247 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 267 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.772A pdb=" N ILE E 416 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 348 through 351 removed outlier: 4.344A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 412 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 401 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.724A pdb=" N LEU E 380 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 384 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 431 " --> pdb=" O LEU E 384 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS E 432 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 445 " --> pdb=" O CYS E 432 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 247 through 248 removed outlier: 3.690A pdb=" N THR H 267 " --> pdb=" O SER H 247 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.506A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.506A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 380 through 384 removed outlier: 3.533A pdb=" N MET H 433 " --> pdb=" O ARG H 382 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 431 " --> pdb=" O LEU H 384 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 248 through 249 removed outlier: 3.735A pdb=" N THR I 265 " --> pdb=" O HIS I 249 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.918A pdb=" N CYS I 323 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 336 " --> pdb=" O CYS I 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'I' and resid 350 through 352 removed outlier: 4.159A pdb=" N THR I 368 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER I 415 " --> pdb=" O CYS I 369 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 416 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 396 " --> pdb=" O ILE I 416 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 388 through 389 removed outlier: 3.670A pdb=" N LEU I 380 " --> pdb=" O GLY I 435 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 433 " --> pdb=" O ARG I 382 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU I 384 " --> pdb=" O SER I 431 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR I 444 " --> pdb=" O VAL I 434 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 245 through 246 removed outlier: 4.109A pdb=" N ARG J 245 " --> pdb=" O THR J 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR J 269 " --> pdb=" O ARG J 245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS J 266 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 348 through 352 removed outlier: 3.962A pdb=" N THR J 368 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL J 413 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA J 412 " --> pdb=" O ARG J 401 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG J 401 " --> pdb=" O ALA J 412 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 382 through 383 593 hydrogen bonds defined for protein. 1476 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: 6.87 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6758 1.34 - 1.46: 5228 1.46 - 1.59: 9690 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 21808 Sorted by residual: bond pdb=" C THR J 282 " pdb=" N PRO J 283 " ideal model delta sigma weight residual 1.333 1.388 -0.054 1.01e-02 9.80e+03 2.89e+01 bond pdb=" C GLN F 313 " pdb=" N PRO F 314 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.25e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" N GLU C 504 " pdb=" CA GLU C 504 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.44e+00 ... (remaining 21803 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.27: 665 105.27 - 112.61: 11921 112.61 - 119.95: 7091 119.95 - 127.29: 9895 127.29 - 134.63: 371 Bond angle restraints: 29943 Sorted by residual: angle pdb=" N PRO J 455 " pdb=" CA PRO J 455 " pdb=" CB PRO J 455 " ideal model delta sigma weight residual 103.25 111.96 -8.71 1.05e+00 9.07e-01 6.88e+01 angle pdb=" C ASN D 49 " pdb=" N ILE D 50 " pdb=" CA ILE D 50 " ideal model delta sigma weight residual 121.65 116.41 5.24 9.40e-01 1.13e+00 3.10e+01 angle pdb=" C LEU D 79 " pdb=" N ASP D 80 " pdb=" CA ASP D 80 " ideal model delta sigma weight residual 122.44 116.59 5.85 1.19e+00 7.06e-01 2.42e+01 angle pdb=" C LYS A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta sigma weight residual 120.60 128.42 -7.82 1.60e+00 3.91e-01 2.39e+01 angle pdb=" C ASN G 337 " pdb=" N ILE G 338 " pdb=" CA ILE G 338 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.00e+00 1.00e+00 2.32e+01 ... (remaining 29938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 12170 21.10 - 42.19: 954 42.19 - 63.29: 107 63.29 - 84.39: 30 84.39 - 105.49: 15 Dihedral angle restraints: 13276 sinusoidal: 4923 harmonic: 8353 Sorted by residual: dihedral pdb=" CB CYS E 369 " pdb=" SG CYS E 369 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS I 369 " pdb=" SG CYS I 369 " pdb=" SG CYS I 432 " pdb=" CB CYS I 432 " ideal model delta sinusoidal sigma weight residual 93.00 167.06 -74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ASN G 337 " pdb=" C ASN G 337 " pdb=" N ILE G 338 " pdb=" CA ILE G 338 " ideal model delta harmonic sigma weight residual 180.00 138.47 41.53 0 5.00e+00 4.00e-02 6.90e+01 ... (remaining 13273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3515 0.147 - 0.294: 117 0.294 - 0.441: 7 0.441 - 0.588: 0 0.588 - 0.735: 2 Chirality restraints: 3641 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN G 337 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 3638 not shown) Planarity restraints: 3838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 313 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO J 314 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO J 314 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 314 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 292 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO K 293 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO K 293 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 293 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 166 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO C 167 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " -0.043 5.00e-02 4.00e+02 ... (remaining 3835 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 726 2.69 - 3.24: 17451 3.24 - 3.79: 30297 3.79 - 4.35: 35726 4.35 - 4.90: 63891 Nonbonded interactions: 148091 Sorted by model distance: nonbonded pdb=" CG GLU C 504 " pdb=" N ASN C 505 " model vdw 2.132 3.520 nonbonded pdb=" O CYS E 432 " pdb=" OG1 THR E 444 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR L 320 " pdb=" O ILE L 338 " model vdw 2.243 2.440 nonbonded pdb=" N ASP C 503 " pdb=" OD1 ASP C 503 " model vdw 2.274 2.520 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.278 2.520 ... (remaining 148086 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 242 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 253 or (resid 254 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 25 \ 9 or (resid 260 through 262 and (name N or name CA or name C or name O or name C \ B )) or resid 263 through 270 or (resid 271 through 272 and (name N or name CA o \ r name C or name O or name CB )) or resid 276 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 through 387 or (resid 388 and (name N or name CA or name C or name O o \ r name CB )) or resid 389 through 391 or (resid 392 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 404 or (resid 405 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 417 or (resid 418 and (name N or name CA or name C or name O or name C \ B )) or resid 419 through 424 or (resid 425 through 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 or (resid 428 and (name N or name \ CA or name C or name O or name CB )) or resid 429 through 445 or (resid 446 and \ (name N or name CA or name C or name O or name CB )) or resid 447 through 449 or \ (resid 450 and (name N or name CA or name C or name O or name CB )) or (resid 4 \ 57 through 459 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 356 or (resid 357 through 363 and (name N or name CA or name \ C or name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 3 \ 91 or (resid 392 through 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 404 or (resid 405 through 406 and (name N or name CA \ or name C or name O or name CB )) or resid 407 through 417 or (resid 418 and (na \ me N or name CA or name C or name O or name CB )) or resid 419 through 424 or (r \ esid 425 through 426 and (name N or name CA or name C or name O or name CB )) or \ resid 427 or (resid 428 and (name N or name CA or name C or name O or name CB ) \ ) or resid 429 through 445 or (resid 446 and (name N or name CA or name C or nam \ e O or name CB )) or resid 447 through 449 or (resid 450 and (name N or name CA \ or name C or name O or name CB )) or (resid 457 through 459 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 417 o \ r (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 19 through 450 or (resid 457 through 459 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'F' and (resid 242 through 259 or (resid 260 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 272 or resid 276 t \ hrough 310 or (resid 311 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 356 or (resid \ 357 through 363 and (name N or name CA or name C or name O or name CB )) or res \ id 364 through 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 417 or (resid 418 and (name N or name CA or name C or nam \ e O or name CB )) or resid 419 through 424 or (resid 425 through 426 and (name N \ or name CA or name C or name O or name CB )) or resid 427 through 445 or (resid \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 449 or (resid 450 and (name N or name CA or name C or name O or name CB )) or \ (resid 457 through 459 and (name N or name CA or name C or name O or name CB )) \ )) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 316 or (resid 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 340 or (resid 341 and (name N or name CA \ or name C or name O or name CB )) or resid 342 through 345 or (resid 346 and (na \ me N or name CA or name C or name O or name CB )) or resid 347 through 356 or (r \ esid 357 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 4 \ 04 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 417 or (resid 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 421 or (resid 422 and (name N or name \ CA or name C or name O or name CB )) or resid 423 through 424 or (resid 425 thr \ ough 426 and (name N or name CA or name C or name O or name CB )) or resid 427 t \ hrough 445 or (resid 446 and (name N or name CA or name C or name O or name CB ) \ ) or resid 447 through 449 or (resid 450 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 457 through 459 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'H' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 14 through 417 or (resid 418 and (name N or name CA or name C or name O or name \ CB )) or resid 419 through 424 or (resid 425 through 426 and (name N or name CA \ or name C or name O or name CB )) or resid 427 through 450 or (resid 457 through \ 459 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 417 or (resid 418 and (na \ me N or name CA or name C or name O or name CB )) or resid 419 through 450 or (r \ esid 457 through 459 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 450 o \ r resid 457 through 459)) selection = (chain 'K' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 340 or (resid 341 and (na \ me N or name CA or name C or name O or name CB )) or resid 342 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 356 or (resid 357 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 392 or (resid \ 393 through 394 and (name N or name CA or name C or name O or name CB )) or res \ id 395 through 404 or (resid 405 through 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 417 or (resid 418 and (name N or name \ CA or name C or name O or name CB )) or resid 419 through 445 or (resid 446 and \ (name N or name CA or name C or name O or name CB )) or resid 447 through 450 o \ r (resid 457 through 459 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'L' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 345 or (resid 346 and (name N or name CA or name C or nam \ e O or name CB )) or resid 347 through 358 or (resid 359 through 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 376 or (resid \ 377 and (name N or name CA or name C or name O or name CB )) or resid 378 throu \ gh 392 or (resid 393 through 394 and (name N or name CA or name C or name O or n \ ame CB )) or resid 395 through 417 or (resid 418 and (name N or name CA or name \ C or name O or name CB )) or resid 419 through 425 or (resid 426 and (name N or \ name CA or name C or name O or name CB )) or resid 427 through 450 or (resid 457 \ through 459 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' } 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: 3.150 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: 0.020 Extract box with map and model: 13.390 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 56.310 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.130 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 0.009 0.097 21808 Z= 0.573 Angle : 1.161 13.926 29943 Z= 0.603 Chirality : 0.067 0.735 3641 Planarity : 0.009 0.089 3829 Dihedral : 15.177 105.485 7737 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.42 % Favored : 86.55 % Rotamer: Outliers : 0.84 % Allowed : 10.49 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -4.63 (0.13), residues: 2869 helix: -4.13 (0.23), residues: 178 sheet: -2.21 (0.16), residues: 898 loop : -3.62 (0.11), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 369 HIS 0.014 0.002 HIS H 436 PHE 0.032 0.003 PHE C 136 TYR 0.021 0.003 TYR F 395 ARG 0.006 0.001 ARG C 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 574 time to evaluate : 2.472 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: K 317 HIS cc_start: 0.6463 (m90) cc_final: 0.5538 (m90) REVERT: L 248 LEU cc_start: 0.7575 (pt) cc_final: 0.7372 (pt) REVERT: I 356 SER cc_start: 0.8219 (p) cc_final: 0.7804 (t) REVERT: J 265 THR cc_start: 0.6187 (t) cc_final: 0.5977 (m) REVERT: J 413 VAL cc_start: 0.6064 (t) cc_final: 0.5822 (p) REVERT: J 430 PHE cc_start: 0.7779 (m-80) cc_final: 0.7458 (m-80) outliers start: 18 outliers final: 9 residues processed: 588 average time/residue: 1.1844 time to fit residues: 794.3418 Evaluate side-chains 344 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 335 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 434 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 0.0020 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 343 ASN A 445 GLN B 327 HIS B 343 ASN B 406 GLN C 16 ASN C 133 ASN C 282 ASN C 314 GLN C 329 ASN C 530 GLN D 81 ASN ** K 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS H 459 ASN I 337 ASN J 385 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21808 Z= 0.329 Angle : 0.857 10.898 29943 Z= 0.417 Chirality : 0.050 0.634 3641 Planarity : 0.007 0.082 3829 Dihedral : 9.814 104.508 3453 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.60 % Favored : 89.37 % Rotamer: Outliers : 6.40 % Allowed : 20.79 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -3.83 (0.14), residues: 2869 helix: -3.15 (0.28), residues: 184 sheet: -1.78 (0.15), residues: 953 loop : -3.07 (0.13), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 424 HIS 0.011 0.001 HIS B 243 PHE 0.022 0.002 PHE E 430 TYR 0.012 0.002 TYR H 411 ARG 0.010 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 372 time to evaluate : 2.218 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: K 358 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6516 (tm-30) REVERT: I 380 LEU cc_start: 0.6152 (tt) cc_final: 0.5929 (tt) REVERT: I 395 TYR cc_start: 0.7110 (p90) cc_final: 0.5926 (p90) REVERT: J 265 THR cc_start: 0.6053 (t) cc_final: 0.5813 (m) REVERT: J 370 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8548 (tp) REVERT: J 410 THR cc_start: 0.7393 (t) cc_final: 0.6696 (t) REVERT: J 414 THR cc_start: 0.7434 (p) cc_final: 0.6848 (p) REVERT: J 430 PHE cc_start: 0.7811 (m-80) cc_final: 0.7508 (m-80) outliers start: 138 outliers final: 59 residues processed: 460 average time/residue: 1.0462 time to fit residues: 560.2650 Evaluate side-chains 382 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 322 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 315 TRP Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 306 SER Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 415 SER Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.0070 chunk 81 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 259 optimal weight: 0.3980 chunk 89 optimal weight: 0.0470 chunk 210 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN F 327 HIS K 291 GLN ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21808 Z= 0.201 Angle : 0.779 11.336 29943 Z= 0.372 Chirality : 0.047 0.607 3641 Planarity : 0.006 0.068 3829 Dihedral : 8.407 81.964 3443 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.30 % Favored : 91.67 % Rotamer: Outliers : 5.75 % Allowed : 23.76 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -3.24 (0.14), residues: 2869 helix: -2.52 (0.32), residues: 189 sheet: -1.18 (0.16), residues: 946 loop : -2.82 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.017 0.001 HIS K 317 PHE 0.022 0.001 PHE I 321 TYR 0.011 0.001 TYR E 395 ARG 0.012 0.001 ARG F 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 358 time to evaluate : 2.446 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: C 287 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6036 (p0) REVERT: D 45 ASN cc_start: 0.7767 (m-40) cc_final: 0.7402 (m110) REVERT: G 243 HIS cc_start: 0.6681 (t70) cc_final: 0.6306 (t70) REVERT: G 466 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7218 (pt0) REVERT: K 351 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8391 (tp) REVERT: K 358 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6514 (tm-30) REVERT: I 383 TRP cc_start: 0.7929 (m100) cc_final: 0.7624 (m-10) REVERT: J 257 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.4996 (tm) REVERT: J 265 THR cc_start: 0.6000 (t) cc_final: 0.5773 (m) REVERT: J 282 THR cc_start: 0.5891 (OUTLIER) cc_final: 0.5617 (p) REVERT: J 430 PHE cc_start: 0.7783 (m-80) cc_final: 0.7531 (m-80) outliers start: 124 outliers final: 57 residues processed: 437 average time/residue: 1.0161 time to fit residues: 516.8148 Evaluate side-chains 366 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 304 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 459 ASN Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 444 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 388 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN F 385 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 21808 Z= 0.331 Angle : 0.828 11.277 29943 Z= 0.398 Chirality : 0.048 0.653 3641 Planarity : 0.006 0.062 3829 Dihedral : 7.810 59.908 3443 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.15 % Favored : 88.81 % Rotamer: Outliers : 7.70 % Allowed : 23.48 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -3.10 (0.14), residues: 2869 helix: -2.03 (0.33), residues: 207 sheet: -1.14 (0.16), residues: 970 loop : -2.74 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 424 HIS 0.012 0.001 HIS K 317 PHE 0.018 0.002 PHE C 75 TYR 0.015 0.002 TYR H 411 ARG 0.016 0.001 ARG F 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 320 time to evaluate : 2.305 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: B 243 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6906 (t70) REVERT: C 138 THR cc_start: 0.3813 (OUTLIER) cc_final: 0.3594 (p) REVERT: G 243 HIS cc_start: 0.6550 (t70) cc_final: 0.5932 (t70) REVERT: G 466 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: K 358 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6589 (tm-30) REVERT: I 383 TRP cc_start: 0.8143 (m100) cc_final: 0.7853 (m-10) REVERT: I 433 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7075 (tmt) REVERT: J 370 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8308 (tt) REVERT: J 430 PHE cc_start: 0.7868 (m-80) cc_final: 0.7652 (m-80) outliers start: 166 outliers final: 88 residues processed: 438 average time/residue: 1.0294 time to fit residues: 525.3634 Evaluate side-chains 380 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 287 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 459 ASN Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 444 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 4.9990 chunk 158 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 249 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 388 GLN C 329 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21808 Z= 0.254 Angle : 0.778 11.183 29943 Z= 0.372 Chirality : 0.047 0.663 3641 Planarity : 0.005 0.062 3829 Dihedral : 7.422 59.860 3443 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.06 % Favored : 90.90 % Rotamer: Outliers : 7.24 % Allowed : 26.64 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.86 (0.15), residues: 2869 helix: -1.60 (0.36), residues: 200 sheet: -1.01 (0.16), residues: 986 loop : -2.61 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 315 HIS 0.022 0.001 HIS K 327 PHE 0.031 0.001 PHE I 321 TYR 0.011 0.001 TYR H 411 ARG 0.013 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 308 time to evaluate : 3.281 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: B 243 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6903 (t70) REVERT: C 192 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7537 (mm) REVERT: D 48 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7031 (mp0) REVERT: G 243 HIS cc_start: 0.6548 (t70) cc_final: 0.5913 (t70) REVERT: K 358 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6579 (tm-30) REVERT: L 433 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7050 (tpt) REVERT: I 433 MET cc_start: 0.7486 (ppp) cc_final: 0.7029 (tmt) REVERT: J 282 THR cc_start: 0.5533 (OUTLIER) cc_final: 0.5266 (p) outliers start: 156 outliers final: 95 residues processed: 421 average time/residue: 1.0094 time to fit residues: 497.2910 Evaluate side-chains 378 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 279 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 448 ILE Chi-restraints excluded: chain K residue 459 ASN Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.4980 chunk 250 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 388 GLN C 191 GLN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21808 Z= 0.214 Angle : 0.768 10.986 29943 Z= 0.363 Chirality : 0.046 0.681 3641 Planarity : 0.005 0.063 3829 Dihedral : 7.069 59.192 3443 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.32 % Rotamer: Outliers : 6.59 % Allowed : 28.07 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.66 (0.15), residues: 2869 helix: -1.40 (0.37), residues: 200 sheet: -0.78 (0.16), residues: 956 loop : -2.51 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 424 HIS 0.010 0.001 HIS H 327 PHE 0.021 0.001 PHE I 321 TYR 0.009 0.001 TYR H 411 ARG 0.014 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 311 time to evaluate : 2.751 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: F 338 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8569 (tp) REVERT: F 346 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7318 (ptt-90) REVERT: G 243 HIS cc_start: 0.6595 (t70) cc_final: 0.5950 (t70) REVERT: G 278 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (p) REVERT: G 466 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6871 (pt0) REVERT: K 358 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6623 (tm-30) REVERT: L 433 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6889 (tpt) REVERT: E 445 GLN cc_start: 0.7597 (tp-100) cc_final: 0.6010 (mt0) REVERT: I 351 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8043 (tt) REVERT: I 433 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7000 (tmt) REVERT: J 282 THR cc_start: 0.5548 (OUTLIER) cc_final: 0.5283 (p) REVERT: J 430 PHE cc_start: 0.7570 (m-80) cc_final: 0.7350 (m-80) outliers start: 142 outliers final: 86 residues processed: 413 average time/residue: 1.0273 time to fit residues: 495.2876 Evaluate side-chains 378 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 284 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 203 optimal weight: 0.1980 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 388 GLN C 373 GLN D 45 ASN D 81 ASN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 445 GLN ** L 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 HIS H 337 ASN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21808 Z= 0.271 Angle : 0.787 11.059 29943 Z= 0.375 Chirality : 0.047 0.690 3641 Planarity : 0.005 0.058 3829 Dihedral : 7.073 59.799 3442 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.62 % Favored : 90.35 % Rotamer: Outliers : 7.19 % Allowed : 28.31 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.61 (0.15), residues: 2869 helix: -1.22 (0.37), residues: 200 sheet: -0.78 (0.16), residues: 964 loop : -2.48 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 281 HIS 0.012 0.001 HIS H 327 PHE 0.019 0.001 PHE H 321 TYR 0.010 0.001 TYR B 472 ARG 0.016 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 296 time to evaluate : 2.488 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: C 192 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7494 (mm) REVERT: F 338 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8538 (tp) REVERT: F 346 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7294 (ptt-90) REVERT: G 243 HIS cc_start: 0.6620 (t70) cc_final: 0.6377 (t70) REVERT: G 278 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8025 (p) REVERT: G 466 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6803 (pt0) REVERT: K 358 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6738 (tm-30) REVERT: L 433 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: E 445 GLN cc_start: 0.7506 (tp-100) cc_final: 0.6034 (mt0) REVERT: I 351 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8076 (tt) REVERT: I 433 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7064 (tmt) REVERT: J 282 THR cc_start: 0.5417 (OUTLIER) cc_final: 0.5144 (p) REVERT: J 437 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7428 (pm20) outliers start: 155 outliers final: 92 residues processed: 406 average time/residue: 1.0190 time to fit residues: 484.3923 Evaluate side-chains 381 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 280 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 388 GLN C 329 ASN C 373 GLN ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 HIS H 327 HIS H 337 ASN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21808 Z= 0.266 Angle : 0.808 11.099 29943 Z= 0.385 Chirality : 0.047 0.687 3641 Planarity : 0.005 0.081 3829 Dihedral : 7.018 57.247 3442 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.13 % Favored : 90.83 % Rotamer: Outliers : 6.73 % Allowed : 28.63 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2869 helix: -1.10 (0.37), residues: 206 sheet: -0.78 (0.16), residues: 987 loop : -2.46 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 281 HIS 0.009 0.001 HIS H 327 PHE 0.017 0.001 PHE C 75 TYR 0.014 0.001 TYR D 63 ARG 0.018 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 292 time to evaluate : 2.275 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: C 453 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8024 (t) REVERT: F 338 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8520 (tp) REVERT: F 346 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7432 (ptt-90) REVERT: G 243 HIS cc_start: 0.6573 (t70) cc_final: 0.6262 (t70) REVERT: G 278 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8018 (p) REVERT: G 466 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6653 (pt0) REVERT: K 279 PHE cc_start: 0.7779 (m-80) cc_final: 0.7460 (m-80) REVERT: K 358 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6781 (tm-30) REVERT: L 433 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6213 (tpt) REVERT: E 445 GLN cc_start: 0.7539 (tp-100) cc_final: 0.6276 (mt0) REVERT: E 451 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5171 (pt) REVERT: I 345 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6561 (t80) REVERT: I 351 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8106 (tt) REVERT: I 433 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7086 (tmt) REVERT: I 449 ASP cc_start: 0.6906 (t0) cc_final: 0.6617 (t0) REVERT: J 282 THR cc_start: 0.5589 (OUTLIER) cc_final: 0.5312 (p) REVERT: J 364 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5651 (mm) REVERT: J 437 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7481 (pm20) outliers start: 145 outliers final: 85 residues processed: 397 average time/residue: 1.0057 time to fit residues: 466.2981 Evaluate side-chains 372 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 275 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 242 optimal weight: 0.7980 chunk 258 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 233 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 257 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 388 GLN C 373 GLN D 45 ASN ** G 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21808 Z= 0.209 Angle : 0.797 12.199 29943 Z= 0.377 Chirality : 0.046 0.681 3641 Planarity : 0.005 0.075 3829 Dihedral : 6.712 56.590 3442 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.95 % Rotamer: Outliers : 4.87 % Allowed : 30.53 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.15), residues: 2869 helix: -1.03 (0.38), residues: 207 sheet: -0.57 (0.16), residues: 974 loop : -2.36 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 281 HIS 0.008 0.001 HIS K 317 PHE 0.024 0.001 PHE H 321 TYR 0.010 0.001 TYR E 395 ARG 0.020 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 304 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LEU cc_start: 0.8378 (tt) cc_final: 0.8146 (mp) REVERT: C 453 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (t) REVERT: F 338 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8545 (tp) REVERT: F 346 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7480 (ptt-90) REVERT: G 243 HIS cc_start: 0.6558 (t70) cc_final: 0.6230 (t70) REVERT: G 466 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6530 (pt0) REVERT: K 279 PHE cc_start: 0.7775 (m-80) cc_final: 0.7472 (m-10) REVERT: K 358 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6740 (tm-30) REVERT: E 315 TRP cc_start: 0.5179 (t-100) cc_final: 0.4906 (t-100) REVERT: I 345 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6530 (t80) REVERT: I 351 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (tt) REVERT: I 433 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7150 (tmm) REVERT: I 449 ASP cc_start: 0.6943 (t0) cc_final: 0.6616 (t0) REVERT: J 282 THR cc_start: 0.5678 (OUTLIER) cc_final: 0.5396 (p) REVERT: J 376 PRO cc_start: 0.6003 (Cg_exo) cc_final: 0.5690 (Cg_endo) REVERT: J 437 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7634 (pm20) outliers start: 105 outliers final: 72 residues processed: 379 average time/residue: 1.0387 time to fit residues: 465.7196 Evaluate side-chains 362 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 282 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 343 ASN Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 6.9990 chunk 273 optimal weight: 0.0970 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 190 optimal weight: 0.0030 chunk 286 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 176 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 388 GLN C 329 ASN C 373 GLN ** G 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 21808 Z= 0.318 Angle : 1.041 59.176 29943 Z= 0.552 Chirality : 0.047 0.681 3641 Planarity : 0.005 0.074 3829 Dihedral : 6.705 56.599 3442 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.84 % Rotamer: Outliers : 4.32 % Allowed : 31.18 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.15), residues: 2869 helix: -1.01 (0.38), residues: 207 sheet: -0.56 (0.17), residues: 974 loop : -2.35 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 281 HIS 0.008 0.001 HIS K 317 PHE 0.015 0.001 PHE C 275 TYR 0.010 0.001 TYR E 395 ARG 0.017 0.001 ARG G 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 280 time to evaluate : 2.591 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: B 264 LEU cc_start: 0.8377 (tt) cc_final: 0.8148 (mp) REVERT: C 453 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7928 (t) REVERT: F 338 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8545 (tp) REVERT: F 346 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7478 (ptt-90) REVERT: G 243 HIS cc_start: 0.6556 (t70) cc_final: 0.6229 (t70) REVERT: G 278 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7976 (p) REVERT: G 466 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: K 279 PHE cc_start: 0.7775 (m-80) cc_final: 0.7475 (m-10) REVERT: K 358 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6740 (tm-30) REVERT: E 315 TRP cc_start: 0.5180 (t-100) cc_final: 0.4935 (t-100) REVERT: I 345 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6532 (t80) REVERT: I 351 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8072 (tt) REVERT: I 433 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7142 (tmm) REVERT: I 449 ASP cc_start: 0.6886 (t0) cc_final: 0.6571 (t0) REVERT: J 282 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5396 (p) REVERT: J 376 PRO cc_start: 0.6002 (Cg_exo) cc_final: 0.5770 (Cg_endo) REVERT: J 437 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7598 (pm20) outliers start: 93 outliers final: 78 residues processed: 349 average time/residue: 1.0396 time to fit residues: 424.4019 Evaluate side-chains 364 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 277 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 464 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 433 MET Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 378 ASP Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain J residue 282 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 0.0000 chunk 210 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 234 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN C 373 GLN D 45 ASN ** G 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.135319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100484 restraints weight = 55144.102| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.65 r_work: 0.3489 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 21808 Z= 0.351 Angle : 1.026 58.939 29943 Z= 0.575 Chirality : 0.047 0.681 3641 Planarity : 0.005 0.114 3829 Dihedral : 6.705 56.599 3442 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.84 % Rotamer: Outliers : 4.08 % Allowed : 31.42 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.15), residues: 2869 helix: -1.01 (0.38), residues: 207 sheet: -0.56 (0.17), residues: 974 loop : -2.35 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 281 HIS 0.008 0.001 HIS K 317 PHE 0.015 0.001 PHE C 275 TYR 0.010 0.001 TYR E 395 ARG 0.017 0.001 ARG G 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8618.10 seconds wall clock time: 152 minutes 22.34 seconds (9142.34 seconds total)