Starting phenix.real_space_refine on Sat Sep 28 12:51:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p62_20259/09_2024/6p62_20259.cif" } resolution = 3.57 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= -0.000 sd= 0.010 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 132 5.16 5 C 12021 2.51 5 N 3171 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "I" 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: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" 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: "Z" 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: "a" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.50, per 1000 atoms: 0.60 Number of scatterers: 19203 At special positions: 0 Unit cell: (149.35, 149.35, 115.36, 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 132 16.00 O 3879 8.00 N 3171 7.00 C 12021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.11 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.10 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.11 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.01 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.10 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35A" - pdb=" SG CYS C 50 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.11 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.10 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " BMA Q 3 " - " MAN Q 7 " " BMA W 3 " - " MAN W 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 703 " - " ASN A 160 " " NAG A 704 " - " ASN A 197 " " NAG A 718 " - " ASN A 295 " " NAG A 719 " - " ASN A 301 " " NAG A 720 " - " ASN A 332 " " NAG A 721 " - " ASN A 133 " " NAG A 722 " - " ASN A 339 " " NAG A 727 " - " ASN A 392 " " NAG A 728 " - " ASN A 448 " " NAG B 703 " - " ASN B 160 " " NAG B 704 " - " ASN B 197 " " NAG B 718 " - " ASN B 295 " " NAG B 719 " - " ASN B 301 " " NAG B 720 " - " ASN B 332 " " NAG B 721 " - " ASN B 133 " " NAG B 722 " - " ASN B 339 " " NAG B 727 " - " ASN B 392 " " NAG B 728 " - " ASN B 448 " " NAG E 703 " - " ASN E 160 " " NAG E 704 " - " ASN E 197 " " NAG E 718 " - " ASN E 295 " " NAG E 719 " - " ASN E 301 " " NAG E 720 " - " ASN E 332 " " NAG E 721 " - " ASN E 133 " " NAG E 722 " - " ASN E 339 " " NAG E 727 " - " ASN E 392 " " NAG E 728 " - " ASN E 448 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN B 156 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 276 " " NAG T 1 " - " ASN B 363 " " NAG U 1 " - " ASN B 386 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 234 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 363 " " NAG a 1 " - " ASN E 386 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.3 seconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 20.7% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.169A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.591A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 596 Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.907A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.864A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.593A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.898A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.592A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 544 " --> pdb=" O GLN E 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 546 " --> pdb=" O ARG E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 657 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 497 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.580A pdb=" N LEU H 18 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR B 132 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.828A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA B 316 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 309 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR B 318 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 301 " --> pdb=" O ILE B 323A" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU C 18 " --> pdb=" O MET C 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS E 201 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'G' and resid 48 through 49 745 hydrogen bonds defined for protein. 1866 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: 7.34 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5903 1.34 - 1.48: 5988 1.48 - 1.63: 7519 1.63 - 1.78: 83 1.78 - 1.93: 94 Bond restraints: 19587 Sorted by residual: bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.351 0.161 2.20e-02 2.07e+03 5.34e+01 bond pdb=" CB TYR D 36 " pdb=" CG TYR D 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.31e+01 bond pdb=" CB TYR G 36 " pdb=" CG TYR G 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.29e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.09e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.08e+01 ... (remaining 19582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 23757 2.82 - 5.64: 2539 5.64 - 8.46: 284 8.46 - 11.28: 36 11.28 - 14.10: 6 Bond angle restraints: 26622 Sorted by residual: angle pdb=" N ASP D 95B" pdb=" CA ASP D 95B" pdb=" C ASP D 95B" ideal model delta sigma weight residual 109.79 123.89 -14.10 1.56e+00 4.11e-01 8.17e+01 angle pdb=" N ASP G 95B" pdb=" CA ASP G 95B" pdb=" C ASP G 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.16e+01 angle pdb=" N ASP L 95B" pdb=" CA ASP L 95B" pdb=" C ASP L 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.15e+01 angle pdb=" N ARG G 61 " pdb=" CA ARG G 61 " pdb=" C ARG G 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.49e+01 angle pdb=" N ARG D 61 " pdb=" CA ARG D 61 " pdb=" C ARG D 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.48e+01 ... (remaining 26617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 12245 21.72 - 43.45: 316 43.45 - 65.17: 108 65.17 - 86.90: 45 86.90 - 108.62: 24 Dihedral angle restraints: 12738 sinusoidal: 6063 harmonic: 6675 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.36 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.39 47.61 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 12735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2398 0.109 - 0.218: 751 0.218 - 0.326: 88 0.326 - 0.435: 6 0.435 - 0.544: 12 Chirality restraints: 3255 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.51e+01 ... (remaining 3252 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN B 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN A 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.067 2.00e-02 2.50e+03 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5208 2.80 - 3.32: 17127 3.32 - 3.85: 31345 3.85 - 4.37: 37289 4.37 - 4.90: 61179 Nonbonded interactions: 152148 Sorted by model distance: nonbonded pdb=" O PRO H 100F" pdb=" OH TYR L 36 " model vdw 2.272 3.040 nonbonded pdb=" O PRO C 100F" pdb=" OH TYR D 36 " model vdw 2.272 3.040 nonbonded pdb=" O PRO F 100F" pdb=" OH TYR G 36 " model vdw 2.272 3.040 nonbonded pdb=" O3 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.363 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 2.363 3.040 ... (remaining 152143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'R' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.730 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.023 0.161 19587 Z= 1.461 Angle : 1.814 14.101 26622 Z= 1.165 Chirality : 0.103 0.544 3255 Planarity : 0.009 0.046 3273 Dihedral : 12.688 108.619 8337 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2286 helix: -0.34 (0.25), residues: 378 sheet: 0.04 (0.18), residues: 756 loop : -0.33 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP E 479 HIS 0.013 0.003 HIS B 105 PHE 0.044 0.007 PHE F 95 TYR 0.055 0.008 TYR L 92 ARG 0.008 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 578 time to evaluate : 2.020 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: A 99 ASN cc_start: 0.7815 (p0) cc_final: 0.7535 (t0) REVERT: A 424 ILE cc_start: 0.9068 (pt) cc_final: 0.8787 (pt) REVERT: A 426 MET cc_start: 0.8732 (tpt) cc_final: 0.8520 (tpt) REVERT: A 577 GLN cc_start: 0.7460 (mt0) cc_final: 0.7252 (tp40) REVERT: H 2 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7436 (mp10) REVERT: H 75 THR cc_start: 0.7991 (p) cc_final: 0.7631 (t) REVERT: L 65 SER cc_start: 0.8755 (p) cc_final: 0.8476 (m) REVERT: B 130 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7195 (mm-40) REVERT: B 174 SER cc_start: 0.8911 (t) cc_final: 0.8642 (p) REVERT: B 302 TYR cc_start: 0.7788 (m-80) cc_final: 0.7577 (m-10) REVERT: C 77 VAL cc_start: 0.8581 (t) cc_final: 0.8322 (p) REVERT: D 8 PRO cc_start: 0.7436 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: D 65 SER cc_start: 0.8689 (p) cc_final: 0.8377 (m) REVERT: E 54 CYS cc_start: 0.8508 (p) cc_final: 0.8114 (m) REVERT: E 99 ASN cc_start: 0.7591 (p0) cc_final: 0.7319 (t0) REVERT: E 104 MET cc_start: 0.8587 (ttt) cc_final: 0.8372 (ttt) REVERT: E 174 SER cc_start: 0.8972 (t) cc_final: 0.8748 (p) REVERT: E 577 GLN cc_start: 0.7692 (mt0) cc_final: 0.7435 (tp40) REVERT: F 2 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7295 (mp10) REVERT: F 86 ASP cc_start: 0.8065 (m-30) cc_final: 0.7712 (m-30) REVERT: G 52 SER cc_start: 0.9125 (p) cc_final: 0.8921 (t) REVERT: G 65 SER cc_start: 0.8669 (p) cc_final: 0.8356 (m) REVERT: G 74 THR cc_start: 0.8637 (m) cc_final: 0.8430 (p) outliers start: 3 outliers final: 3 residues processed: 581 average time/residue: 0.3176 time to fit residues: 274.0212 Evaluate side-chains 326 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 323 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain E residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 246 GLN A 352 HIS H 80 GLN B 103 GLN B 105 HIS B 352 HIS B 356 ASN B 425 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN E 105 HIS E 137 ASN E 352 HIS E 425 ASN E 428 GLN E 653 GLN F 80 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19587 Z= 0.263 Angle : 0.803 13.080 26622 Z= 0.423 Chirality : 0.049 0.194 3255 Planarity : 0.005 0.042 3273 Dihedral : 9.626 63.632 4209 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.65 % Allowed : 8.20 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2286 helix: 0.69 (0.28), residues: 384 sheet: -0.31 (0.18), residues: 738 loop : -0.61 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 479 HIS 0.003 0.001 HIS B 330 PHE 0.024 0.003 PHE H 95 TYR 0.017 0.002 TYR A 217 ARG 0.007 0.001 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 375 time to evaluate : 2.133 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: A 130 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7139 (mm-40) REVERT: A 530 MET cc_start: 0.7638 (mtp) cc_final: 0.7340 (mtp) REVERT: H 75 THR cc_start: 0.7878 (p) cc_final: 0.7557 (t) REVERT: L 65 SER cc_start: 0.8979 (p) cc_final: 0.8662 (m) REVERT: C 23 LYS cc_start: 0.8546 (tttt) cc_final: 0.8254 (tptt) REVERT: C 75 THR cc_start: 0.7883 (p) cc_final: 0.7658 (p) REVERT: D 8 PRO cc_start: 0.7137 (Cg_endo) cc_final: 0.6854 (Cg_exo) REVERT: D 61 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6844 (mtp180) REVERT: D 65 SER cc_start: 0.8877 (p) cc_final: 0.8608 (m) REVERT: D 77 ASP cc_start: 0.6540 (t0) cc_final: 0.6263 (t0) REVERT: E 54 CYS cc_start: 0.8480 (p) cc_final: 0.8224 (m) REVERT: E 130 GLN cc_start: 0.7671 (mm-40) cc_final: 0.6827 (mm-40) REVERT: E 461 THR cc_start: 0.8686 (m) cc_final: 0.8458 (m) REVERT: E 530 MET cc_start: 0.7614 (mtp) cc_final: 0.7328 (mtp) REVERT: E 577 GLN cc_start: 0.7663 (mt0) cc_final: 0.7409 (tp40) REVERT: F 23 LYS cc_start: 0.8589 (tttt) cc_final: 0.8146 (tptt) REVERT: F 102 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8122 (mp) REVERT: G 65 SER cc_start: 0.8843 (p) cc_final: 0.8592 (m) REVERT: G 74 THR cc_start: 0.8765 (m) cc_final: 0.8547 (p) outliers start: 53 outliers final: 32 residues processed: 402 average time/residue: 0.2750 time to fit residues: 173.7135 Evaluate side-chains 323 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 290 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN E 540 GLN F 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19587 Z= 0.343 Angle : 0.744 10.868 26622 Z= 0.387 Chirality : 0.047 0.205 3255 Planarity : 0.005 0.044 3273 Dihedral : 7.895 47.977 4209 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.75 % Allowed : 9.20 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2286 helix: 0.60 (0.28), residues: 387 sheet: -0.38 (0.18), residues: 744 loop : -0.95 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 47 HIS 0.008 0.001 HIS A 66 PHE 0.025 0.003 PHE C 95 TYR 0.018 0.002 TYR D 36 ARG 0.008 0.001 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 293 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 THR cc_start: 0.9218 (t) cc_final: 0.8998 (m) REVERT: L 63 SER cc_start: 0.8984 (m) cc_final: 0.8712 (p) REVERT: L 65 SER cc_start: 0.8859 (p) cc_final: 0.8614 (m) REVERT: B 104 MET cc_start: 0.8715 (ttm) cc_final: 0.8399 (ttt) REVERT: B 652 GLN cc_start: 0.7099 (tp40) cc_final: 0.6896 (tp40) REVERT: D 8 PRO cc_start: 0.7380 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: D 61 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7129 (mtp85) REVERT: D 65 SER cc_start: 0.8841 (p) cc_final: 0.8602 (m) REVERT: D 74 THR cc_start: 0.8990 (m) cc_final: 0.8666 (p) REVERT: E 54 CYS cc_start: 0.8490 (p) cc_final: 0.8273 (m) REVERT: F 80 GLN cc_start: 0.7249 (mp-120) cc_final: 0.7036 (mp10) REVERT: F 102 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8179 (mp) outliers start: 75 outliers final: 47 residues processed: 338 average time/residue: 0.2809 time to fit residues: 152.2422 Evaluate side-chains 308 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19587 Z= 0.233 Angle : 0.656 10.360 26622 Z= 0.337 Chirality : 0.045 0.208 3255 Planarity : 0.004 0.046 3273 Dihedral : 6.708 38.210 4209 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.55 % Allowed : 10.14 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2286 helix: 0.70 (0.28), residues: 387 sheet: -0.24 (0.19), residues: 747 loop : -1.05 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 62 HIS 0.003 0.001 HIS A 352 PHE 0.020 0.002 PHE A 522 TYR 0.020 0.002 TYR G 67 ARG 0.007 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 284 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7231 (tp40) cc_final: 0.7022 (tp40) REVERT: L 63 SER cc_start: 0.8921 (m) cc_final: 0.8671 (p) REVERT: L 65 SER cc_start: 0.8786 (p) cc_final: 0.8510 (m) REVERT: L 105 VAL cc_start: 0.6086 (t) cc_final: 0.5847 (t) REVERT: B 104 MET cc_start: 0.8682 (ttm) cc_final: 0.8360 (ttt) REVERT: B 323 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 482 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7512 (mm-30) REVERT: D 8 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.7127 (Cg_exo) REVERT: E 54 CYS cc_start: 0.8565 (p) cc_final: 0.8228 (m) REVERT: E 651 ASN cc_start: 0.7498 (m-40) cc_final: 0.7213 (t0) REVERT: F 80 GLN cc_start: 0.7247 (mp-120) cc_final: 0.6995 (mp10) REVERT: F 86 ASP cc_start: 0.7800 (m-30) cc_final: 0.7255 (m-30) REVERT: G 103 GLU cc_start: 0.7827 (tp30) cc_final: 0.7558 (tt0) outliers start: 71 outliers final: 57 residues processed: 326 average time/residue: 0.2844 time to fit residues: 149.2527 Evaluate side-chains 306 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 248 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN D 38 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN G 37 GLN G 38 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19587 Z= 0.484 Angle : 0.822 13.660 26622 Z= 0.415 Chirality : 0.049 0.200 3255 Planarity : 0.005 0.054 3273 Dihedral : 7.378 43.431 4209 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.25 % Allowed : 10.49 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2286 helix: 0.36 (0.27), residues: 387 sheet: -0.57 (0.19), residues: 777 loop : -1.31 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 623 HIS 0.006 0.001 HIS A 352 PHE 0.028 0.003 PHE F 95 TYR 0.027 0.002 TYR G 67 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 276 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7543 (tp40) cc_final: 0.7330 (tp40) REVERT: H 2 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7531 (mp10) REVERT: L 63 SER cc_start: 0.9054 (m) cc_final: 0.8781 (p) REVERT: L 65 SER cc_start: 0.8697 (p) cc_final: 0.8458 (m) REVERT: L 105 VAL cc_start: 0.6032 (t) cc_final: 0.5653 (m) REVERT: B 323 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 482 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 54 CYS cc_start: 0.8646 (p) cc_final: 0.8200 (m) REVERT: E 482 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 651 ASN cc_start: 0.7575 (m-40) cc_final: 0.7356 (t0) REVERT: F 2 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7201 (mp10) REVERT: F 81 MET cc_start: 0.6929 (mtm) cc_final: 0.6553 (mtm) outliers start: 85 outliers final: 63 residues processed: 332 average time/residue: 0.2482 time to fit residues: 135.3671 Evaluate side-chains 316 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 252 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19587 Z= 0.205 Angle : 0.652 11.016 26622 Z= 0.333 Chirality : 0.045 0.301 3255 Planarity : 0.004 0.052 3273 Dihedral : 6.453 36.851 4207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.50 % Allowed : 12.09 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2286 helix: 0.93 (0.29), residues: 369 sheet: -0.48 (0.18), residues: 798 loop : -1.38 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 62 HIS 0.004 0.001 HIS B 66 PHE 0.013 0.002 PHE F 95 TYR 0.021 0.001 TYR G 67 ARG 0.005 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 272 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7205 (t0) REVERT: H 2 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7395 (mp10) REVERT: H 81 MET cc_start: 0.6852 (mtm) cc_final: 0.6644 (mtm) REVERT: L 65 SER cc_start: 0.8658 (p) cc_final: 0.8390 (m) REVERT: L 103 GLU cc_start: 0.8035 (tp30) cc_final: 0.7507 (tt0) REVERT: B 323 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8900 (tt) REVERT: B 482 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 2 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7654 (mp10) REVERT: C 62 TRP cc_start: 0.8268 (p-90) cc_final: 0.7774 (p-90) REVERT: C 81 MET cc_start: 0.6817 (mtm) cc_final: 0.6488 (mtt) REVERT: E 54 CYS cc_start: 0.8523 (p) cc_final: 0.8238 (m) REVERT: E 103 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8269 (tm-30) REVERT: E 482 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7660 (mm-30) REVERT: F 2 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7560 (mp10) REVERT: F 7 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7136 (m) REVERT: F 86 ASP cc_start: 0.7869 (m-30) cc_final: 0.7440 (m-30) outliers start: 70 outliers final: 52 residues processed: 314 average time/residue: 0.2430 time to fit residues: 126.5157 Evaluate side-chains 307 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19587 Z= 0.342 Angle : 0.711 9.843 26622 Z= 0.361 Chirality : 0.046 0.214 3255 Planarity : 0.004 0.053 3273 Dihedral : 6.604 40.788 4207 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.65 % Allowed : 11.99 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2286 helix: 0.86 (0.29), residues: 369 sheet: -0.50 (0.19), residues: 777 loop : -1.46 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS L 38 PHE 0.018 0.002 PHE H 95 TYR 0.026 0.002 TYR G 67 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 256 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7686 (mp10) REVERT: H 33 TYR cc_start: 0.8518 (m-80) cc_final: 0.8279 (m-10) REVERT: L 65 SER cc_start: 0.8701 (p) cc_final: 0.8368 (m) REVERT: B 323 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 482 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 651 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7027 (t0) REVERT: C 2 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7714 (mp10) REVERT: C 33 TYR cc_start: 0.8454 (m-80) cc_final: 0.8176 (m-10) REVERT: C 70 SER cc_start: 0.8619 (t) cc_final: 0.8400 (m) REVERT: C 81 MET cc_start: 0.6877 (mtm) cc_final: 0.6604 (mtt) REVERT: E 54 CYS cc_start: 0.8609 (p) cc_final: 0.8256 (m) REVERT: E 103 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 482 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7723 (mm-30) REVERT: F 2 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7586 (mp10) REVERT: F 7 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7239 (m) outliers start: 73 outliers final: 64 residues processed: 302 average time/residue: 0.2418 time to fit residues: 120.6549 Evaluate side-chains 307 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19587 Z= 0.235 Angle : 0.660 13.189 26622 Z= 0.337 Chirality : 0.045 0.442 3255 Planarity : 0.004 0.052 3273 Dihedral : 6.337 38.655 4207 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.25 % Allowed : 13.09 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2286 helix: 1.07 (0.29), residues: 363 sheet: -0.47 (0.18), residues: 813 loop : -1.56 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 62 HIS 0.003 0.001 HIS L 38 PHE 0.014 0.002 PHE H 95 TYR 0.022 0.001 TYR G 67 ARG 0.004 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 259 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7110 (t0) REVERT: H 2 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7466 (mp10) REVERT: L 103 GLU cc_start: 0.8184 (tp30) cc_final: 0.7688 (tt0) REVERT: B 323 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8913 (tt) REVERT: B 482 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 2 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7717 (mp10) REVERT: C 81 MET cc_start: 0.6833 (mtm) cc_final: 0.6616 (mtt) REVERT: E 54 CYS cc_start: 0.8530 (p) cc_final: 0.8246 (m) REVERT: E 103 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8337 (tm-30) REVERT: E 150 MET cc_start: 0.7578 (ttm) cc_final: 0.7271 (ttm) REVERT: E 482 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 577 GLN cc_start: 0.7615 (mt0) cc_final: 0.7402 (tp40) REVERT: F 2 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7592 (mp10) REVERT: F 7 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7399 (m) REVERT: F 86 ASP cc_start: 0.7901 (m-30) cc_final: 0.7457 (m-30) outliers start: 65 outliers final: 54 residues processed: 300 average time/residue: 0.2535 time to fit residues: 125.3796 Evaluate side-chains 303 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 246 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19587 Z= 0.249 Angle : 0.665 12.887 26622 Z= 0.338 Chirality : 0.045 0.323 3255 Planarity : 0.004 0.053 3273 Dihedral : 6.237 39.160 4207 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.05 % Allowed : 13.89 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2286 helix: 1.13 (0.29), residues: 360 sheet: -0.42 (0.19), residues: 777 loop : -1.57 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 571 HIS 0.002 0.001 HIS L 38 PHE 0.015 0.002 PHE H 95 TYR 0.023 0.001 TYR G 67 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 253 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7475 (mp10) REVERT: L 103 GLU cc_start: 0.8169 (tp30) cc_final: 0.7692 (tt0) REVERT: B 323 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8917 (tt) REVERT: B 482 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7513 (mm-30) REVERT: C 2 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7623 (mp10) REVERT: E 54 CYS cc_start: 0.8522 (p) cc_final: 0.8245 (m) REVERT: E 103 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8348 (tm-30) REVERT: E 150 MET cc_start: 0.7628 (ttm) cc_final: 0.7313 (ttm) REVERT: E 482 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7658 (mm-30) REVERT: E 577 GLN cc_start: 0.7637 (mt0) cc_final: 0.7419 (tp40) REVERT: F 2 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7564 (mp10) REVERT: F 7 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7431 (m) REVERT: F 86 ASP cc_start: 0.7912 (m-30) cc_final: 0.7516 (m-30) outliers start: 61 outliers final: 53 residues processed: 295 average time/residue: 0.2390 time to fit residues: 117.0529 Evaluate side-chains 301 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19587 Z= 0.304 Angle : 0.698 13.293 26622 Z= 0.356 Chirality : 0.046 0.300 3255 Planarity : 0.004 0.054 3273 Dihedral : 6.522 56.680 4207 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.10 % Allowed : 13.74 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2286 helix: 1.01 (0.29), residues: 363 sheet: -0.53 (0.19), residues: 792 loop : -1.65 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 571 HIS 0.003 0.001 HIS G 38 PHE 0.017 0.002 PHE H 95 TYR 0.025 0.002 TYR G 67 ARG 0.006 0.000 ARG D 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 253 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7445 (mp10) REVERT: H 33 TYR cc_start: 0.8487 (m-80) cc_final: 0.8263 (m-10) REVERT: B 246 GLN cc_start: 0.6931 (pm20) cc_final: 0.6373 (tt0) REVERT: B 323 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8928 (tt) REVERT: B 482 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 2 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7679 (mp10) REVERT: C 7 SER cc_start: 0.8331 (p) cc_final: 0.7612 (m) REVERT: E 54 CYS cc_start: 0.8557 (p) cc_final: 0.8260 (m) REVERT: E 103 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 150 MET cc_start: 0.7735 (ttm) cc_final: 0.7447 (ttm) REVERT: E 482 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7721 (mm-30) REVERT: E 577 GLN cc_start: 0.7689 (mt0) cc_final: 0.7474 (tp40) REVERT: F 2 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7607 (mp10) REVERT: F 7 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7522 (m) REVERT: F 86 ASP cc_start: 0.7950 (m-30) cc_final: 0.7568 (m-30) outliers start: 62 outliers final: 54 residues processed: 293 average time/residue: 0.2436 time to fit residues: 118.3463 Evaluate side-chains 303 residues out of total 2001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 651 ASN B 72 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092134 restraints weight = 37256.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094838 restraints weight = 22665.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096651 restraints weight = 16429.561| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19587 Z= 0.186 Angle : 0.630 14.214 26622 Z= 0.324 Chirality : 0.044 0.289 3255 Planarity : 0.004 0.054 3273 Dihedral : 6.091 54.605 4207 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.45 % Allowed : 14.54 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.18), residues: 2286 helix: 1.16 (0.29), residues: 363 sheet: -0.37 (0.19), residues: 777 loop : -1.57 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 571 HIS 0.002 0.001 HIS B 249 PHE 0.013 0.001 PHE C 95 TYR 0.022 0.001 TYR G 67 ARG 0.004 0.000 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.54 seconds wall clock time: 65 minutes 46.44 seconds (3946.44 seconds total)