Starting phenix.real_space_refine on Sat Mar 23 02:54:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooi_17016/03_2024/8ooi_17016_updated.pdb" } resolution = 2.61 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= 0.001 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: 7 Type Number sf(0) Gaussians K 6 8.98 5 P 42 5.49 5 Mg 18 5.21 5 S 180 5.16 5 C 21966 2.51 5 N 6210 2.21 5 O 6834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 673": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35256 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "F" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "B" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "D" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "C" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "E" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 734, 5754 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 5818 Chain: "A" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "F" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "B" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "D" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "C" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "E" Number of atoms: 72 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Conformer: "B" Number of residues, atoms: 6, 66 Unusual residues: {' K': 1, ' MG': 2, 'ADP': 1, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} bond proxies already assigned to first conformer: 62 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AHIS A 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 384 " occ=0.50 residue: pdb=" N AHIS F 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 384 " occ=0.50 residue: pdb=" N AHIS B 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 384 " occ=0.50 residue: pdb=" N AHIS D 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 384 " occ=0.50 residue: pdb=" N AHIS C 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 384 " occ=0.50 residue: pdb=" N AHIS E 384 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 384 " occ=0.50 residue: pdb="MG A MG A 904 " occ=0.50 pdb="MG B MG A 904 " occ=0.50 residue: pdb=" O1 APO4 A 906 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 A 906 " occ=0.50 residue: pdb=" O1 APO4 F 901 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 F 901 " occ=0.50 residue: pdb="MG A MG F 905 " occ=0.50 pdb="MG B MG F 905 " occ=0.50 residue: pdb="MG A MG B 904 " occ=0.50 pdb="MG B MG B 904 " occ=0.50 residue: pdb=" O1 APO4 B 906 " occ=0.50 ... (8 atoms not shown) pdb=" P BPO4 B 906 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 33.09, per 1000 atoms: 0.94 Number of scatterers: 35256 At special positions: 0 Unit cell: (170.64, 177.84, 100.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 6 19.00 S 180 16.00 P 42 15.00 Mg 18 11.99 O 6834 8.00 N 6210 7.00 C 21966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 695 " distance=2.06 Simple disulfide: pdb=" SG CYS F 691 " - pdb=" SG CYS F 695 " distance=2.06 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 695 " distance=2.06 Simple disulfide: pdb=" SG CYS D 691 " - pdb=" SG CYS D 695 " distance=2.06 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 695 " distance=2.06 Simple disulfide: pdb=" SG CYS E 691 " - pdb=" SG CYS E 695 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.78 Conformation dependent library (CDL) restraints added in 13.4 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 36 sheets defined 39.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.02 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.511A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.785A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.696A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.769A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 709 removed outlier: 3.799A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.949A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.511A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 398 through 401 No H-bonds generated for 'chain 'F' and resid 398 through 401' Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.784A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.696A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.769A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 709 removed outlier: 3.800A pdb=" N LYS F 696 " --> pdb=" O GLN F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.949A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 763 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.511A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.785A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.696A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.768A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 709 removed outlier: 3.799A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.949A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 763 Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.510A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 231' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 398 through 401 No H-bonds generated for 'chain 'D' and resid 398 through 401' Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.784A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.697A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.769A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 709 removed outlier: 3.799A pdb=" N LYS D 696 " --> pdb=" O GLN D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.949A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 763 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.511A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 231' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 398 through 401 No H-bonds generated for 'chain 'C' and resid 398 through 401' Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.784A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.696A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.769A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 709 removed outlier: 3.799A pdb=" N LYS C 696 " --> pdb=" O GLN C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.948A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.452A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.511A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 231' Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 336 removed outlier: 3.902A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 398 through 401 No H-bonds generated for 'chain 'E' and resid 398 through 401' Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.785A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.696A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.768A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 709 removed outlier: 3.799A pdb=" N LYS E 696 " --> pdb=" O GLN E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.949A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 763 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 8.521A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= D, first strand: chain 'A' and resid 151 through 156 removed outlier: 7.082A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.387A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 27 through 30 Processing sheet with id= H, first strand: chain 'F' and resid 38 through 41 removed outlier: 8.522A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= J, first strand: chain 'F' and resid 151 through 156 removed outlier: 7.083A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.386A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= N, first strand: chain 'B' and resid 38 through 41 removed outlier: 8.521A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= P, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.083A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.386A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= T, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.521A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= V, first strand: chain 'D' and resid 151 through 156 removed outlier: 7.083A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.387A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= Z, first strand: chain 'C' and resid 38 through 41 removed outlier: 8.521A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= AB, first strand: chain 'C' and resid 151 through 156 removed outlier: 7.082A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.387A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 27 through 30 Processing sheet with id= AF, first strand: chain 'E' and resid 38 through 41 removed outlier: 8.522A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AH, first strand: chain 'E' and resid 151 through 156 removed outlier: 7.082A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.387A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.201A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3060 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: 12.68 Time building geometry restraints manager: 16.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 12060 1.36 - 1.49: 8150 1.49 - 1.63: 15202 1.63 - 1.77: 6 1.77 - 1.91: 282 Bond restraints: 35700 Sorted by residual: bond pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.27e-02 6.20e+03 1.54e+01 bond pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.27e-02 6.20e+03 1.53e+01 bond pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 bond pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 bond pdb=" CA ARG D 349 " pdb=" CB ARG D 349 " ideal model delta sigma weight residual 1.528 1.478 0.049 1.27e-02 6.20e+03 1.52e+01 ... (remaining 35695 not shown) Histogram of bond angle deviations from ideal: 99.01 - 107.15: 1395 107.15 - 115.29: 21725 115.29 - 123.43: 24083 123.43 - 131.57: 1031 131.57 - 139.71: 48 Bond angle restraints: 48282 Sorted by residual: angle pdb=" N ASN E 348 " pdb=" CA ASN E 348 " pdb=" C ASN E 348 " ideal model delta sigma weight residual 113.17 103.62 9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N ASN F 348 " pdb=" CA ASN F 348 " pdb=" C ASN F 348 " ideal model delta sigma weight residual 113.17 103.63 9.54 1.26e+00 6.30e-01 5.74e+01 angle pdb=" N ASN B 348 " pdb=" CA ASN B 348 " pdb=" C ASN B 348 " ideal model delta sigma weight residual 113.17 103.63 9.54 1.26e+00 6.30e-01 5.73e+01 angle pdb=" N ASN D 348 " pdb=" CA ASN D 348 " pdb=" C ASN D 348 " ideal model delta sigma weight residual 113.17 103.68 9.49 1.26e+00 6.30e-01 5.67e+01 angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 113.17 103.69 9.48 1.26e+00 6.30e-01 5.66e+01 ... (remaining 48277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 21480 33.37 - 66.75: 648 66.75 - 100.12: 54 100.12 - 133.50: 12 133.50 - 166.87: 6 Dihedral angle restraints: 22200 sinusoidal: 9474 harmonic: 12726 Sorted by residual: dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 106.88 -166.87 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 106.84 -166.84 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 106.84 -166.83 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 22197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4386 0.058 - 0.116: 862 0.116 - 0.174: 122 0.174 - 0.232: 0 0.232 - 0.290: 12 Chirality restraints: 5382 Sorted by residual: chirality pdb=" CA SER F 352 " pdb=" N SER F 352 " pdb=" C SER F 352 " pdb=" CB SER F 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA SER D 352 " pdb=" N SER D 352 " pdb=" C SER D 352 " pdb=" CB SER D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5379 not shown) Planarity restraints: 6324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO C 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 298 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO E 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 ... (remaining 6321 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.23: 22 2.23 - 2.96: 16617 2.96 - 3.68: 64253 3.68 - 4.41: 107288 4.41 - 5.14: 172154 Nonbonded interactions: 360334 Sorted by model distance: nonbonded pdb=" SD MET A 427 " pdb=" OE2 GLU F 221 " model vdw 1.501 3.400 nonbonded pdb=" SD MET F 427 " pdb=" OE2 GLU E 221 " model vdw 1.501 3.400 nonbonded pdb=" SD MET D 427 " pdb=" OE2 GLU C 221 " model vdw 1.507 3.400 nonbonded pdb=" OE2 GLU B 221 " pdb=" SD MET C 427 " model vdw 1.534 3.400 nonbonded pdb=" OE2 GLU A 221 " pdb=" SD MET B 427 " model vdw 1.630 3.400 ... (remaining 360329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'B' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'C' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'D' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'E' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) selection = (chain 'F' and (resid 22 through 358 or resid 361 through 383 or resid 385 throu \ gh 775)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.720 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 120.790 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.005 0.098 35700 Z= 0.349 Angle : 0.704 9.553 48282 Z= 0.382 Chirality : 0.048 0.290 5382 Planarity : 0.005 0.062 6324 Dihedral : 15.387 166.872 13938 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.53 % Favored : 95.05 % Rotamer: Outliers : 0.16 % Allowed : 11.66 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.61 (0.13), residues: 4398 helix: 0.23 (0.12), residues: 1908 sheet: -0.33 (0.21), residues: 576 loop : -0.99 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 454 HIS 0.004 0.001 HIS F 317 PHE 0.009 0.001 PHE D 736 TYR 0.024 0.002 TYR C 244 ARG 0.006 0.001 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7243 (mm) cc_final: 0.6857 (mp) REVERT: A 388 MET cc_start: 0.7640 (mtp) cc_final: 0.7310 (mtt) REVERT: A 670 VAL cc_start: 0.6916 (m) cc_final: 0.6712 (t) REVERT: F 26 LEU cc_start: 0.7050 (mm) cc_final: 0.6630 (mp) REVERT: F 388 MET cc_start: 0.7490 (mtp) cc_final: 0.7224 (mtt) REVERT: F 670 VAL cc_start: 0.6991 (m) cc_final: 0.6759 (t) REVERT: F 700 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7202 (ttp-170) REVERT: B 26 LEU cc_start: 0.7202 (mm) cc_final: 0.6892 (mp) REVERT: B 45 LYS cc_start: 0.5897 (tppt) cc_final: 0.5600 (tmtt) REVERT: B 288 LYS cc_start: 0.8267 (ttmp) cc_final: 0.8050 (tmmt) REVERT: B 388 MET cc_start: 0.7702 (mtp) cc_final: 0.7441 (mtt) REVERT: B 670 VAL cc_start: 0.6970 (m) cc_final: 0.6725 (t) REVERT: D 26 LEU cc_start: 0.7217 (mm) cc_final: 0.6903 (mp) REVERT: D 388 MET cc_start: 0.7732 (mtp) cc_final: 0.7396 (mtt) REVERT: C 26 LEU cc_start: 0.7137 (mm) cc_final: 0.6806 (mp) REVERT: C 388 MET cc_start: 0.7554 (mtp) cc_final: 0.7309 (mtt) REVERT: E 26 LEU cc_start: 0.7101 (mm) cc_final: 0.6749 (mp) REVERT: E 45 LYS cc_start: 0.5943 (tppt) cc_final: 0.5594 (tmtt) REVERT: E 63 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6964 (tppp) REVERT: E 288 LYS cc_start: 0.8279 (ttmp) cc_final: 0.8063 (tmmt) REVERT: E 388 MET cc_start: 0.7763 (mtp) cc_final: 0.7487 (mtt) REVERT: E 670 VAL cc_start: 0.6888 (m) cc_final: 0.6677 (t) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 1.5688 time to fit residues: 1092.5170 Evaluate side-chains 396 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 397 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN F 215 GLN F 351 ASN F 404 HIS F 760 GLN B 404 HIS D 351 ASN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN E 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 35700 Z= 0.276 Angle : 0.631 9.041 48282 Z= 0.317 Chirality : 0.045 0.135 5382 Planarity : 0.005 0.058 6324 Dihedral : 11.642 179.387 5094 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 3.73 % Allowed : 15.18 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.49 (0.13), residues: 4398 helix: 0.30 (0.12), residues: 1926 sheet: -0.47 (0.20), residues: 648 loop : -0.83 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 454 HIS 0.006 0.001 HIS E 404 PHE 0.011 0.001 PHE E 563 TYR 0.013 0.002 TYR D 203 ARG 0.006 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 400 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7399 (mm) cc_final: 0.7073 (mp) REVERT: A 291 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: A 388 MET cc_start: 0.7677 (mtp) cc_final: 0.7454 (mtt) REVERT: F 26 LEU cc_start: 0.7308 (mm) cc_final: 0.6986 (mp) REVERT: F 60 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6454 (mtmm) REVERT: F 268 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8820 (tt) REVERT: F 670 VAL cc_start: 0.7002 (m) cc_final: 0.6756 (t) REVERT: B 26 LEU cc_start: 0.7518 (mm) cc_final: 0.7108 (mt) REVERT: B 268 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8794 (tt) REVERT: B 288 LYS cc_start: 0.8324 (ttmp) cc_final: 0.8073 (tmmt) REVERT: B 291 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: B 388 MET cc_start: 0.7758 (mtp) cc_final: 0.7527 (mtt) REVERT: D 26 LEU cc_start: 0.7420 (mm) cc_final: 0.7079 (mp) REVERT: D 291 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: D 388 MET cc_start: 0.7738 (mtp) cc_final: 0.7501 (mtt) REVERT: C 26 LEU cc_start: 0.7423 (mm) cc_final: 0.7065 (mp) REVERT: C 60 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6571 (mtmm) REVERT: C 268 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 388 MET cc_start: 0.7715 (mtp) cc_final: 0.7510 (mtt) REVERT: C 700 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7537 (ttp-170) REVERT: C 738 GLU cc_start: 0.7488 (tt0) cc_final: 0.7183 (tt0) REVERT: E 26 LEU cc_start: 0.7382 (mm) cc_final: 0.6992 (mt) REVERT: E 268 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8807 (tt) REVERT: E 288 LYS cc_start: 0.8322 (ttmp) cc_final: 0.8078 (tmmt) REVERT: E 388 MET cc_start: 0.7787 (mtp) cc_final: 0.7538 (mtt) outliers start: 134 outliers final: 68 residues processed: 499 average time/residue: 1.5155 time to fit residues: 902.8001 Evaluate side-chains 424 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 346 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 652 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.0570 chunk 123 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 398 optimal weight: 0.9980 chunk 430 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 319 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS F 226 HIS B 404 HIS D 404 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35700 Z= 0.177 Angle : 0.573 7.423 48282 Z= 0.285 Chirality : 0.043 0.191 5382 Planarity : 0.004 0.060 6324 Dihedral : 11.111 174.443 5094 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.58 % Favored : 95.08 % Rotamer: Outliers : 2.72 % Allowed : 17.60 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.23 (0.13), residues: 4398 helix: 0.60 (0.12), residues: 1884 sheet: -0.48 (0.20), residues: 672 loop : -0.71 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 454 HIS 0.006 0.001 HIS C 226 PHE 0.011 0.001 PHE C 131 TYR 0.019 0.001 TYR F 203 ARG 0.010 0.000 ARG F 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 396 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7305 (mm) cc_final: 0.6980 (mp) REVERT: A 291 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 388 MET cc_start: 0.7693 (mtp) cc_final: 0.7477 (mtt) REVERT: A 761 THR cc_start: 0.7697 (p) cc_final: 0.7493 (t) REVERT: F 268 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8678 (tt) REVERT: F 292 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: F 388 MET cc_start: 0.6445 (mtt) cc_final: 0.6113 (mtp) REVERT: F 670 VAL cc_start: 0.6935 (m) cc_final: 0.6686 (t) REVERT: B 26 LEU cc_start: 0.7334 (mm) cc_final: 0.6964 (mt) REVERT: B 291 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: B 292 GLU cc_start: 0.7376 (tp30) cc_final: 0.7114 (mm-30) REVERT: B 388 MET cc_start: 0.7725 (mtp) cc_final: 0.7499 (mtt) REVERT: B 543 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (mppt) REVERT: B 678 MET cc_start: 0.5629 (mpp) cc_final: 0.5303 (mpm) REVERT: D 26 LEU cc_start: 0.7334 (mm) cc_final: 0.7009 (mp) REVERT: D 291 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: D 388 MET cc_start: 0.7747 (mtp) cc_final: 0.7465 (mtt) REVERT: C 190 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6294 (mppt) REVERT: C 268 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8652 (tt) REVERT: C 495 TYR cc_start: 0.8434 (m-10) cc_final: 0.8225 (m-10) REVERT: E 26 LEU cc_start: 0.7259 (mm) cc_final: 0.6869 (mt) REVERT: E 35 ASP cc_start: 0.6541 (t0) cc_final: 0.6326 (t0) REVERT: E 190 LYS cc_start: 0.7251 (mmtt) cc_final: 0.6421 (mppt) REVERT: E 291 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: E 292 GLU cc_start: 0.7381 (tp30) cc_final: 0.7175 (mm-30) outliers start: 96 outliers final: 51 residues processed: 463 average time/residue: 1.3999 time to fit residues: 785.7402 Evaluate side-chains 410 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 351 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 466 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 399 optimal weight: 0.5980 chunk 423 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 379 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN D 460 ASN E 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 35700 Z= 0.324 Angle : 0.647 8.811 48282 Z= 0.326 Chirality : 0.046 0.199 5382 Planarity : 0.005 0.054 6324 Dihedral : 11.044 163.119 5094 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.79 % Favored : 93.93 % Rotamer: Outliers : 4.07 % Allowed : 17.04 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.42 (0.13), residues: 4398 helix: 0.39 (0.12), residues: 1890 sheet: -0.64 (0.19), residues: 696 loop : -0.70 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 454 HIS 0.005 0.001 HIS D 317 PHE 0.013 0.002 PHE D 736 TYR 0.014 0.002 TYR A 203 ARG 0.009 0.001 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 378 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7529 (mm) cc_final: 0.7197 (mp) REVERT: A 46 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6745 (mpp) REVERT: A 148 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7263 (mmtt) REVERT: A 291 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: A 388 MET cc_start: 0.7757 (mtp) cc_final: 0.7491 (mtt) REVERT: A 427 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5336 (tpp) REVERT: F 38 VAL cc_start: 0.7573 (t) cc_final: 0.7359 (t) REVERT: F 60 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6538 (mtmm) REVERT: F 268 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8797 (tt) REVERT: F 292 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: F 388 MET cc_start: 0.6482 (mtt) cc_final: 0.6132 (mtp) REVERT: F 670 VAL cc_start: 0.6981 (m) cc_final: 0.6713 (t) REVERT: F 753 ARG cc_start: 0.7957 (ttp-110) cc_final: 0.7564 (ttm110) REVERT: B 26 LEU cc_start: 0.7591 (mm) cc_final: 0.7194 (mt) REVERT: B 148 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7384 (mmtt) REVERT: B 162 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 288 LYS cc_start: 0.8329 (ttmp) cc_final: 0.8072 (tmmt) REVERT: B 291 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: B 678 MET cc_start: 0.5670 (mpp) cc_final: 0.5373 (mpm) REVERT: B 700 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7683 (ttm170) REVERT: D 26 LEU cc_start: 0.7551 (mm) cc_final: 0.7191 (mp) REVERT: D 158 MET cc_start: 0.7452 (mtp) cc_final: 0.7163 (mtt) REVERT: D 291 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 60 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6558 (mtmm) REVERT: C 268 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8702 (tt) REVERT: C 388 MET cc_start: 0.6575 (mtt) cc_final: 0.6230 (mtp) REVERT: C 753 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7426 (ttm110) REVERT: E 35 ASP cc_start: 0.6858 (t0) cc_final: 0.6541 (t70) REVERT: E 268 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (tt) REVERT: E 288 LYS cc_start: 0.8329 (ttmp) cc_final: 0.8057 (tmmt) REVERT: E 670 VAL cc_start: 0.6922 (m) cc_final: 0.6698 (t) REVERT: E 678 MET cc_start: 0.5501 (mpp) cc_final: 0.5257 (mpm) outliers start: 147 outliers final: 91 residues processed: 492 average time/residue: 1.4814 time to fit residues: 875.5310 Evaluate side-chains 457 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 352 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 652 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 315 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 380 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN F 351 ASN D 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 35700 Z= 0.237 Angle : 0.597 7.472 48282 Z= 0.298 Chirality : 0.045 0.185 5382 Planarity : 0.004 0.059 6324 Dihedral : 10.778 163.350 5094 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.83 % Favored : 94.89 % Rotamer: Outliers : 3.65 % Allowed : 18.08 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.32 (0.13), residues: 4398 helix: 0.42 (0.12), residues: 1926 sheet: -0.61 (0.19), residues: 690 loop : -0.60 (0.16), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 454 HIS 0.003 0.001 HIS D 317 PHE 0.009 0.001 PHE A 267 TYR 0.026 0.002 TYR B 203 ARG 0.006 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 372 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7491 (mm) cc_final: 0.7135 (mp) REVERT: A 46 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6722 (mpp) REVERT: A 291 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 761 THR cc_start: 0.7666 (p) cc_final: 0.7444 (t) REVERT: F 35 ASP cc_start: 0.6715 (t0) cc_final: 0.6295 (t70) REVERT: F 38 VAL cc_start: 0.7627 (t) cc_final: 0.7045 (t) REVERT: F 60 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6422 (mtmm) REVERT: F 148 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7092 (mmtt) REVERT: F 268 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8780 (tt) REVERT: F 292 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: F 358 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7589 (mtp85) REVERT: F 388 MET cc_start: 0.6506 (mtt) cc_final: 0.6182 (mtp) REVERT: F 670 VAL cc_start: 0.6968 (m) cc_final: 0.6699 (t) REVERT: F 753 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7559 (ttm110) REVERT: B 26 LEU cc_start: 0.7560 (mm) cc_final: 0.7184 (mt) REVERT: B 148 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7270 (mmtt) REVERT: B 288 LYS cc_start: 0.8288 (ttmp) cc_final: 0.8024 (tmmt) REVERT: B 291 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: B 295 LYS cc_start: 0.7435 (mtmm) cc_final: 0.7171 (mmtm) REVERT: B 670 VAL cc_start: 0.6975 (m) cc_final: 0.6696 (t) REVERT: B 678 MET cc_start: 0.5658 (mpp) cc_final: 0.5380 (mpm) REVERT: D 26 LEU cc_start: 0.7491 (mm) cc_final: 0.7134 (mp) REVERT: D 291 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: D 761 THR cc_start: 0.7584 (p) cc_final: 0.7380 (t) REVERT: C 60 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6535 (mtmm) REVERT: C 268 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 388 MET cc_start: 0.6569 (mtt) cc_final: 0.6216 (mtp) REVERT: C 753 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7430 (ttm110) REVERT: E 35 ASP cc_start: 0.6771 (t0) cc_final: 0.6469 (t70) REVERT: E 162 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: E 189 ILE cc_start: 0.7048 (pt) cc_final: 0.6763 (pp) REVERT: E 190 LYS cc_start: 0.7202 (mptt) cc_final: 0.6445 (mppt) REVERT: E 288 LYS cc_start: 0.8290 (ttmp) cc_final: 0.8031 (tmmt) REVERT: E 670 VAL cc_start: 0.6933 (m) cc_final: 0.6714 (t) outliers start: 131 outliers final: 80 residues processed: 477 average time/residue: 1.4480 time to fit residues: 831.8288 Evaluate side-chains 448 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 356 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 652 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 423 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN D 36 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 35700 Z= 0.417 Angle : 0.716 8.830 48282 Z= 0.362 Chirality : 0.049 0.217 5382 Planarity : 0.005 0.053 6324 Dihedral : 11.169 163.967 5094 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.75 % Favored : 92.97 % Rotamer: Outliers : 4.05 % Allowed : 18.13 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.73 (0.13), residues: 4398 helix: 0.15 (0.12), residues: 1884 sheet: -0.88 (0.19), residues: 702 loop : -0.85 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 454 HIS 0.007 0.001 HIS F 317 PHE 0.016 0.002 PHE B 131 TYR 0.019 0.003 TYR D 203 ARG 0.015 0.001 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 371 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6727 (mpp) REVERT: A 291 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: F 38 VAL cc_start: 0.7866 (t) cc_final: 0.7630 (t) REVERT: F 60 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6437 (mtmm) REVERT: F 268 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8759 (tt) REVERT: F 288 LYS cc_start: 0.8392 (ttmp) cc_final: 0.7965 (tmmm) REVERT: F 388 MET cc_start: 0.6560 (mtt) cc_final: 0.6274 (mtm) REVERT: F 670 VAL cc_start: 0.7004 (m) cc_final: 0.6720 (t) REVERT: F 738 GLU cc_start: 0.7527 (tt0) cc_final: 0.7191 (tt0) REVERT: F 753 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7560 (ttm110) REVERT: B 26 LEU cc_start: 0.7668 (mm) cc_final: 0.7062 (mp) REVERT: B 35 ASP cc_start: 0.6837 (t0) cc_final: 0.6581 (t70) REVERT: B 148 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7333 (mmtt) REVERT: B 162 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 198 LEU cc_start: 0.7693 (mt) cc_final: 0.7422 (mt) REVERT: B 288 LYS cc_start: 0.8335 (ttmp) cc_final: 0.8090 (tmmt) REVERT: B 670 VAL cc_start: 0.7004 (m) cc_final: 0.6739 (t) REVERT: B 700 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7673 (ttm170) REVERT: B 741 ARG cc_start: 0.8209 (ttm110) cc_final: 0.8001 (ttm110) REVERT: D 26 LEU cc_start: 0.7612 (mm) cc_final: 0.7113 (mp) REVERT: D 148 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7187 (mmmt) REVERT: D 288 LYS cc_start: 0.8379 (ttmp) cc_final: 0.8034 (tmmt) REVERT: D 291 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: D 427 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5372 (tpp) REVERT: D 511 SER cc_start: 0.8634 (p) cc_final: 0.8385 (m) REVERT: D 761 THR cc_start: 0.7731 (p) cc_final: 0.7518 (t) REVERT: C 60 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6500 (mtmm) REVERT: C 268 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8750 (tt) REVERT: C 388 MET cc_start: 0.6528 (mtt) cc_final: 0.6160 (mtp) REVERT: C 678 MET cc_start: 0.5167 (mpp) cc_final: 0.4891 (mpm) REVERT: C 738 GLU cc_start: 0.7530 (tt0) cc_final: 0.7197 (tt0) REVERT: C 753 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7472 (ttm110) REVERT: E 35 ASP cc_start: 0.6836 (t0) cc_final: 0.6602 (t70) REVERT: E 148 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7412 (mmtt) REVERT: E 162 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: E 189 ILE cc_start: 0.7423 (pt) cc_final: 0.7222 (pp) REVERT: E 288 LYS cc_start: 0.8347 (ttmp) cc_final: 0.8091 (tmmt) REVERT: E 670 VAL cc_start: 0.6970 (m) cc_final: 0.6764 (t) REVERT: E 678 MET cc_start: 0.5617 (mpp) cc_final: 0.5363 (mpm) outliers start: 146 outliers final: 90 residues processed: 493 average time/residue: 1.5260 time to fit residues: 907.2369 Evaluate side-chains 449 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 346 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 613 THR Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 241 optimal weight: 0.0980 chunk 309 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 422 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 257 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN F 285 ASN F 351 ASN B 285 ASN B 460 ASN C 351 ASN E 36 ASN E 351 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35700 Z= 0.176 Angle : 0.585 7.073 48282 Z= 0.290 Chirality : 0.044 0.143 5382 Planarity : 0.004 0.065 6324 Dihedral : 10.325 165.116 5094 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.42 % Favored : 95.31 % Rotamer: Outliers : 2.37 % Allowed : 20.21 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.22 (0.13), residues: 4398 helix: 0.64 (0.12), residues: 1884 sheet: -0.73 (0.19), residues: 660 loop : -0.61 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 454 HIS 0.002 0.001 HIS D 340 PHE 0.012 0.001 PHE B 163 TYR 0.019 0.002 TYR F 203 ARG 0.010 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 370 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7449 (mm) cc_final: 0.7063 (mp) REVERT: A 291 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 295 LYS cc_start: 0.7181 (mtmm) cc_final: 0.6863 (mmtm) REVERT: F 38 VAL cc_start: 0.7621 (t) cc_final: 0.7366 (t) REVERT: F 268 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8701 (tt) REVERT: F 670 VAL cc_start: 0.7018 (m) cc_final: 0.6739 (t) REVERT: F 753 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7563 (ttm110) REVERT: B 26 LEU cc_start: 0.7470 (mm) cc_final: 0.7124 (mt) REVERT: B 35 ASP cc_start: 0.6692 (t0) cc_final: 0.6430 (t70) REVERT: B 291 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: B 670 VAL cc_start: 0.6979 (m) cc_final: 0.6716 (t) REVERT: D 26 LEU cc_start: 0.7423 (mm) cc_final: 0.7031 (mp) REVERT: D 291 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: C 35 ASP cc_start: 0.6771 (t0) cc_final: 0.6475 (t70) REVERT: C 268 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 388 MET cc_start: 0.6488 (mtt) cc_final: 0.6099 (mtp) REVERT: C 753 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7503 (ttm110) REVERT: E 35 ASP cc_start: 0.6566 (t0) cc_final: 0.6262 (t70) REVERT: E 189 ILE cc_start: 0.7241 (pt) cc_final: 0.6959 (pp) REVERT: E 190 LYS cc_start: 0.7223 (mptt) cc_final: 0.6537 (mppt) REVERT: E 288 LYS cc_start: 0.8260 (ttmp) cc_final: 0.7985 (tmmt) REVERT: E 670 VAL cc_start: 0.6878 (m) cc_final: 0.6658 (t) outliers start: 83 outliers final: 48 residues processed: 440 average time/residue: 1.4921 time to fit residues: 784.9098 Evaluate side-chains 398 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 345 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 268 optimal weight: 0.6980 chunk 287 optimal weight: 8.9990 chunk 208 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 331 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN D 460 ASN E 296 ASN E 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35700 Z= 0.207 Angle : 0.593 8.200 48282 Z= 0.293 Chirality : 0.044 0.205 5382 Planarity : 0.004 0.061 6324 Dihedral : 10.221 163.611 5094 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.45 % Favored : 94.28 % Rotamer: Outliers : 2.72 % Allowed : 20.18 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.10 (0.13), residues: 4398 helix: 0.75 (0.12), residues: 1884 sheet: -0.65 (0.20), residues: 654 loop : -0.58 (0.16), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 454 HIS 0.002 0.001 HIS C 183 PHE 0.008 0.001 PHE E 230 TYR 0.020 0.001 TYR B 203 ARG 0.009 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 360 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7495 (mm) cc_final: 0.7110 (mp) REVERT: A 291 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 761 THR cc_start: 0.7610 (p) cc_final: 0.7386 (t) REVERT: F 38 VAL cc_start: 0.7684 (t) cc_final: 0.7422 (t) REVERT: F 268 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8710 (tt) REVERT: F 292 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: F 332 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: F 670 VAL cc_start: 0.7007 (m) cc_final: 0.6719 (t) REVERT: F 753 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7568 (ttm110) REVERT: B 26 LEU cc_start: 0.7530 (mm) cc_final: 0.7145 (mt) REVERT: B 35 ASP cc_start: 0.6717 (t0) cc_final: 0.6428 (t70) REVERT: B 291 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: B 292 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: B 670 VAL cc_start: 0.6932 (m) cc_final: 0.6630 (t) REVERT: B 700 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7653 (ttm170) REVERT: D 26 LEU cc_start: 0.7494 (mm) cc_final: 0.7089 (mp) REVERT: D 291 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: C 35 ASP cc_start: 0.6823 (t0) cc_final: 0.6541 (t70) REVERT: C 268 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8697 (tt) REVERT: C 388 MET cc_start: 0.6560 (mtt) cc_final: 0.6195 (mtp) REVERT: C 753 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7504 (ttm110) REVERT: C 761 THR cc_start: 0.7697 (p) cc_final: 0.7479 (t) REVERT: E 35 ASP cc_start: 0.6574 (t0) cc_final: 0.6278 (t70) REVERT: E 162 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: E 189 ILE cc_start: 0.7238 (pt) cc_final: 0.6958 (pp) REVERT: E 190 LYS cc_start: 0.7207 (mptt) cc_final: 0.6537 (mppt) REVERT: E 198 LEU cc_start: 0.7698 (mp) cc_final: 0.7355 (tp) REVERT: E 288 LYS cc_start: 0.8252 (ttmp) cc_final: 0.7988 (tmmt) REVERT: E 670 VAL cc_start: 0.6877 (m) cc_final: 0.6625 (t) REVERT: E 741 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7639 (ttm110) outliers start: 96 outliers final: 61 residues processed: 439 average time/residue: 1.4623 time to fit residues: 768.8718 Evaluate side-chains 408 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 338 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 308 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 chunk 392 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN D 36 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN E 460 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 35700 Z= 0.367 Angle : 0.687 10.265 48282 Z= 0.345 Chirality : 0.048 0.255 5382 Planarity : 0.005 0.057 6324 Dihedral : 10.786 163.162 5094 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.48 % Favored : 93.25 % Rotamer: Outliers : 2.69 % Allowed : 20.07 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.42 (0.13), residues: 4398 helix: 0.47 (0.12), residues: 1884 sheet: -0.80 (0.19), residues: 666 loop : -0.72 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 454 HIS 0.004 0.001 HIS F 317 PHE 0.013 0.002 PHE D 736 TYR 0.028 0.002 TYR A 203 ARG 0.009 0.001 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 351 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7626 (mm) cc_final: 0.7239 (mp) REVERT: A 239 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6427 (mmm160) REVERT: A 288 LYS cc_start: 0.8390 (ttmp) cc_final: 0.8023 (tmmt) REVERT: A 291 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 761 THR cc_start: 0.7743 (p) cc_final: 0.7509 (t) REVERT: F 38 VAL cc_start: 0.7826 (t) cc_final: 0.7568 (t) REVERT: F 268 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8752 (tt) REVERT: F 292 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: F 670 VAL cc_start: 0.7013 (m) cc_final: 0.6725 (t) REVERT: F 753 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7573 (ttm110) REVERT: B 26 LEU cc_start: 0.7619 (mm) cc_final: 0.7239 (mt) REVERT: B 288 LYS cc_start: 0.8334 (ttmp) cc_final: 0.7936 (tmmm) REVERT: B 670 VAL cc_start: 0.6998 (m) cc_final: 0.6724 (t) REVERT: B 700 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7654 (ttm170) REVERT: D 26 LEU cc_start: 0.7613 (mm) cc_final: 0.7078 (mp) REVERT: D 36 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7722 (t160) REVERT: D 288 LYS cc_start: 0.8363 (ttmp) cc_final: 0.8012 (tmmt) REVERT: D 291 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: D 442 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7029 (mmm) REVERT: D 511 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8355 (m) REVERT: D 761 THR cc_start: 0.7758 (p) cc_final: 0.7510 (t) REVERT: C 268 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8730 (tt) REVERT: C 388 MET cc_start: 0.6533 (mtt) cc_final: 0.6205 (mtp) REVERT: C 753 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7494 (ttm110) REVERT: E 35 ASP cc_start: 0.6753 (t0) cc_final: 0.6416 (t70) REVERT: E 162 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: E 198 LEU cc_start: 0.7693 (mp) cc_final: 0.7370 (tp) REVERT: E 288 LYS cc_start: 0.8341 (ttmp) cc_final: 0.8087 (tmmt) REVERT: E 670 VAL cc_start: 0.6956 (m) cc_final: 0.6727 (t) outliers start: 95 outliers final: 72 residues processed: 430 average time/residue: 1.5338 time to fit residues: 786.9148 Evaluate side-chains 422 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 340 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 7.9990 chunk 415 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 197 optimal weight: 0.0270 chunk 289 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 401 optimal weight: 0.0040 chunk 347 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 overall best weight: 0.9452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN B 460 ASN D 36 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN C 351 ASN E 351 ASN E 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35700 Z= 0.200 Angle : 0.616 11.508 48282 Z= 0.305 Chirality : 0.045 0.254 5382 Planarity : 0.004 0.061 6324 Dihedral : 10.416 163.150 5094 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.70 % Favored : 94.02 % Rotamer: Outliers : 2.18 % Allowed : 20.47 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.19 (0.13), residues: 4398 helix: 0.68 (0.12), residues: 1884 sheet: -0.71 (0.20), residues: 660 loop : -0.62 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 454 HIS 0.002 0.001 HIS C 183 PHE 0.010 0.001 PHE E 163 TYR 0.017 0.002 TYR F 203 ARG 0.009 0.000 ARG B 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 356 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7508 (mm) cc_final: 0.7118 (mp) REVERT: A 288 LYS cc_start: 0.8365 (ttmp) cc_final: 0.7971 (tmmt) REVERT: A 291 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: A 761 THR cc_start: 0.7602 (p) cc_final: 0.7388 (t) REVERT: F 38 VAL cc_start: 0.7785 (t) cc_final: 0.7503 (t) REVERT: F 57 VAL cc_start: 0.6029 (m) cc_final: 0.5822 (m) REVERT: F 268 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8724 (tt) REVERT: F 332 MET cc_start: 0.8241 (mtp) cc_final: 0.8005 (mtp) REVERT: F 454 TRP cc_start: 0.6827 (t60) cc_final: 0.6588 (t60) REVERT: F 670 VAL cc_start: 0.7022 (m) cc_final: 0.6740 (t) REVERT: F 753 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7576 (ttm110) REVERT: B 26 LEU cc_start: 0.7533 (mm) cc_final: 0.7157 (mt) REVERT: B 35 ASP cc_start: 0.6813 (t0) cc_final: 0.6567 (t70) REVERT: B 291 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: B 670 VAL cc_start: 0.6984 (m) cc_final: 0.6708 (t) REVERT: B 700 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7632 (ttm170) REVERT: B 741 ARG cc_start: 0.8230 (ttm110) cc_final: 0.8002 (ttm110) REVERT: D 26 LEU cc_start: 0.7553 (mm) cc_final: 0.7141 (mp) REVERT: D 291 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: D 442 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7015 (mmm) REVERT: D 508 MET cc_start: 0.2789 (mtm) cc_final: 0.1884 (ptp) REVERT: D 761 THR cc_start: 0.7669 (p) cc_final: 0.7446 (t) REVERT: C 268 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8701 (tt) REVERT: C 388 MET cc_start: 0.6501 (mtt) cc_final: 0.6227 (mtp) REVERT: C 753 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7526 (ttm110) REVERT: E 35 ASP cc_start: 0.6615 (t0) cc_final: 0.6311 (t70) REVERT: E 162 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: E 198 LEU cc_start: 0.7674 (mp) cc_final: 0.7320 (tp) REVERT: E 288 LYS cc_start: 0.8265 (ttmp) cc_final: 0.8009 (tmmt) REVERT: E 292 GLU cc_start: 0.7387 (tp30) cc_final: 0.7011 (tp30) REVERT: E 670 VAL cc_start: 0.6944 (m) cc_final: 0.6720 (t) REVERT: E 741 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7608 (ttm110) outliers start: 76 outliers final: 61 residues processed: 417 average time/residue: 1.5091 time to fit residues: 750.4615 Evaluate side-chains 414 residues out of total 3726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 346 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 511 SER Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 320 optimal weight: 0.0370 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 348 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 357 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 ASN B 85 ASN B 460 ASN D 460 ASN C 351 ASN E 460 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.140061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109024 restraints weight = 143494.670| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.32 r_work: 0.3358 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 35700 Z= 0.193 Angle : 0.601 11.399 48282 Z= 0.296 Chirality : 0.044 0.248 5382 Planarity : 0.004 0.063 6324 Dihedral : 10.186 163.083 5094 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.98 % Favored : 93.75 % Rotamer: Outliers : 2.26 % Allowed : 20.42 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.10 (0.13), residues: 4398 helix: 0.78 (0.12), residues: 1884 sheet: -0.67 (0.20), residues: 648 loop : -0.61 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 454 HIS 0.002 0.001 HIS C 183 PHE 0.009 0.001 PHE E 163 TYR 0.014 0.001 TYR F 203 ARG 0.009 0.000 ARG B 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13662.06 seconds wall clock time: 241 minutes 42.66 seconds (14502.66 seconds total)