Starting phenix.real_space_refine on Sat Mar 23 16:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boy_30136/03_2024/7boy_30136.pdb" } resolution = 3.8 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= 0.035 sd= 0.651 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 23970 2.51 5 N 6504 2.21 5 O 7230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "s ARG 288": "NH1" <-> "NH2" Residue "s PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 288": "NH1" <-> "NH2" Residue "t PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 288": "NH1" <-> "NH2" Residue "u PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 288": "NH1" <-> "NH2" Residue "v PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 288": "NH1" <-> "NH2" Residue "w PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 288": "NH1" <-> "NH2" Residue "x PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37794 Number of models: 1 Model: "" Number of chains: 6 Chain: "s" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "t" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "u" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "v" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "w" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "x" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Time building chain proxies: 17.74, per 1000 atoms: 0.47 Number of scatterers: 37794 At special positions: 0 Unit cell: (161.29, 176.53, 160.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 7230 8.00 N 6504 7.00 C 23970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.78 Conformation dependent library (CDL) restraints added in 6.0 seconds 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8760 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 114 sheets defined 5.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 's' and resid 111 through 115 Processing helix chain 's' and resid 168 through 172 removed outlier: 3.503A pdb=" N GLY s 171 " --> pdb=" O HIS s 168 " (cutoff:3.500A) Processing helix chain 's' and resid 184 through 189 removed outlier: 4.114A pdb=" N ASN s 189 " --> pdb=" O PRO s 185 " (cutoff:3.500A) Processing helix chain 's' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU s 196 " --> pdb=" O ASP s 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU s 198 " --> pdb=" O GLN s 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA s 201 " --> pdb=" O ALA s 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN s 203 " --> pdb=" O GLU s 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET s 204 " --> pdb=" O LEU s 200 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR s 206 " --> pdb=" O LYS s 202 " (cutoff:3.500A) Processing helix chain 's' and resid 617 through 621 Processing helix chain 's' and resid 662 through 666 removed outlier: 3.728A pdb=" N ARG s 665 " --> pdb=" O LEU s 662 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET s 666 " --> pdb=" O GLU s 663 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 662 through 666' Processing helix chain 't' and resid 111 through 115 Processing helix chain 't' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY t 171 " --> pdb=" O HIS t 168 " (cutoff:3.500A) Processing helix chain 't' and resid 184 through 189 removed outlier: 4.112A pdb=" N ASN t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 207 removed outlier: 4.083A pdb=" N LEU t 196 " --> pdb=" O ASP t 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU t 198 " --> pdb=" O GLN t 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA t 201 " --> pdb=" O ALA t 197 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN t 203 " --> pdb=" O GLU t 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET t 204 " --> pdb=" O LEU t 200 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR t 206 " --> pdb=" O LYS t 202 " (cutoff:3.500A) Processing helix chain 't' and resid 617 through 621 Processing helix chain 't' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG t 665 " --> pdb=" O LEU t 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET t 666 " --> pdb=" O GLU t 663 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 662 through 666' Processing helix chain 'u' and resid 111 through 115 Processing helix chain 'u' and resid 168 through 172 removed outlier: 3.503A pdb=" N GLY u 171 " --> pdb=" O HIS u 168 " (cutoff:3.500A) Processing helix chain 'u' and resid 184 through 189 removed outlier: 4.113A pdb=" N ASN u 189 " --> pdb=" O PRO u 185 " (cutoff:3.500A) Processing helix chain 'u' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU u 196 " --> pdb=" O ASP u 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU u 198 " --> pdb=" O GLN u 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA u 201 " --> pdb=" O ALA u 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN u 203 " --> pdb=" O GLU u 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET u 204 " --> pdb=" O LEU u 200 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR u 206 " --> pdb=" O LYS u 202 " (cutoff:3.500A) Processing helix chain 'u' and resid 617 through 621 Processing helix chain 'u' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG u 665 " --> pdb=" O LEU u 662 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET u 666 " --> pdb=" O GLU u 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 662 through 666' Processing helix chain 'v' and resid 111 through 115 Processing helix chain 'v' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY v 171 " --> pdb=" O HIS v 168 " (cutoff:3.500A) Processing helix chain 'v' and resid 184 through 189 removed outlier: 4.112A pdb=" N ASN v 189 " --> pdb=" O PRO v 185 " (cutoff:3.500A) Processing helix chain 'v' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU v 196 " --> pdb=" O ASP v 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU v 198 " --> pdb=" O GLN v 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA v 201 " --> pdb=" O ALA v 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN v 203 " --> pdb=" O GLU v 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET v 204 " --> pdb=" O LEU v 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR v 206 " --> pdb=" O LYS v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 617 through 621 Processing helix chain 'v' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG v 665 " --> pdb=" O LEU v 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET v 666 " --> pdb=" O GLU v 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 662 through 666' Processing helix chain 'w' and resid 111 through 115 Processing helix chain 'w' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY w 171 " --> pdb=" O HIS w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 184 through 189 removed outlier: 4.113A pdb=" N ASN w 189 " --> pdb=" O PRO w 185 " (cutoff:3.500A) Processing helix chain 'w' and resid 192 through 207 removed outlier: 4.082A pdb=" N LEU w 196 " --> pdb=" O ASP w 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU w 198 " --> pdb=" O GLN w 194 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA w 201 " --> pdb=" O ALA w 197 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN w 203 " --> pdb=" O GLU w 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET w 204 " --> pdb=" O LEU w 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR w 206 " --> pdb=" O LYS w 202 " (cutoff:3.500A) Processing helix chain 'w' and resid 617 through 621 Processing helix chain 'w' and resid 662 through 666 removed outlier: 3.728A pdb=" N ARG w 665 " --> pdb=" O LEU w 662 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET w 666 " --> pdb=" O GLU w 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 662 through 666' Processing helix chain 'x' and resid 111 through 115 Processing helix chain 'x' and resid 168 through 172 removed outlier: 3.501A pdb=" N GLY x 171 " --> pdb=" O HIS x 168 " (cutoff:3.500A) Processing helix chain 'x' and resid 184 through 189 removed outlier: 4.114A pdb=" N ASN x 189 " --> pdb=" O PRO x 185 " (cutoff:3.500A) Processing helix chain 'x' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU x 196 " --> pdb=" O ASP x 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU x 198 " --> pdb=" O GLN x 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA x 201 " --> pdb=" O ALA x 197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN x 203 " --> pdb=" O GLU x 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET x 204 " --> pdb=" O LEU x 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR x 206 " --> pdb=" O LYS x 202 " (cutoff:3.500A) Processing helix chain 'x' and resid 617 through 621 Processing helix chain 'x' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG x 665 " --> pdb=" O LEU x 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET x 666 " --> pdb=" O GLU x 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 662 through 666' Processing sheet with id=AA1, first strand: chain 's' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY s 780 " --> pdb=" O ASN s 709 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU s 784 " --> pdb=" O ARG s 705 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG s 705 " --> pdb=" O GLU s 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN s 786 " --> pdb=" O LEU s 703 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU s 703 " --> pdb=" O ASN s 786 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU s 788 " --> pdb=" O LEU s 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU s 701 " --> pdb=" O LEU s 788 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 's' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY s 780 " --> pdb=" O ASN s 709 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU s 784 " --> pdb=" O ARG s 705 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG s 705 " --> pdb=" O GLU s 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN s 786 " --> pdb=" O LEU s 703 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU s 703 " --> pdb=" O ASN s 786 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU s 788 " --> pdb=" O LEU s 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU s 701 " --> pdb=" O LEU s 788 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 's' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 's' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 's' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL s 88 " --> pdb=" O LYS s 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 's' and resid 69 through 70 Processing sheet with id=AA7, first strand: chain 's' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR s 125 " --> pdb=" O LEU s 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 's' and resid 221 through 222 removed outlier: 3.585A pdb=" N VAL s 222 " --> pdb=" O GLY s 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 's' and resid 164 through 167 removed outlier: 6.695A pdb=" N LEU s 165 " --> pdb=" O LYS s 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS s 176 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 's' and resid 250 through 251 Processing sheet with id=AB2, first strand: chain 's' and resid 359 through 362 removed outlier: 3.543A pdb=" N VAL s 393 " --> pdb=" O ILE s 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 's' and resid 406 through 409 removed outlier: 3.686A pdb=" N GLU s 412 " --> pdb=" O PHE s 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 's' and resid 458 through 459 Processing sheet with id=AB5, first strand: chain 's' and resid 511 through 512 removed outlier: 3.622A pdb=" N SER s 541 " --> pdb=" O MET s 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 's' and resid 530 through 531 Processing sheet with id=AB7, first strand: chain 's' and resid 551 through 557 removed outlier: 4.733A pdb=" N ALA s 553 " --> pdb=" O ILE s 564 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE s 564 " --> pdb=" O ALA s 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 's' and resid 598 through 600 Processing sheet with id=AB9, first strand: chain 's' and resid 607 through 608 removed outlier: 3.732A pdb=" N ASN s 608 " --> pdb=" O THR s 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR s 613 " --> pdb=" O ASN s 608 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 685 through 686 Processing sheet with id=AC2, first strand: chain 't' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY t 780 " --> pdb=" O ASN t 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU t 784 " --> pdb=" O ARG t 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG t 705 " --> pdb=" O GLU t 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN t 786 " --> pdb=" O LEU t 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU t 703 " --> pdb=" O ASN t 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU t 788 " --> pdb=" O LEU t 701 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU t 701 " --> pdb=" O LEU t 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 't' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY t 780 " --> pdb=" O ASN t 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU t 784 " --> pdb=" O ARG t 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG t 705 " --> pdb=" O GLU t 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN t 786 " --> pdb=" O LEU t 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU t 703 " --> pdb=" O ASN t 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU t 788 " --> pdb=" O LEU t 701 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU t 701 " --> pdb=" O LEU t 788 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 't' and resid 31 through 32 Processing sheet with id=AC5, first strand: chain 't' and resid 42 through 43 Processing sheet with id=AC6, first strand: chain 't' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE t 564 " --> pdb=" O ALA t 553 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA t 553 " --> pdb=" O ILE t 564 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 't' and resid 65 through 66 removed outlier: 4.180A pdb=" N VAL t 88 " --> pdb=" O LYS t 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 't' and resid 69 through 70 Processing sheet with id=AC9, first strand: chain 't' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR t 125 " --> pdb=" O LEU t 312 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 't' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL t 222 " --> pdb=" O GLY t 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 't' and resid 164 through 167 removed outlier: 6.694A pdb=" N LEU t 165 " --> pdb=" O LYS t 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS t 176 " --> pdb=" O LEU t 165 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 't' and resid 250 through 251 Processing sheet with id=AD4, first strand: chain 't' and resid 359 through 362 removed outlier: 3.545A pdb=" N VAL t 393 " --> pdb=" O ILE t 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU t 412 " --> pdb=" O PHE t 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 458 through 459 Processing sheet with id=AD7, first strand: chain 't' and resid 511 through 512 removed outlier: 3.620A pdb=" N SER t 541 " --> pdb=" O MET t 525 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 530 through 531 Processing sheet with id=AD9, first strand: chain 't' and resid 598 through 600 Processing sheet with id=AE1, first strand: chain 't' and resid 607 through 608 removed outlier: 3.732A pdb=" N ASN t 608 " --> pdb=" O THR t 613 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR t 613 " --> pdb=" O ASN t 608 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 't' and resid 685 through 686 Processing sheet with id=AE3, first strand: chain 'u' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY u 780 " --> pdb=" O ASN u 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU u 784 " --> pdb=" O ARG u 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG u 705 " --> pdb=" O GLU u 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN u 786 " --> pdb=" O LEU u 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU u 703 " --> pdb=" O ASN u 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU u 788 " --> pdb=" O LEU u 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU u 701 " --> pdb=" O LEU u 788 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'u' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY u 780 " --> pdb=" O ASN u 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU u 784 " --> pdb=" O ARG u 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG u 705 " --> pdb=" O GLU u 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN u 786 " --> pdb=" O LEU u 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU u 703 " --> pdb=" O ASN u 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU u 788 " --> pdb=" O LEU u 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU u 701 " --> pdb=" O LEU u 788 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'u' and resid 31 through 32 Processing sheet with id=AE6, first strand: chain 'u' and resid 42 through 43 Processing sheet with id=AE7, first strand: chain 'u' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL u 88 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 69 through 70 Processing sheet with id=AE9, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR u 125 " --> pdb=" O LEU u 312 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'u' and resid 221 through 222 removed outlier: 3.585A pdb=" N VAL u 222 " --> pdb=" O GLY u 152 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'u' and resid 164 through 167 removed outlier: 6.693A pdb=" N LEU u 165 " --> pdb=" O LYS u 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS u 176 " --> pdb=" O LEU u 165 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'u' and resid 250 through 251 Processing sheet with id=AF4, first strand: chain 'u' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL u 393 " --> pdb=" O ILE u 366 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'u' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU u 412 " --> pdb=" O PHE u 409 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'u' and resid 458 through 459 Processing sheet with id=AF7, first strand: chain 'u' and resid 511 through 512 removed outlier: 3.621A pdb=" N SER u 541 " --> pdb=" O MET u 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'u' and resid 530 through 531 Processing sheet with id=AF9, first strand: chain 'u' and resid 551 through 557 removed outlier: 4.734A pdb=" N ALA u 553 " --> pdb=" O ILE u 564 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE u 564 " --> pdb=" O ALA u 553 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'u' and resid 598 through 600 Processing sheet with id=AG2, first strand: chain 'u' and resid 607 through 608 removed outlier: 3.730A pdb=" N ASN u 608 " --> pdb=" O THR u 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR u 613 " --> pdb=" O ASN u 608 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'u' and resid 685 through 686 Processing sheet with id=AG4, first strand: chain 'v' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY v 780 " --> pdb=" O ASN v 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU v 784 " --> pdb=" O ARG v 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG v 705 " --> pdb=" O GLU v 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN v 786 " --> pdb=" O LEU v 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU v 703 " --> pdb=" O ASN v 786 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU v 788 " --> pdb=" O LEU v 701 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU v 701 " --> pdb=" O LEU v 788 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'v' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY v 780 " --> pdb=" O ASN v 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU v 784 " --> pdb=" O ARG v 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG v 705 " --> pdb=" O GLU v 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN v 786 " --> pdb=" O LEU v 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU v 703 " --> pdb=" O ASN v 786 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU v 788 " --> pdb=" O LEU v 701 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU v 701 " --> pdb=" O LEU v 788 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'v' and resid 31 through 32 Processing sheet with id=AG7, first strand: chain 'v' and resid 42 through 43 Processing sheet with id=AG8, first strand: chain 'v' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE v 564 " --> pdb=" O ALA v 553 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA v 553 " --> pdb=" O ILE v 564 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'v' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL v 88 " --> pdb=" O LYS v 96 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'v' and resid 69 through 70 Processing sheet with id=AH2, first strand: chain 'v' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR v 125 " --> pdb=" O LEU v 312 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'v' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL v 222 " --> pdb=" O GLY v 152 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'v' and resid 164 through 167 removed outlier: 6.693A pdb=" N LEU v 165 " --> pdb=" O LYS v 176 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS v 176 " --> pdb=" O LEU v 165 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'v' and resid 250 through 251 Processing sheet with id=AH6, first strand: chain 'v' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL v 393 " --> pdb=" O ILE v 366 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'v' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU v 412 " --> pdb=" O PHE v 409 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'v' and resid 458 through 459 Processing sheet with id=AH9, first strand: chain 'v' and resid 511 through 512 removed outlier: 3.623A pdb=" N SER v 541 " --> pdb=" O MET v 525 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'v' and resid 530 through 531 Processing sheet with id=AI2, first strand: chain 'v' and resid 598 through 600 Processing sheet with id=AI3, first strand: chain 'v' and resid 607 through 608 removed outlier: 3.730A pdb=" N ASN v 608 " --> pdb=" O THR v 613 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR v 613 " --> pdb=" O ASN v 608 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'v' and resid 685 through 686 Processing sheet with id=AI5, first strand: chain 'w' and resid 4 through 8 removed outlier: 3.841A pdb=" N GLY w 780 " --> pdb=" O ASN w 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU w 784 " --> pdb=" O ARG w 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG w 705 " --> pdb=" O GLU w 784 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN w 786 " --> pdb=" O LEU w 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU w 703 " --> pdb=" O ASN w 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU w 788 " --> pdb=" O LEU w 701 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU w 701 " --> pdb=" O LEU w 788 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'w' and resid 4 through 8 removed outlier: 3.841A pdb=" N GLY w 780 " --> pdb=" O ASN w 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU w 784 " --> pdb=" O ARG w 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG w 705 " --> pdb=" O GLU w 784 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN w 786 " --> pdb=" O LEU w 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU w 703 " --> pdb=" O ASN w 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU w 788 " --> pdb=" O LEU w 701 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU w 701 " --> pdb=" O LEU w 788 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'w' and resid 31 through 32 Processing sheet with id=AI8, first strand: chain 'w' and resid 42 through 43 Processing sheet with id=AI9, first strand: chain 'w' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE w 564 " --> pdb=" O ALA w 553 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA w 553 " --> pdb=" O ILE w 564 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'w' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL w 88 " --> pdb=" O LYS w 96 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'w' and resid 69 through 70 Processing sheet with id=AJ3, first strand: chain 'w' and resid 116 through 120 removed outlier: 4.318A pdb=" N THR w 125 " --> pdb=" O LEU w 312 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'w' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL w 222 " --> pdb=" O GLY w 152 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'w' and resid 164 through 167 removed outlier: 6.694A pdb=" N LEU w 165 " --> pdb=" O LYS w 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS w 176 " --> pdb=" O LEU w 165 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'w' and resid 250 through 251 Processing sheet with id=AJ7, first strand: chain 'w' and resid 359 through 362 removed outlier: 3.543A pdb=" N VAL w 393 " --> pdb=" O ILE w 366 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'w' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU w 412 " --> pdb=" O PHE w 409 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'w' and resid 458 through 459 Processing sheet with id=AK1, first strand: chain 'w' and resid 511 through 512 removed outlier: 3.621A pdb=" N SER w 541 " --> pdb=" O MET w 525 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'w' and resid 530 through 531 Processing sheet with id=AK3, first strand: chain 'w' and resid 598 through 600 Processing sheet with id=AK4, first strand: chain 'w' and resid 607 through 608 removed outlier: 3.731A pdb=" N ASN w 608 " --> pdb=" O THR w 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR w 613 " --> pdb=" O ASN w 608 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'w' and resid 685 through 686 Processing sheet with id=AK6, first strand: chain 'x' and resid 4 through 8 removed outlier: 3.839A pdb=" N GLY x 780 " --> pdb=" O ASN x 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU x 784 " --> pdb=" O ARG x 705 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG x 705 " --> pdb=" O GLU x 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN x 786 " --> pdb=" O LEU x 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU x 703 " --> pdb=" O ASN x 786 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU x 788 " --> pdb=" O LEU x 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU x 701 " --> pdb=" O LEU x 788 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'x' and resid 4 through 8 removed outlier: 3.839A pdb=" N GLY x 780 " --> pdb=" O ASN x 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU x 784 " --> pdb=" O ARG x 705 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG x 705 " --> pdb=" O GLU x 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN x 786 " --> pdb=" O LEU x 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU x 703 " --> pdb=" O ASN x 786 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU x 788 " --> pdb=" O LEU x 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU x 701 " --> pdb=" O LEU x 788 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'x' and resid 31 through 32 Processing sheet with id=AK9, first strand: chain 'x' and resid 42 through 43 Processing sheet with id=AL1, first strand: chain 'x' and resid 48 through 49 removed outlier: 3.574A pdb=" N ARG x 575 " --> pdb=" O VAL x 49 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE x 564 " --> pdb=" O ALA x 553 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA x 553 " --> pdb=" O ILE x 564 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'x' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL x 88 " --> pdb=" O LYS x 96 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'x' and resid 69 through 70 Processing sheet with id=AL4, first strand: chain 'x' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR x 125 " --> pdb=" O LEU x 312 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'x' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL x 222 " --> pdb=" O GLY x 152 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'x' and resid 164 through 167 removed outlier: 6.695A pdb=" N LEU x 165 " --> pdb=" O LYS x 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS x 176 " --> pdb=" O LEU x 165 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'x' and resid 250 through 251 Processing sheet with id=AL8, first strand: chain 'x' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL x 393 " --> pdb=" O ILE x 366 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'x' and resid 406 through 409 removed outlier: 3.686A pdb=" N GLU x 412 " --> pdb=" O PHE x 409 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'x' and resid 458 through 459 Processing sheet with id=AM2, first strand: chain 'x' and resid 511 through 512 removed outlier: 3.622A pdb=" N SER x 541 " --> pdb=" O MET x 525 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'x' and resid 530 through 531 Processing sheet with id=AM4, first strand: chain 'x' and resid 598 through 600 Processing sheet with id=AM5, first strand: chain 'x' and resid 607 through 608 removed outlier: 3.733A pdb=" N ASN x 608 " --> pdb=" O THR x 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR x 613 " --> pdb=" O ASN x 608 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'x' and resid 685 through 686 715 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.61 Time building geometry restraints manager: 15.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7814 1.33 - 1.45: 9897 1.45 - 1.57: 20887 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 38748 Sorted by residual: bond pdb=" N PRO u 64 " pdb=" CD PRO u 64 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" N PRO w 64 " pdb=" CD PRO w 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" N PRO v 64 " pdb=" CD PRO v 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" N PRO s 64 " pdb=" CD PRO s 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" N PRO t 64 " pdb=" CD PRO t 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 38743 not shown) Histogram of bond angle deviations from ideal: 92.66 - 102.97: 244 102.97 - 113.28: 20775 113.28 - 123.59: 29510 123.59 - 133.90: 2074 133.90 - 144.21: 89 Bond angle restraints: 52692 Sorted by residual: angle pdb=" N GLY s 218 " pdb=" CA GLY s 218 " pdb=" C GLY s 218 " ideal model delta sigma weight residual 113.18 133.49 -20.31 2.37e+00 1.78e-01 7.34e+01 angle pdb=" N GLY u 218 " pdb=" CA GLY u 218 " pdb=" C GLY u 218 " ideal model delta sigma weight residual 113.18 133.43 -20.25 2.37e+00 1.78e-01 7.30e+01 angle pdb=" N GLY v 218 " pdb=" CA GLY v 218 " pdb=" C GLY v 218 " ideal model delta sigma weight residual 113.18 133.42 -20.24 2.37e+00 1.78e-01 7.29e+01 angle pdb=" N GLY t 218 " pdb=" CA GLY t 218 " pdb=" C GLY t 218 " ideal model delta sigma weight residual 113.18 133.40 -20.22 2.37e+00 1.78e-01 7.28e+01 angle pdb=" N GLY x 218 " pdb=" CA GLY x 218 " pdb=" C GLY x 218 " ideal model delta sigma weight residual 113.18 133.40 -20.22 2.37e+00 1.78e-01 7.28e+01 ... (remaining 52687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.69: 21800 23.69 - 47.39: 864 47.39 - 71.08: 62 71.08 - 94.78: 8 94.78 - 118.47: 12 Dihedral angle restraints: 22746 sinusoidal: 9030 harmonic: 13716 Sorted by residual: dihedral pdb=" CA ALA u 688 " pdb=" C ALA u 688 " pdb=" N ASP u 689 " pdb=" CA ASP u 689 " ideal model delta harmonic sigma weight residual 180.00 61.53 118.47 0 5.00e+00 4.00e-02 5.61e+02 dihedral pdb=" CA ALA w 688 " pdb=" C ALA w 688 " pdb=" N ASP w 689 " pdb=" CA ASP w 689 " ideal model delta harmonic sigma weight residual 180.00 61.53 118.47 0 5.00e+00 4.00e-02 5.61e+02 dihedral pdb=" CA ALA t 688 " pdb=" C ALA t 688 " pdb=" N ASP t 689 " pdb=" CA ASP t 689 " ideal model delta harmonic sigma weight residual 180.00 61.54 118.46 0 5.00e+00 4.00e-02 5.61e+02 ... (remaining 22743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 5038 0.111 - 0.223: 518 0.223 - 0.334: 78 0.334 - 0.446: 1 0.446 - 0.557: 5 Chirality restraints: 5640 Sorted by residual: chirality pdb=" CA PHE u 50 " pdb=" N PHE u 50 " pdb=" C PHE u 50 " pdb=" CB PHE u 50 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" CA PHE t 50 " pdb=" N PHE t 50 " pdb=" C PHE t 50 " pdb=" CB PHE t 50 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA PHE s 50 " pdb=" N PHE s 50 " pdb=" C PHE s 50 " pdb=" CB PHE s 50 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.24e+00 ... (remaining 5637 not shown) Planarity restraints: 6918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP x 595 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ASP x 595 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP x 595 " -0.029 2.00e-02 2.50e+03 pdb=" N MET x 596 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP v 595 " -0.021 2.00e-02 2.50e+03 4.35e-02 1.90e+01 pdb=" C ASP v 595 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP v 595 " -0.029 2.00e-02 2.50e+03 pdb=" N MET v 596 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP u 595 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ASP u 595 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP u 595 " 0.029 2.00e-02 2.50e+03 pdb=" N MET u 596 " 0.025 2.00e-02 2.50e+03 ... (remaining 6915 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 70 2.35 - 2.99: 19403 2.99 - 3.63: 55470 3.63 - 4.26: 86754 4.26 - 4.90: 144020 Nonbonded interactions: 305717 Sorted by model distance: nonbonded pdb=" O GLY u 55 " pdb=" OD1 ASN u 570 " model vdw 1.717 3.040 nonbonded pdb=" O GLY x 55 " pdb=" OD1 ASN x 570 " model vdw 1.735 3.040 nonbonded pdb=" O GLY s 55 " pdb=" OD1 ASN s 570 " model vdw 1.916 3.040 nonbonded pdb=" O GLY v 55 " pdb=" OD1 ASN v 570 " model vdw 1.947 3.040 nonbonded pdb=" O GLY w 55 " pdb=" OD1 ASN w 570 " model vdw 1.962 3.040 ... (remaining 305712 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 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 11.030 Check model and map are aligned: 0.600 Set scattering table: 0.330 Process input model: 95.440 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.008 0.074 38748 Z= 0.548 Angle : 1.495 22.916 52692 Z= 0.816 Chirality : 0.073 0.557 5640 Planarity : 0.007 0.068 6918 Dihedral : 12.884 118.469 13986 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 1.15 % Allowed : 16.14 % Favored : 82.72 % Rotamer: Outliers : 1.21 % Allowed : 7.25 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 6.02 % Twisted General : 3.72 % 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: -5.15 (0.10), residues: 4716 helix: -5.02 (0.10), residues: 156 sheet: -3.32 (0.12), residues: 1584 loop : -3.55 (0.09), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP v 297 HIS 0.011 0.003 HIS u 491 PHE 0.052 0.004 PHE x 50 TYR 0.030 0.004 TYR u 767 ARG 0.014 0.002 ARG v 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1137 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.8989 (m) cc_final: 0.8596 (t) REVERT: s 239 TYR cc_start: 0.8465 (t80) cc_final: 0.7999 (t80) REVERT: s 278 ASP cc_start: 0.8249 (m-30) cc_final: 0.8030 (t0) REVERT: s 342 SER cc_start: 0.8130 (m) cc_final: 0.7920 (p) REVERT: s 367 ILE cc_start: 0.9070 (mp) cc_final: 0.8799 (mm) REVERT: s 374 TYR cc_start: 0.8245 (m-10) cc_final: 0.7894 (m-80) REVERT: s 417 SER cc_start: 0.9144 (m) cc_final: 0.8821 (p) REVERT: s 567 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: s 631 ILE cc_start: 0.9514 (mt) cc_final: 0.9127 (tt) REVERT: s 741 LEU cc_start: 0.9213 (tp) cc_final: 0.8884 (tt) REVERT: t 228 GLN cc_start: 0.8659 (mp-120) cc_final: 0.8014 (mp10) REVERT: t 367 ILE cc_start: 0.8913 (mp) cc_final: 0.8640 (mm) REVERT: t 788 LEU cc_start: 0.8901 (tm) cc_final: 0.8633 (tp) REVERT: u 336 ASP cc_start: 0.7688 (p0) cc_final: 0.7342 (p0) REVERT: u 352 PHE cc_start: 0.8830 (m-10) cc_final: 0.8267 (m-80) REVERT: u 367 ILE cc_start: 0.8943 (mp) cc_final: 0.8731 (mm) REVERT: u 417 SER cc_start: 0.9028 (m) cc_final: 0.8752 (p) REVERT: u 439 LEU cc_start: 0.9195 (tm) cc_final: 0.8977 (tp) REVERT: u 477 GLN cc_start: 0.8560 (mt0) cc_final: 0.7964 (mt0) REVERT: u 542 HIS cc_start: 0.7344 (m-70) cc_final: 0.6981 (m-70) REVERT: u 550 GLN cc_start: 0.8278 (mt0) cc_final: 0.7726 (mp10) REVERT: v 20 ASP cc_start: 0.7976 (p0) cc_final: 0.7651 (t0) REVERT: v 180 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8425 (Cg_exo) REVERT: v 255 SER cc_start: 0.9029 (m) cc_final: 0.8823 (p) REVERT: v 269 ILE cc_start: 0.9223 (mm) cc_final: 0.8988 (tp) REVERT: v 342 SER cc_start: 0.8291 (m) cc_final: 0.7975 (p) REVERT: v 417 SER cc_start: 0.8985 (m) cc_final: 0.8673 (t) REVERT: v 644 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6269 (tm-30) REVERT: v 701 LEU cc_start: 0.9398 (tm) cc_final: 0.9184 (tp) REVERT: v 742 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7835 (mmm160) REVERT: w 336 ASP cc_start: 0.7875 (p0) cc_final: 0.7644 (p0) REVERT: w 367 ILE cc_start: 0.8867 (mp) cc_final: 0.8517 (mm) REVERT: w 425 THR cc_start: 0.8610 (p) cc_final: 0.8394 (p) REVERT: w 550 GLN cc_start: 0.8116 (mt0) cc_final: 0.7885 (mp10) REVERT: x 138 THR cc_start: 0.9144 (p) cc_final: 0.8851 (p) REVERT: x 336 ASP cc_start: 0.8080 (p0) cc_final: 0.7864 (p0) REVERT: x 352 PHE cc_start: 0.8694 (m-10) cc_final: 0.8460 (m-80) REVERT: x 417 SER cc_start: 0.9156 (m) cc_final: 0.8895 (p) REVERT: x 441 THR cc_start: 0.8945 (p) cc_final: 0.8673 (p) REVERT: x 477 GLN cc_start: 0.8118 (mt0) cc_final: 0.7342 (mt0) REVERT: x 788 LEU cc_start: 0.8824 (tm) cc_final: 0.8579 (tp) outliers start: 50 outliers final: 13 residues processed: 1175 average time/residue: 0.5700 time to fit residues: 1047.0324 Evaluate side-chains 568 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 554 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 64 PRO Chi-restraints excluded: chain s residue 414 LEU Chi-restraints excluded: chain s residue 567 ASN Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 64 PRO Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.8980 chunk 359 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 191 optimal weight: 0.0570 chunk 371 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 430 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 31 GLN s 67 HIS s 114 ASN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 252 GLN s 376 ASN ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 457 ASN s 494 ASN s 532 ASN s 570 ASN s 777 ASN t 62 GLN t 74 HIS t 111 ASN t 114 ASN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 245 ASN t 252 GLN t 376 ASN t 457 ASN t 494 ASN ** t 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 764 ASN t 777 ASN u 67 HIS u 114 ASN u 187 HIS u 207 ASN u 376 ASN u 457 ASN u 494 ASN u 570 ASN u 764 ASN u 777 ASN v 67 HIS v 74 HIS v 114 ASN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 189 ASN v 252 GLN v 376 ASN v 457 ASN v 491 HIS v 532 ASN v 538 GLN ** v 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 764 ASN v 777 ASN w 114 ASN ** w 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 245 ASN w 252 GLN w 260 ASN w 376 ASN w 457 ASN w 494 ASN w 764 ASN w 777 ASN x 67 HIS x 74 HIS x 114 ASN x 187 HIS ** x 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 376 ASN x 457 ASN x 494 ASN x 570 ASN x 726 ASN x 764 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38748 Z= 0.261 Angle : 0.998 18.473 52692 Z= 0.507 Chirality : 0.055 0.271 5640 Planarity : 0.005 0.069 6918 Dihedral : 10.137 71.534 5233 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.91 % Allowed : 15.95 % Favored : 83.14 % Rotamer: Outliers : 3.66 % Allowed : 14.43 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.11), residues: 4716 helix: -4.25 (0.22), residues: 132 sheet: -2.75 (0.12), residues: 1584 loop : -3.34 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP t 305 HIS 0.008 0.002 HIS t 74 PHE 0.028 0.002 PHE s 352 TYR 0.017 0.002 TYR x 495 ARG 0.010 0.001 ARG v 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 617 time to evaluate : 4.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.8959 (m) cc_final: 0.8334 (t) REVERT: s 266 MET cc_start: 0.8397 (mtt) cc_final: 0.8184 (ttm) REVERT: s 308 MET cc_start: 0.8730 (mmm) cc_final: 0.8070 (mmm) REVERT: s 364 GLU cc_start: 0.6721 (mp0) cc_final: 0.6347 (pm20) REVERT: s 367 ILE cc_start: 0.9072 (mp) cc_final: 0.8845 (mm) REVERT: s 439 LEU cc_start: 0.9221 (tt) cc_final: 0.9020 (tp) REVERT: s 460 PHE cc_start: 0.8703 (m-10) cc_final: 0.8375 (m-10) REVERT: s 519 ASP cc_start: 0.6681 (p0) cc_final: 0.6472 (p0) REVERT: s 534 GLU cc_start: 0.9311 (pt0) cc_final: 0.8760 (mm-30) REVERT: s 550 GLN cc_start: 0.7876 (mt0) cc_final: 0.7654 (mp10) REVERT: s 631 ILE cc_start: 0.9591 (mt) cc_final: 0.9280 (tt) REVERT: t 29 SER cc_start: 0.9259 (m) cc_final: 0.8713 (t) REVERT: t 51 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (pp) REVERT: t 228 GLN cc_start: 0.8398 (mp-120) cc_final: 0.8002 (mp10) REVERT: t 245 ASN cc_start: 0.8158 (m110) cc_final: 0.7354 (m-40) REVERT: t 255 SER cc_start: 0.9075 (m) cc_final: 0.8852 (p) REVERT: t 283 ARG cc_start: 0.8445 (ttt90) cc_final: 0.8132 (ttt90) REVERT: t 326 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7456 (mm-30) REVERT: t 367 ILE cc_start: 0.9061 (mp) cc_final: 0.8708 (mm) REVERT: t 416 TRP cc_start: 0.8718 (m-10) cc_final: 0.8379 (m-10) REVERT: t 596 MET cc_start: 0.7471 (tpp) cc_final: 0.7260 (tpp) REVERT: t 598 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8705 (tp) REVERT: t 721 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6705 (tm-30) REVERT: u 29 SER cc_start: 0.9049 (m) cc_final: 0.8733 (t) REVERT: u 71 ARG cc_start: 0.7231 (ttm110) cc_final: 0.6846 (mtt-85) REVERT: u 324 TRP cc_start: 0.8442 (p-90) cc_final: 0.8117 (p-90) REVERT: u 336 ASP cc_start: 0.7801 (p0) cc_final: 0.7511 (p0) REVERT: u 364 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6096 (mt-10) REVERT: u 367 ILE cc_start: 0.9111 (mp) cc_final: 0.8898 (mm) REVERT: u 405 TYR cc_start: 0.7324 (m-80) cc_final: 0.7068 (m-80) REVERT: u 413 LEU cc_start: 0.9008 (tt) cc_final: 0.8633 (tt) REVERT: u 416 TRP cc_start: 0.9153 (m-10) cc_final: 0.8320 (m-10) REVERT: u 417 SER cc_start: 0.8992 (m) cc_final: 0.8606 (t) REVERT: u 477 GLN cc_start: 0.8577 (mt0) cc_final: 0.8175 (mt0) REVERT: u 550 GLN cc_start: 0.8152 (mt0) cc_final: 0.7786 (mp10) REVERT: u 594 MET cc_start: 0.8298 (tpp) cc_final: 0.8097 (tpp) REVERT: v 308 MET cc_start: 0.8596 (mmm) cc_final: 0.8008 (mmm) REVERT: v 314 ARG cc_start: 0.7741 (ttt90) cc_final: 0.7356 (ttt90) REVERT: v 405 TYR cc_start: 0.7619 (m-80) cc_final: 0.7399 (m-10) REVERT: v 416 TRP cc_start: 0.8941 (m-10) cc_final: 0.8739 (m-10) REVERT: v 417 SER cc_start: 0.8921 (m) cc_final: 0.8352 (t) REVERT: v 644 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6521 (tm-30) REVERT: v 645 GLN cc_start: 0.7874 (pp30) cc_final: 0.7652 (pp30) REVERT: v 701 LEU cc_start: 0.9426 (tm) cc_final: 0.9149 (tp) REVERT: v 742 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7665 (mmm160) REVERT: v 757 VAL cc_start: 0.8609 (t) cc_final: 0.8405 (t) REVERT: v 788 LEU cc_start: 0.8320 (tt) cc_final: 0.8075 (tp) REVERT: w 115 ASP cc_start: 0.7157 (m-30) cc_final: 0.6857 (m-30) REVERT: w 220 ILE cc_start: 0.8822 (mm) cc_final: 0.8555 (mm) REVERT: w 255 SER cc_start: 0.9164 (m) cc_final: 0.8641 (p) REVERT: w 308 MET cc_start: 0.8443 (mmm) cc_final: 0.7818 (mmm) REVERT: w 314 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7403 (ttm-80) REVERT: w 367 ILE cc_start: 0.9019 (mp) cc_final: 0.8649 (mm) REVERT: w 416 TRP cc_start: 0.8875 (m-10) cc_final: 0.8646 (m-10) REVERT: w 550 GLN cc_start: 0.8184 (mt0) cc_final: 0.7954 (mp10) REVERT: w 656 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8449 (mp) REVERT: w 718 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7054 (mt) REVERT: w 731 MET cc_start: 0.8165 (tmm) cc_final: 0.7819 (ttt) REVERT: x 138 THR cc_start: 0.9069 (p) cc_final: 0.8838 (p) REVERT: x 308 MET cc_start: 0.8710 (mmm) cc_final: 0.8485 (mmm) REVERT: x 405 TYR cc_start: 0.7502 (m-80) cc_final: 0.7190 (m-80) REVERT: x 413 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8540 (tp) REVERT: x 416 TRP cc_start: 0.9030 (m-10) cc_final: 0.8675 (m-10) REVERT: x 417 SER cc_start: 0.8904 (m) cc_final: 0.8390 (t) REVERT: x 477 GLN cc_start: 0.8270 (mt0) cc_final: 0.7833 (mt0) REVERT: x 550 GLN cc_start: 0.8223 (mt0) cc_final: 0.7842 (mp10) REVERT: x 561 MET cc_start: 0.8224 (tpp) cc_final: 0.7864 (ttt) REVERT: x 718 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7660 (mt) REVERT: x 726 ASN cc_start: 0.8288 (m110) cc_final: 0.7416 (t0) outliers start: 151 outliers final: 57 residues processed: 744 average time/residue: 0.5021 time to fit residues: 604.2326 Evaluate side-chains 535 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 470 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 123 ASP Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 414 LEU Chi-restraints excluded: chain s residue 479 VAL Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 770 SER Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 26 ASP Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 123 ASP Chi-restraints excluded: chain t residue 214 ASN Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 572 PHE Chi-restraints excluded: chain t residue 598 ILE Chi-restraints excluded: chain t residue 770 SER Chi-restraints excluded: chain u residue 26 ASP Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 344 VAL Chi-restraints excluded: chain u residue 346 SER Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 414 LEU Chi-restraints excluded: chain u residue 770 SER Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 74 HIS Chi-restraints excluded: chain v residue 123 ASP Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 746 LEU Chi-restraints excluded: chain v residue 764 ASN Chi-restraints excluded: chain v residue 770 SER Chi-restraints excluded: chain w residue 12 LYS Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 92 SER Chi-restraints excluded: chain w residue 123 ASP Chi-restraints excluded: chain w residue 314 ARG Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 572 PHE Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain w residue 770 SER Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 123 ASP Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 413 LEU Chi-restraints excluded: chain x residue 572 PHE Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 770 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 chunk 358 optimal weight: 0.2980 chunk 293 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 431 optimal weight: 0.9980 chunk 465 optimal weight: 0.6980 chunk 384 optimal weight: 4.9990 chunk 427 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 345 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 31 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 538 GLN s 542 HIS s 747 ASN t 6 GLN t 187 HIS ** t 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 67 HIS u 672 ASN v 10 ASN ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 207 ASN v 661 ASN w 10 ASN w 187 HIS w 207 ASN x 538 GLN ** x 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 672 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38748 Z= 0.223 Angle : 0.923 17.626 52692 Z= 0.464 Chirality : 0.053 0.222 5640 Planarity : 0.005 0.070 6918 Dihedral : 9.130 57.779 5218 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.76 % Allowed : 16.48 % Favored : 82.76 % Rotamer: Outliers : 3.93 % Allowed : 17.15 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 1.33 % Twisted Proline : 1.85 % Twisted General : 1.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.11), residues: 4716 helix: -3.93 (0.21), residues: 168 sheet: -2.88 (0.12), residues: 1602 loop : -3.01 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP w 195 HIS 0.026 0.002 HIS v 74 PHE 0.034 0.002 PHE u 352 TYR 0.024 0.002 TYR v 473 ARG 0.010 0.001 ARG t 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 554 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.8957 (m) cc_final: 0.8327 (t) REVERT: s 78 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7015 (t80) REVERT: s 308 MET cc_start: 0.8770 (mmm) cc_final: 0.8280 (mtm) REVERT: s 364 GLU cc_start: 0.6660 (mp0) cc_final: 0.6276 (pm20) REVERT: s 367 ILE cc_start: 0.9135 (mp) cc_final: 0.8866 (mm) REVERT: s 403 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8065 (tt) REVERT: s 561 MET cc_start: 0.8749 (tpp) cc_final: 0.8536 (ttm) REVERT: s 596 MET cc_start: 0.7265 (tpp) cc_final: 0.7040 (tpp) REVERT: s 631 ILE cc_start: 0.9590 (mt) cc_final: 0.9299 (tt) REVERT: t 29 SER cc_start: 0.9237 (m) cc_final: 0.8736 (t) REVERT: t 78 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.6643 (t80) REVERT: t 187 HIS cc_start: 0.7820 (m90) cc_final: 0.7010 (m90) REVERT: t 228 GLN cc_start: 0.8442 (mp-120) cc_final: 0.8124 (mp10) REVERT: t 255 SER cc_start: 0.9296 (m) cc_final: 0.8878 (p) REVERT: t 308 MET cc_start: 0.8431 (mmm) cc_final: 0.7824 (mmm) REVERT: t 367 ILE cc_start: 0.9086 (mp) cc_final: 0.8718 (mm) REVERT: t 400 ILE cc_start: 0.8887 (mt) cc_final: 0.8647 (mt) REVERT: t 430 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (mt) REVERT: t 531 LEU cc_start: 0.8780 (mm) cc_final: 0.8579 (mt) REVERT: t 697 ASP cc_start: 0.6693 (p0) cc_final: 0.6483 (p0) REVERT: t 721 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6656 (tm-30) REVERT: u 29 SER cc_start: 0.9057 (m) cc_final: 0.8690 (t) REVERT: u 115 ASP cc_start: 0.7239 (m-30) cc_final: 0.6860 (m-30) REVERT: u 123 ASP cc_start: 0.7789 (p0) cc_final: 0.7534 (p0) REVERT: u 145 ASN cc_start: 0.8194 (p0) cc_final: 0.7873 (t0) REVERT: u 283 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7734 (ttt90) REVERT: u 304 LEU cc_start: 0.8724 (tp) cc_final: 0.8425 (mt) REVERT: u 324 TRP cc_start: 0.8564 (p-90) cc_final: 0.7833 (p-90) REVERT: u 336 ASP cc_start: 0.7847 (p0) cc_final: 0.7552 (p0) REVERT: u 352 PHE cc_start: 0.8055 (m-80) cc_final: 0.7807 (m-80) REVERT: u 417 SER cc_start: 0.8924 (m) cc_final: 0.8586 (t) REVERT: u 477 GLN cc_start: 0.8551 (mt0) cc_final: 0.8245 (mt0) REVERT: u 486 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7202 (mt-10) REVERT: u 697 ASP cc_start: 0.7529 (p0) cc_final: 0.7210 (p0) REVERT: v 115 ASP cc_start: 0.7416 (m-30) cc_final: 0.6604 (m-30) REVERT: v 283 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7853 (tpp-160) REVERT: v 308 MET cc_start: 0.8633 (mmm) cc_final: 0.8143 (mmm) REVERT: v 352 PHE cc_start: 0.7731 (m-10) cc_final: 0.7509 (m-80) REVERT: v 364 GLU cc_start: 0.7244 (mp0) cc_final: 0.7028 (pm20) REVERT: v 460 PHE cc_start: 0.8714 (m-10) cc_final: 0.8337 (m-10) REVERT: v 492 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9042 (p) REVERT: v 644 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6525 (tm-30) REVERT: v 666 MET cc_start: 0.7772 (ppp) cc_final: 0.7157 (ppp) REVERT: v 701 LEU cc_start: 0.9552 (tm) cc_final: 0.9229 (tp) REVERT: v 742 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7575 (mmp-170) REVERT: w 29 SER cc_start: 0.9230 (m) cc_final: 0.8877 (t) REVERT: w 115 ASP cc_start: 0.7212 (m-30) cc_final: 0.6837 (m-30) REVERT: w 255 SER cc_start: 0.9148 (m) cc_final: 0.8706 (p) REVERT: w 308 MET cc_start: 0.8519 (mmm) cc_final: 0.7868 (mmm) REVERT: w 367 ILE cc_start: 0.9051 (mp) cc_final: 0.8627 (mm) REVERT: w 416 TRP cc_start: 0.8892 (m-10) cc_final: 0.8644 (m-10) REVERT: w 417 SER cc_start: 0.9082 (m) cc_final: 0.8753 (t) REVERT: x 138 THR cc_start: 0.9031 (p) cc_final: 0.8602 (p) REVERT: x 417 SER cc_start: 0.8993 (m) cc_final: 0.8580 (t) REVERT: x 477 GLN cc_start: 0.8061 (mt0) cc_final: 0.7682 (mt0) REVERT: x 550 GLN cc_start: 0.8227 (mt0) cc_final: 0.7827 (mp10) REVERT: x 561 MET cc_start: 0.8201 (tpp) cc_final: 0.7775 (ttt) REVERT: x 697 ASP cc_start: 0.7706 (p0) cc_final: 0.7486 (p0) REVERT: x 726 ASN cc_start: 0.7654 (m110) cc_final: 0.7303 (m-40) outliers start: 162 outliers final: 76 residues processed: 679 average time/residue: 0.4785 time to fit residues: 532.6473 Evaluate side-chains 545 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 464 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 123 ASP Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 403 LEU Chi-restraints excluded: chain s residue 407 VAL Chi-restraints excluded: chain s residue 423 VAL Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 542 HIS Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 123 ASP Chi-restraints excluded: chain t residue 214 ASN Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain u residue 26 ASP Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 335 VAL Chi-restraints excluded: chain u residue 344 VAL Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 403 LEU Chi-restraints excluded: chain u residue 414 LEU Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 661 ASN Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain w residue 26 ASP Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 123 ASP Chi-restraints excluded: chain w residue 207 ASN Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 532 ASN Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 123 ASP Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 492 VAL Chi-restraints excluded: chain x residue 673 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 205 optimal weight: 0.4980 chunk 289 optimal weight: 0.6980 chunk 432 optimal weight: 0.6980 chunk 458 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 410 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 491 HIS s 764 ASN t 168 HIS ** t 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 302 GLN t 517 HIS ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 252 GLN u 491 HIS u 538 GLN v 10 ASN v 31 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 10 ASN w 517 HIS ** w 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 207 ASN ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38748 Z= 0.229 Angle : 0.883 16.036 52692 Z= 0.443 Chirality : 0.052 0.227 5640 Planarity : 0.005 0.068 6918 Dihedral : 8.659 56.349 5216 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.55 % Allowed : 16.60 % Favored : 82.85 % Rotamer: Outliers : 4.17 % Allowed : 17.90 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 1.33 % Twisted Proline : 1.39 % Twisted General : 1.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.11), residues: 4716 helix: -3.20 (0.36), residues: 132 sheet: -2.57 (0.13), residues: 1560 loop : -3.05 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP v 416 HIS 0.013 0.001 HIS s 542 PHE 0.035 0.002 PHE s 50 TYR 0.021 0.002 TYR w 405 ARG 0.009 0.001 ARG s 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 518 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9082 (m) cc_final: 0.8367 (t) REVERT: s 78 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7146 (t80) REVERT: s 283 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7894 (ttt90) REVERT: s 308 MET cc_start: 0.8852 (mmm) cc_final: 0.8346 (mtm) REVERT: s 364 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: s 417 SER cc_start: 0.9004 (m) cc_final: 0.8521 (t) REVERT: s 550 GLN cc_start: 0.7901 (mt0) cc_final: 0.7649 (mp10) REVERT: s 561 MET cc_start: 0.8740 (tpp) cc_final: 0.8508 (ttm) REVERT: s 591 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7490 (tpt170) REVERT: s 596 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7316 (tpp) REVERT: s 631 ILE cc_start: 0.9587 (mt) cc_final: 0.9300 (tt) REVERT: t 29 SER cc_start: 0.9229 (m) cc_final: 0.8784 (t) REVERT: t 78 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6750 (t80) REVERT: t 138 THR cc_start: 0.9168 (m) cc_final: 0.8893 (p) REVERT: t 139 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8626 (mmmt) REVERT: t 228 GLN cc_start: 0.8576 (mp-120) cc_final: 0.8297 (mp10) REVERT: t 255 SER cc_start: 0.9255 (m) cc_final: 0.8833 (p) REVERT: t 308 MET cc_start: 0.8585 (mmm) cc_final: 0.8200 (mmm) REVERT: t 348 ILE cc_start: 0.8432 (mt) cc_final: 0.8172 (tt) REVERT: t 360 PHE cc_start: 0.8594 (m-10) cc_final: 0.8257 (m-10) REVERT: t 367 ILE cc_start: 0.9109 (mp) cc_final: 0.8678 (mm) REVERT: t 417 SER cc_start: 0.9045 (m) cc_final: 0.8711 (t) REVERT: t 430 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8265 (mt) REVERT: t 697 ASP cc_start: 0.6927 (p0) cc_final: 0.6688 (p0) REVERT: t 731 MET cc_start: 0.8864 (tmm) cc_final: 0.8588 (tmm) REVERT: u 29 SER cc_start: 0.9115 (m) cc_final: 0.8747 (t) REVERT: u 115 ASP cc_start: 0.7247 (m-30) cc_final: 0.6855 (m-30) REVERT: u 283 ARG cc_start: 0.8317 (ttt90) cc_final: 0.7708 (ttt90) REVERT: u 336 ASP cc_start: 0.7825 (p0) cc_final: 0.7543 (p0) REVERT: u 387 ASP cc_start: 0.7782 (t0) cc_final: 0.7225 (t0) REVERT: u 477 GLN cc_start: 0.8549 (mt0) cc_final: 0.8203 (mm-40) REVERT: u 486 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7132 (tt0) REVERT: u 534 GLU cc_start: 0.9126 (pp20) cc_final: 0.8781 (pp20) REVERT: u 542 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6829 (m90) REVERT: u 591 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7521 (tpt170) REVERT: u 656 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9003 (mp) REVERT: u 697 ASP cc_start: 0.7572 (p0) cc_final: 0.7291 (p0) REVERT: u 730 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7867 (t) REVERT: v 115 ASP cc_start: 0.7366 (m-30) cc_final: 0.6501 (m-30) REVERT: v 308 MET cc_start: 0.8753 (mmm) cc_final: 0.8199 (mmm) REVERT: v 364 GLU cc_start: 0.7242 (mp0) cc_final: 0.7016 (pm20) REVERT: v 416 TRP cc_start: 0.9090 (m-10) cc_final: 0.8810 (m-10) REVERT: v 591 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6618 (tpt170) REVERT: v 644 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6149 (tm-30) REVERT: v 742 ARG cc_start: 0.8143 (mmt180) cc_final: 0.7746 (mmp-170) REVERT: w 29 SER cc_start: 0.9234 (m) cc_final: 0.8895 (t) REVERT: w 115 ASP cc_start: 0.7206 (m-30) cc_final: 0.6834 (m-30) REVERT: w 168 HIS cc_start: 0.8128 (t-90) cc_final: 0.7704 (t70) REVERT: w 255 SER cc_start: 0.9166 (m) cc_final: 0.8737 (p) REVERT: w 283 ARG cc_start: 0.8318 (ttt90) cc_final: 0.7816 (tpm170) REVERT: w 308 MET cc_start: 0.8530 (mmm) cc_final: 0.7762 (mmm) REVERT: w 332 CYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7568 (p) REVERT: w 367 ILE cc_start: 0.9072 (mp) cc_final: 0.8629 (mm) REVERT: w 477 GLN cc_start: 0.7916 (mt0) cc_final: 0.7585 (mt0) REVERT: w 701 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8957 (tp) REVERT: x 9 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7925 (mmtm) REVERT: x 283 ARG cc_start: 0.8455 (ttt90) cc_final: 0.8240 (ttt90) REVERT: x 325 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6972 (pp) REVERT: x 417 SER cc_start: 0.8850 (m) cc_final: 0.8432 (t) REVERT: x 477 GLN cc_start: 0.8127 (mt0) cc_final: 0.7826 (mm-40) REVERT: x 495 TYR cc_start: 0.8825 (t80) cc_final: 0.8560 (t80) REVERT: x 550 GLN cc_start: 0.8232 (mt0) cc_final: 0.7800 (mp10) REVERT: x 561 MET cc_start: 0.8249 (tpp) cc_final: 0.7825 (ttt) REVERT: x 591 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7542 (tpt170) REVERT: x 697 ASP cc_start: 0.7597 (p0) cc_final: 0.7383 (p0) REVERT: x 726 ASN cc_start: 0.7624 (m110) cc_final: 0.7235 (m-40) outliers start: 172 outliers final: 103 residues processed: 652 average time/residue: 0.4903 time to fit residues: 521.6966 Evaluate side-chains 571 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 453 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 423 VAL Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 591 ARG Chi-restraints excluded: chain s residue 596 MET Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 730 THR Chi-restraints excluded: chain t residue 26 ASP Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 123 ASP Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 407 VAL Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 517 HIS Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain t residue 730 THR Chi-restraints excluded: chain u residue 26 ASP Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 412 GLU Chi-restraints excluded: chain u residue 421 GLN Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 656 LEU Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain u residue 730 THR Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain w residue 26 ASP Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 123 ASP Chi-restraints excluded: chain w residue 207 ASN Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 517 HIS Chi-restraints excluded: chain w residue 532 ASN Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 730 THR Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 123 ASP Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 414 LEU Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 730 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 341 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 411 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 542 HIS ** s 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 GLN t 190 ASN t 302 GLN ** t 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN ** v 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 6 GLN w 10 ASN w 190 ASN w 207 ASN ** w 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38748 Z= 0.262 Angle : 0.879 15.473 52692 Z= 0.440 Chirality : 0.051 0.185 5640 Planarity : 0.005 0.068 6918 Dihedral : 8.381 59.683 5216 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 17.30 % Favored : 82.23 % Rotamer: Outliers : 4.66 % Allowed : 18.53 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 1.33 % Twisted Proline : 1.39 % Twisted General : 1.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.11), residues: 4716 helix: -2.96 (0.36), residues: 132 sheet: -2.59 (0.13), residues: 1584 loop : -2.94 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP v 416 HIS 0.016 0.001 HIS w 517 PHE 0.041 0.002 PHE s 50 TYR 0.020 0.002 TYR w 177 ARG 0.007 0.001 ARG s 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 504 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9110 (m) cc_final: 0.8419 (t) REVERT: s 78 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7317 (t80) REVERT: s 115 ASP cc_start: 0.7651 (m-30) cc_final: 0.7308 (m-30) REVERT: s 283 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7985 (ttt90) REVERT: s 308 MET cc_start: 0.8858 (mmm) cc_final: 0.8392 (mtm) REVERT: s 332 CYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6942 (p) REVERT: s 403 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8025 (tt) REVERT: s 417 SER cc_start: 0.9003 (m) cc_final: 0.8570 (t) REVERT: s 550 GLN cc_start: 0.7843 (mt0) cc_final: 0.7634 (mp10) REVERT: s 591 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (tpt170) REVERT: s 730 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7628 (t) REVERT: t 29 SER cc_start: 0.9254 (m) cc_final: 0.8835 (t) REVERT: t 78 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.6714 (t80) REVERT: t 91 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (mm) REVERT: t 228 GLN cc_start: 0.8618 (mp-120) cc_final: 0.8399 (mp10) REVERT: t 255 SER cc_start: 0.9265 (m) cc_final: 0.8870 (p) REVERT: t 308 MET cc_start: 0.8617 (mmm) cc_final: 0.8287 (mmm) REVERT: t 325 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7512 (pp) REVERT: t 348 ILE cc_start: 0.8493 (mt) cc_final: 0.8264 (tt) REVERT: t 360 PHE cc_start: 0.8605 (m-10) cc_final: 0.8226 (m-10) REVERT: t 367 ILE cc_start: 0.9140 (mp) cc_final: 0.8681 (mm) REVERT: t 430 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8255 (mt) REVERT: t 697 ASP cc_start: 0.6913 (p0) cc_final: 0.6587 (p0) REVERT: u 29 SER cc_start: 0.9148 (m) cc_final: 0.8818 (t) REVERT: u 115 ASP cc_start: 0.7306 (m-30) cc_final: 0.6859 (m-30) REVERT: u 283 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7702 (ttt90) REVERT: u 332 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6702 (p) REVERT: u 336 ASP cc_start: 0.7925 (p0) cc_final: 0.7660 (p0) REVERT: u 477 GLN cc_start: 0.8610 (mt0) cc_final: 0.8297 (mm-40) REVERT: u 486 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7114 (tt0) REVERT: u 525 MET cc_start: 0.8598 (tpp) cc_final: 0.8347 (tpp) REVERT: u 542 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.6769 (m90) REVERT: u 591 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7313 (tpt170) REVERT: u 697 ASP cc_start: 0.7637 (p0) cc_final: 0.7360 (p0) REVERT: u 730 THR cc_start: 0.7909 (m) cc_final: 0.7664 (t) REVERT: v 115 ASP cc_start: 0.7376 (m-30) cc_final: 0.6460 (m-30) REVERT: v 308 MET cc_start: 0.8731 (mmm) cc_final: 0.8291 (mmm) REVERT: v 591 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6341 (tpt170) REVERT: v 644 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6470 (tm-30) REVERT: v 742 ARG cc_start: 0.8198 (mmt180) cc_final: 0.7830 (mmp-170) REVERT: w 29 SER cc_start: 0.9299 (m) cc_final: 0.8927 (t) REVERT: w 115 ASP cc_start: 0.7264 (m-30) cc_final: 0.6846 (m-30) REVERT: w 150 GLN cc_start: 0.6521 (mm-40) cc_final: 0.5951 (tp-100) REVERT: w 308 MET cc_start: 0.8607 (mmm) cc_final: 0.8220 (mmm) REVERT: w 332 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7590 (p) REVERT: w 364 GLU cc_start: 0.6505 (pm20) cc_final: 0.6292 (pm20) REVERT: w 367 ILE cc_start: 0.9084 (mp) cc_final: 0.8611 (mm) REVERT: w 477 GLN cc_start: 0.8060 (mt0) cc_final: 0.7843 (mt0) REVERT: w 567 ASN cc_start: 0.7612 (m-40) cc_final: 0.7310 (m-40) REVERT: w 701 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8985 (tp) REVERT: x 9 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7921 (mmtm) REVERT: x 29 SER cc_start: 0.9136 (m) cc_final: 0.8880 (t) REVERT: x 325 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6934 (pp) REVERT: x 332 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7208 (p) REVERT: x 412 GLU cc_start: 0.7517 (pm20) cc_final: 0.7267 (pm20) REVERT: x 417 SER cc_start: 0.8874 (m) cc_final: 0.8505 (t) REVERT: x 477 GLN cc_start: 0.8726 (mt0) cc_final: 0.8488 (mm-40) REVERT: x 495 TYR cc_start: 0.8809 (t80) cc_final: 0.8432 (t80) REVERT: x 550 GLN cc_start: 0.8269 (mt0) cc_final: 0.7832 (mp10) REVERT: x 561 MET cc_start: 0.8544 (tpp) cc_final: 0.7938 (ttt) REVERT: x 591 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7715 (tpt170) REVERT: x 594 MET cc_start: 0.8109 (tpp) cc_final: 0.7642 (tpp) REVERT: x 726 ASN cc_start: 0.7720 (m110) cc_final: 0.7270 (m-40) REVERT: x 730 THR cc_start: 0.8205 (m) cc_final: 0.7800 (t) outliers start: 192 outliers final: 108 residues processed: 650 average time/residue: 0.4804 time to fit residues: 509.7191 Evaluate side-chains 578 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 452 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 403 LEU Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 563 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 591 ARG Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 730 THR Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 423 VAL Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 591 ARG Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain t residue 769 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 332 CYS Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 414 LEU Chi-restraints excluded: chain u residue 421 GLN Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 213 VAL Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 661 ASN Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 717 ASP Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 352 PHE Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 407 VAL Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 532 ASN Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 123 ASP Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 292 THR Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 0.0870 chunk 412 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 458 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS t 207 ASN ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN v 62 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 10 ASN ** w 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38748 Z= 0.251 Angle : 0.866 15.301 52692 Z= 0.435 Chirality : 0.051 0.174 5640 Planarity : 0.005 0.064 6918 Dihedral : 8.112 52.731 5214 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 17.41 % Favored : 82.29 % Rotamer: Outliers : 4.42 % Allowed : 19.51 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 1.33 % Twisted Proline : 0.93 % Twisted General : 1.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.11), residues: 4716 helix: -2.50 (0.37), residues: 168 sheet: -2.47 (0.13), residues: 1512 loop : -2.90 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP v 416 HIS 0.007 0.001 HIS w 74 PHE 0.031 0.002 PHE s 352 TYR 0.027 0.002 TYR s 405 ARG 0.007 0.001 ARG v 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 499 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9139 (m) cc_final: 0.8412 (t) REVERT: s 78 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7402 (t80) REVERT: s 115 ASP cc_start: 0.7641 (m-30) cc_final: 0.7237 (m-30) REVERT: s 283 ARG cc_start: 0.8300 (ttt90) cc_final: 0.7949 (ttt90) REVERT: s 308 MET cc_start: 0.8823 (mmm) cc_final: 0.8365 (mtm) REVERT: s 332 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7112 (p) REVERT: s 403 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7988 (tt) REVERT: s 417 SER cc_start: 0.8861 (m) cc_final: 0.8553 (t) REVERT: s 525 MET cc_start: 0.8553 (mmm) cc_final: 0.8265 (tpp) REVERT: s 730 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7401 (t) REVERT: t 29 SER cc_start: 0.9215 (m) cc_final: 0.8936 (t) REVERT: t 78 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.6706 (t80) REVERT: t 91 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8742 (mm) REVERT: t 190 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7576 (t0) REVERT: t 255 SER cc_start: 0.9254 (m) cc_final: 0.8875 (p) REVERT: t 283 ARG cc_start: 0.7089 (tpp-160) cc_final: 0.6774 (tpp-160) REVERT: t 308 MET cc_start: 0.8630 (mmm) cc_final: 0.8304 (mmm) REVERT: t 325 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7496 (pp) REVERT: t 348 ILE cc_start: 0.8519 (mt) cc_final: 0.8304 (tt) REVERT: t 360 PHE cc_start: 0.8678 (m-10) cc_final: 0.8293 (m-10) REVERT: t 367 ILE cc_start: 0.9176 (mp) cc_final: 0.8715 (mm) REVERT: t 430 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8196 (mt) REVERT: t 542 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7164 (m90) REVERT: t 697 ASP cc_start: 0.7132 (p0) cc_final: 0.6917 (p0) REVERT: u 29 SER cc_start: 0.9135 (m) cc_final: 0.8845 (t) REVERT: u 115 ASP cc_start: 0.7303 (m-30) cc_final: 0.6860 (m-30) REVERT: u 332 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7086 (p) REVERT: u 364 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: u 412 GLU cc_start: 0.7779 (pm20) cc_final: 0.7532 (pm20) REVERT: u 525 MET cc_start: 0.8732 (tpp) cc_final: 0.8377 (tpp) REVERT: u 542 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.6718 (m90) REVERT: u 591 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7457 (tpt170) REVERT: u 697 ASP cc_start: 0.7622 (p0) cc_final: 0.7386 (p0) REVERT: v 91 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8893 (mm) REVERT: v 115 ASP cc_start: 0.7455 (m-30) cc_final: 0.6514 (m-30) REVERT: v 308 MET cc_start: 0.8758 (mmm) cc_final: 0.8277 (mmm) REVERT: v 332 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7503 (p) REVERT: v 367 ILE cc_start: 0.9304 (mp) cc_final: 0.9063 (mm) REVERT: v 644 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6530 (tm-30) REVERT: v 742 ARG cc_start: 0.8179 (mmt180) cc_final: 0.7849 (mmm160) REVERT: w 29 SER cc_start: 0.9349 (m) cc_final: 0.9002 (t) REVERT: w 115 ASP cc_start: 0.7267 (m-30) cc_final: 0.6811 (m-30) REVERT: w 308 MET cc_start: 0.8657 (mmm) cc_final: 0.8245 (mmm) REVERT: w 332 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7551 (p) REVERT: w 364 GLU cc_start: 0.6910 (pm20) cc_final: 0.6642 (pm20) REVERT: w 367 ILE cc_start: 0.9091 (mp) cc_final: 0.8620 (mm) REVERT: w 542 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.7114 (m90) REVERT: w 567 ASN cc_start: 0.7731 (m-40) cc_final: 0.7488 (m-40) REVERT: w 570 ASN cc_start: 0.8025 (m-40) cc_final: 0.7530 (m110) REVERT: w 701 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.8997 (tp) REVERT: x 9 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7907 (mmtm) REVERT: x 29 SER cc_start: 0.9149 (m) cc_final: 0.8844 (t) REVERT: x 115 ASP cc_start: 0.7367 (m-30) cc_final: 0.7028 (m-30) REVERT: x 133 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9150 (p) REVERT: x 325 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6953 (pp) REVERT: x 332 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7342 (p) REVERT: x 550 GLN cc_start: 0.8248 (mt0) cc_final: 0.7819 (mp10) REVERT: x 561 MET cc_start: 0.8558 (tpp) cc_final: 0.7841 (ttt) REVERT: x 591 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7649 (tpt170) outliers start: 182 outliers final: 109 residues processed: 641 average time/residue: 0.4934 time to fit residues: 517.0845 Evaluate side-chains 589 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 457 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 403 LEU Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 563 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 730 THR Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 190 ASN Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 292 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 542 HIS Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain t residue 769 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 332 CYS Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 421 GLN Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 717 ASP Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 91 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 214 ASN Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 332 CYS Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 661 ASN Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 717 ASP Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 415 ILE Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 542 HIS Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 123 ASP Chi-restraints excluded: chain x residue 133 VAL Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 352 PHE Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 334 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 386 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 456 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 278 optimal weight: 0.4980 chunk 210 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 6 GLN s 31 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 491 HIS t 567 ASN ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN v 74 HIS ** v 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 190 ASN ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 477 GLN v 532 ASN w 10 ASN ** w 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 477 GLN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38748 Z= 0.216 Angle : 0.857 15.061 52692 Z= 0.429 Chirality : 0.051 0.189 5640 Planarity : 0.004 0.065 6918 Dihedral : 7.857 49.910 5214 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.26 % Favored : 82.49 % Rotamer: Outliers : 3.74 % Allowed : 20.79 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 1.33 % Twisted Proline : 0.46 % Twisted General : 0.91 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.11), residues: 4716 helix: -2.32 (0.38), residues: 168 sheet: -2.38 (0.13), residues: 1524 loop : -2.85 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP v 416 HIS 0.007 0.001 HIS v 74 PHE 0.032 0.002 PHE u 352 TYR 0.022 0.002 TYR x 77 ARG 0.009 0.001 ARG u 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 501 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9091 (m) cc_final: 0.8494 (t) REVERT: s 51 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (pp) REVERT: s 78 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7417 (t80) REVERT: s 115 ASP cc_start: 0.7654 (m-30) cc_final: 0.7215 (m-30) REVERT: s 283 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7817 (ttt90) REVERT: s 308 MET cc_start: 0.8810 (mmm) cc_final: 0.8334 (mtm) REVERT: s 332 CYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7188 (p) REVERT: s 525 MET cc_start: 0.8499 (mmm) cc_final: 0.8280 (tpp) REVERT: s 561 MET cc_start: 0.8707 (tpp) cc_final: 0.8284 (ttt) REVERT: s 596 MET cc_start: 0.7835 (ttp) cc_final: 0.7558 (tpp) REVERT: s 697 ASP cc_start: 0.6797 (p0) cc_final: 0.6567 (p0) REVERT: s 730 THR cc_start: 0.7341 (m) cc_final: 0.7052 (t) REVERT: t 29 SER cc_start: 0.9213 (m) cc_final: 0.8994 (t) REVERT: t 51 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8677 (pp) REVERT: t 91 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8719 (mm) REVERT: t 190 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7589 (t0) REVERT: t 308 MET cc_start: 0.8625 (mmm) cc_final: 0.8318 (mmm) REVERT: t 325 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7452 (pp) REVERT: t 348 ILE cc_start: 0.8477 (mt) cc_final: 0.8250 (tt) REVERT: t 360 PHE cc_start: 0.8650 (m-10) cc_final: 0.8176 (m-10) REVERT: t 367 ILE cc_start: 0.9121 (mp) cc_final: 0.8636 (mm) REVERT: t 430 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8080 (mt) REVERT: t 770 SER cc_start: 0.2192 (OUTLIER) cc_final: 0.1857 (t) REVERT: u 29 SER cc_start: 0.9115 (m) cc_final: 0.8844 (t) REVERT: u 332 CYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7111 (p) REVERT: u 364 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: u 525 MET cc_start: 0.8763 (tpp) cc_final: 0.8433 (tpp) REVERT: u 542 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.6660 (m90) REVERT: u 591 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7478 (tpt170) REVERT: u 697 ASP cc_start: 0.7715 (p0) cc_final: 0.7402 (p0) REVERT: v 91 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8668 (mm) REVERT: v 115 ASP cc_start: 0.7479 (m-30) cc_final: 0.6496 (m-30) REVERT: v 308 MET cc_start: 0.8754 (mmm) cc_final: 0.8280 (mmm) REVERT: v 314 ARG cc_start: 0.7814 (tpt-90) cc_final: 0.7032 (tpt-90) REVERT: v 332 CYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7547 (p) REVERT: v 367 ILE cc_start: 0.9238 (mp) cc_final: 0.9003 (mm) REVERT: v 591 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6606 (tpt90) REVERT: v 644 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6429 (tm-30) REVERT: v 742 ARG cc_start: 0.8201 (mmt180) cc_final: 0.7891 (mmm160) REVERT: w 29 SER cc_start: 0.9319 (m) cc_final: 0.8963 (t) REVERT: w 51 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8691 (pp) REVERT: w 115 ASP cc_start: 0.7308 (m-30) cc_final: 0.6849 (m-30) REVERT: w 308 MET cc_start: 0.8635 (mmm) cc_final: 0.8248 (mmm) REVERT: w 332 CYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7578 (p) REVERT: w 364 GLU cc_start: 0.7112 (pm20) cc_final: 0.6908 (pm20) REVERT: w 367 ILE cc_start: 0.9070 (mp) cc_final: 0.8577 (mm) REVERT: w 399 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7308 (ttm-80) REVERT: w 542 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.7081 (m90) REVERT: w 570 ASN cc_start: 0.7931 (m-40) cc_final: 0.7433 (m110) REVERT: w 701 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8936 (tp) REVERT: x 29 SER cc_start: 0.9158 (m) cc_final: 0.8807 (t) REVERT: x 115 ASP cc_start: 0.7329 (m-30) cc_final: 0.6985 (m-30) REVERT: x 133 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9227 (p) REVERT: x 314 ARG cc_start: 0.8483 (tpt-90) cc_final: 0.8188 (tpt-90) REVERT: x 325 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6848 (pp) REVERT: x 332 CYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7329 (p) REVERT: x 519 ASP cc_start: 0.7175 (p0) cc_final: 0.6973 (p0) REVERT: x 550 GLN cc_start: 0.8206 (mt0) cc_final: 0.7674 (mp10) REVERT: x 561 MET cc_start: 0.8566 (tpp) cc_final: 0.7822 (ttt) REVERT: x 591 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7553 (tpt170) REVERT: x 726 ASN cc_start: 0.7775 (m110) cc_final: 0.7353 (m-40) outliers start: 154 outliers final: 102 residues processed: 618 average time/residue: 0.4808 time to fit residues: 485.9052 Evaluate side-chains 572 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 446 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 591 ARG Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 190 ASN Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 292 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 415 ILE Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain t residue 770 SER Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 332 CYS Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 717 ASP Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 74 HIS Chi-restraints excluded: chain v residue 91 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 332 CYS Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 438 ASN Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 661 ASN Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 717 ASP Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 415 ILE Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 542 HIS Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 133 VAL Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 359 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 6 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN ** s 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 GLN t 168 HIS ** t 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 ASN ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 421 GLN v 10 ASN ** v 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 10 ASN ** w 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 567 ASN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 38748 Z= 0.252 Angle : 0.870 14.932 52692 Z= 0.435 Chirality : 0.051 0.235 5640 Planarity : 0.004 0.063 6918 Dihedral : 7.728 56.219 5214 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.71 % Favored : 82.04 % Rotamer: Outliers : 3.81 % Allowed : 21.30 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 1.33 % Twisted Proline : 0.46 % Twisted General : 0.73 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.11), residues: 4716 helix: -2.14 (0.38), residues: 168 sheet: -2.35 (0.13), residues: 1554 loop : -2.78 (0.10), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP v 416 HIS 0.026 0.001 HIS v 74 PHE 0.025 0.002 PHE s 352 TYR 0.026 0.002 TYR t 124 ARG 0.010 0.001 ARG u 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 467 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9094 (m) cc_final: 0.8501 (t) REVERT: s 51 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8167 (pp) REVERT: s 78 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7427 (t80) REVERT: s 308 MET cc_start: 0.8818 (mmm) cc_final: 0.8380 (mtm) REVERT: s 332 CYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7305 (p) REVERT: s 364 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6715 (mm-30) REVERT: s 561 MET cc_start: 0.8701 (tpp) cc_final: 0.8310 (ttt) REVERT: s 697 ASP cc_start: 0.6815 (p0) cc_final: 0.6486 (p0) REVERT: s 730 THR cc_start: 0.7216 (m) cc_final: 0.6882 (t) REVERT: t 29 SER cc_start: 0.9286 (m) cc_final: 0.9041 (t) REVERT: t 51 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8704 (pp) REVERT: t 78 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6598 (t80) REVERT: t 91 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8724 (mm) REVERT: t 190 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7604 (t0) REVERT: t 308 MET cc_start: 0.8656 (mmm) cc_final: 0.8334 (mmm) REVERT: t 325 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7389 (pp) REVERT: t 360 PHE cc_start: 0.8687 (m-10) cc_final: 0.8236 (m-10) REVERT: t 367 ILE cc_start: 0.9142 (mp) cc_final: 0.8666 (mm) REVERT: t 430 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (mt) REVERT: u 29 SER cc_start: 0.9094 (m) cc_final: 0.8869 (t) REVERT: u 283 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7951 (ttt90) REVERT: u 364 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6344 (pm20) REVERT: u 525 MET cc_start: 0.8770 (tpp) cc_final: 0.8376 (tpp) REVERT: u 591 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7499 (tpt170) REVERT: u 697 ASP cc_start: 0.7648 (p0) cc_final: 0.7330 (p0) REVERT: v 91 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8691 (mm) REVERT: v 115 ASP cc_start: 0.7481 (m-30) cc_final: 0.6464 (m-30) REVERT: v 308 MET cc_start: 0.8764 (mmm) cc_final: 0.8291 (mmm) REVERT: v 314 ARG cc_start: 0.7794 (tpt-90) cc_final: 0.7341 (tpt-90) REVERT: v 332 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7526 (p) REVERT: v 367 ILE cc_start: 0.9255 (mp) cc_final: 0.8989 (mm) REVERT: v 591 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6519 (tpt90) REVERT: v 644 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6470 (tm-30) REVERT: v 742 ARG cc_start: 0.8259 (mmt180) cc_final: 0.7910 (mmm160) REVERT: w 29 SER cc_start: 0.9290 (m) cc_final: 0.8973 (t) REVERT: w 51 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8702 (pp) REVERT: w 115 ASP cc_start: 0.7366 (m-30) cc_final: 0.6887 (m-30) REVERT: w 308 MET cc_start: 0.8745 (mmm) cc_final: 0.8372 (mmm) REVERT: w 325 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7551 (pp) REVERT: w 332 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7613 (p) REVERT: w 367 ILE cc_start: 0.9069 (mp) cc_final: 0.8580 (mm) REVERT: w 542 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.7127 (m90) REVERT: w 701 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8983 (tp) REVERT: w 731 MET cc_start: 0.8357 (tmm) cc_final: 0.7647 (tmm) REVERT: x 29 SER cc_start: 0.9101 (m) cc_final: 0.8861 (t) REVERT: x 115 ASP cc_start: 0.7400 (m-30) cc_final: 0.7055 (m-30) REVERT: x 325 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6887 (pp) REVERT: x 332 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7393 (p) REVERT: x 364 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: x 550 GLN cc_start: 0.8236 (mt0) cc_final: 0.7692 (mp10) REVERT: x 561 MET cc_start: 0.8647 (tpp) cc_final: 0.8355 (ttt) REVERT: x 591 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7025 (tpt170) REVERT: x 726 ASN cc_start: 0.7796 (m110) cc_final: 0.7369 (m-40) outliers start: 157 outliers final: 105 residues processed: 587 average time/residue: 0.4867 time to fit residues: 466.4335 Evaluate side-chains 572 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 444 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 563 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 703 LEU Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 190 ASN Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 292 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 717 ASP Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 91 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 332 CYS Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 416 TRP Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 438 ASN Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 717 ASP Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 542 HIS Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 438 ASN Chi-restraints excluded: chain x residue 495 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 9.9990 chunk 437 optimal weight: 4.9990 chunk 399 optimal weight: 0.0970 chunk 425 optimal weight: 0.5980 chunk 256 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 130 optimal weight: 0.0050 chunk 384 optimal weight: 0.2980 chunk 402 optimal weight: 0.7980 chunk 424 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 491 HIS ** v 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 10 ASN ** w 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 570 ASN x 76 GLN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 38748 Z= 0.206 Angle : 0.857 15.261 52692 Z= 0.428 Chirality : 0.050 0.206 5640 Planarity : 0.004 0.060 6918 Dihedral : 7.517 50.320 5214 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.03 % Favored : 82.72 % Rotamer: Outliers : 3.42 % Allowed : 21.98 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.11), residues: 4716 helix: -2.10 (0.34), residues: 204 sheet: -2.55 (0.13), residues: 1530 loop : -2.63 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP u 416 HIS 0.006 0.001 HIS u 471 PHE 0.060 0.002 PHE x 50 TYR 0.021 0.001 TYR s 405 ARG 0.010 0.001 ARG u 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 482 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 20 ASP cc_start: 0.8054 (t0) cc_final: 0.7851 (t0) REVERT: s 29 SER cc_start: 0.9100 (m) cc_final: 0.8525 (t) REVERT: s 51 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8081 (pp) REVERT: s 78 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.7403 (t80) REVERT: s 308 MET cc_start: 0.8781 (mmm) cc_final: 0.8350 (mtm) REVERT: s 332 CYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7333 (p) REVERT: s 364 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6626 (mm-30) REVERT: s 525 MET cc_start: 0.8487 (mmm) cc_final: 0.8181 (tpp) REVERT: s 561 MET cc_start: 0.8693 (tpp) cc_final: 0.8267 (ttt) REVERT: s 697 ASP cc_start: 0.6916 (p0) cc_final: 0.6529 (p0) REVERT: s 730 THR cc_start: 0.6989 (m) cc_final: 0.6713 (t) REVERT: t 29 SER cc_start: 0.9295 (m) cc_final: 0.9036 (t) REVERT: t 51 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8639 (pp) REVERT: t 78 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6609 (t80) REVERT: t 91 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8739 (mm) REVERT: t 115 ASP cc_start: 0.7346 (m-30) cc_final: 0.6856 (m-30) REVERT: t 190 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7616 (t0) REVERT: t 308 MET cc_start: 0.8601 (mmm) cc_final: 0.8325 (mmm) REVERT: t 325 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7277 (pp) REVERT: t 367 ILE cc_start: 0.9102 (mp) cc_final: 0.8612 (mm) REVERT: t 430 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7788 (mt) REVERT: t 542 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.7016 (m90) REVERT: u 29 SER cc_start: 0.9106 (m) cc_final: 0.8769 (t) REVERT: u 283 ARG cc_start: 0.8279 (ttt90) cc_final: 0.7873 (tpm170) REVERT: u 326 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6844 (tm-30) REVERT: u 364 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: u 416 TRP cc_start: 0.8995 (m-10) cc_final: 0.8647 (m100) REVERT: u 594 MET cc_start: 0.8380 (tpp) cc_final: 0.8025 (tpp) REVERT: u 697 ASP cc_start: 0.7708 (p0) cc_final: 0.7374 (p0) REVERT: v 91 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8766 (mm) REVERT: v 115 ASP cc_start: 0.7447 (m-30) cc_final: 0.6424 (m-30) REVERT: v 308 MET cc_start: 0.8727 (mmm) cc_final: 0.8290 (mmm) REVERT: v 314 ARG cc_start: 0.7864 (tpt-90) cc_final: 0.7645 (tpt-90) REVERT: v 367 ILE cc_start: 0.9139 (mp) cc_final: 0.8881 (mm) REVERT: v 473 TYR cc_start: 0.9066 (t80) cc_final: 0.8686 (t80) REVERT: v 591 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7034 (tpt90) REVERT: v 644 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6389 (tm-30) REVERT: v 703 LEU cc_start: 0.8481 (tt) cc_final: 0.8143 (tt) REVERT: v 742 ARG cc_start: 0.8233 (mmt180) cc_final: 0.7910 (mmm160) REVERT: w 29 SER cc_start: 0.9180 (m) cc_final: 0.8852 (t) REVERT: w 51 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8620 (pp) REVERT: w 115 ASP cc_start: 0.7294 (m-30) cc_final: 0.6792 (m-30) REVERT: w 308 MET cc_start: 0.8735 (mmm) cc_final: 0.8410 (mmm) REVERT: w 325 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7547 (pp) REVERT: w 367 ILE cc_start: 0.9054 (mp) cc_final: 0.8554 (mm) REVERT: w 542 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6972 (m90) REVERT: w 701 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8973 (tp) REVERT: w 731 MET cc_start: 0.8246 (tmm) cc_final: 0.7503 (tmm) REVERT: x 29 SER cc_start: 0.9115 (m) cc_final: 0.8852 (t) REVERT: x 115 ASP cc_start: 0.7407 (m-30) cc_final: 0.7051 (m-30) REVERT: x 325 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6839 (pp) REVERT: x 332 CYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7438 (p) REVERT: x 352 PHE cc_start: 0.7979 (m-80) cc_final: 0.7778 (m-80) REVERT: x 364 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: x 550 GLN cc_start: 0.8160 (mt0) cc_final: 0.7644 (mp10) REVERT: x 561 MET cc_start: 0.8685 (tpp) cc_final: 0.8356 (ttt) REVERT: x 591 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7036 (tpt170) REVERT: x 726 ASN cc_start: 0.7795 (m110) cc_final: 0.7400 (m-40) outliers start: 141 outliers final: 97 residues processed: 593 average time/residue: 0.4882 time to fit residues: 477.1695 Evaluate side-chains 548 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 430 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 563 VAL Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 717 ASP Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 190 ASN Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 292 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 415 ILE Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 542 HIS Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 717 ASP Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 91 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 416 TRP Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 438 ASN Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 344 VAL Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 542 HIS Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 438 ASN Chi-restraints excluded: chain x residue 495 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 666 MET Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.0270 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 472 optimal weight: 2.9990 chunk 434 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 10 ASN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 570 ASN ** s 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 168 HIS ** t 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 567 ASN ** t 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 GLN u 168 HIS ** u 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN ** v 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 764 ASN w 190 ASN ** w 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 712 ASN ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 38748 Z= 0.457 Angle : 0.958 16.760 52692 Z= 0.485 Chirality : 0.054 0.229 5640 Planarity : 0.005 0.065 6918 Dihedral : 7.930 54.399 5214 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 19.25 % Favored : 80.47 % Rotamer: Outliers : 3.08 % Allowed : 22.83 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 1.33 % Twisted Proline : 0.46 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.11), residues: 4716 helix: -1.48 (0.47), residues: 132 sheet: -2.49 (0.12), residues: 1632 loop : -2.76 (0.10), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP v 416 HIS 0.006 0.002 HIS u 542 PHE 0.049 0.003 PHE x 50 TYR 0.020 0.002 TYR x 405 ARG 0.010 0.001 ARG u 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 433 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 29 SER cc_start: 0.9161 (m) cc_final: 0.8589 (t) REVERT: s 51 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8337 (pp) REVERT: s 78 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7373 (t80) REVERT: s 308 MET cc_start: 0.8879 (mmm) cc_final: 0.8497 (mmm) REVERT: s 332 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7395 (p) REVERT: s 352 PHE cc_start: 0.8089 (m-80) cc_final: 0.7755 (m-80) REVERT: s 525 MET cc_start: 0.8696 (mmm) cc_final: 0.8427 (tpp) REVERT: s 561 MET cc_start: 0.8696 (tpp) cc_final: 0.8470 (ttt) REVERT: s 730 THR cc_start: 0.8162 (m) cc_final: 0.7758 (t) REVERT: t 29 SER cc_start: 0.9356 (m) cc_final: 0.9055 (t) REVERT: t 51 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8795 (pp) REVERT: t 78 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.7169 (t80) REVERT: t 91 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8862 (mm) REVERT: t 190 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7769 (t0) REVERT: t 308 MET cc_start: 0.8783 (mmm) cc_final: 0.8398 (mmm) REVERT: t 325 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7905 (pp) REVERT: t 367 ILE cc_start: 0.9264 (mp) cc_final: 0.8815 (mm) REVERT: t 542 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7287 (m90) REVERT: t 561 MET cc_start: 0.8608 (tpp) cc_final: 0.8042 (ttt) REVERT: t 772 GLU cc_start: 0.6873 (tp30) cc_final: 0.6416 (tp30) REVERT: u 29 SER cc_start: 0.9103 (m) cc_final: 0.8818 (t) REVERT: u 416 TRP cc_start: 0.9016 (m-10) cc_final: 0.8724 (m-10) REVERT: u 417 SER cc_start: 0.8975 (m) cc_final: 0.8741 (t) REVERT: u 594 MET cc_start: 0.8472 (tpp) cc_final: 0.8041 (tpp) REVERT: u 697 ASP cc_start: 0.7920 (p0) cc_final: 0.7527 (p0) REVERT: v 115 ASP cc_start: 0.7538 (m-30) cc_final: 0.6524 (m-30) REVERT: v 308 MET cc_start: 0.8862 (mmm) cc_final: 0.8412 (mmm) REVERT: v 367 ILE cc_start: 0.9267 (mp) cc_final: 0.9050 (mm) REVERT: v 742 ARG cc_start: 0.8459 (mmt180) cc_final: 0.8082 (mmp-170) REVERT: w 29 SER cc_start: 0.9344 (m) cc_final: 0.9136 (t) REVERT: w 51 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8791 (pp) REVERT: w 115 ASP cc_start: 0.7495 (m-30) cc_final: 0.7215 (m-30) REVERT: w 308 MET cc_start: 0.8897 (mmm) cc_final: 0.8461 (mmm) REVERT: w 325 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7527 (pp) REVERT: w 332 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7610 (p) REVERT: w 367 ILE cc_start: 0.9205 (mp) cc_final: 0.8743 (mm) REVERT: w 542 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7642 (m90) REVERT: w 731 MET cc_start: 0.8814 (tmm) cc_final: 0.7888 (tmm) REVERT: w 772 GLU cc_start: 0.7149 (tp30) cc_final: 0.6718 (tp30) REVERT: x 29 SER cc_start: 0.9147 (m) cc_final: 0.8858 (t) REVERT: x 51 LEU cc_start: 0.8433 (pp) cc_final: 0.8207 (pp) REVERT: x 115 ASP cc_start: 0.7619 (m-30) cc_final: 0.7236 (m-30) REVERT: x 325 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7385 (pp) REVERT: x 332 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7379 (p) REVERT: x 550 GLN cc_start: 0.8410 (mt0) cc_final: 0.7779 (mp10) REVERT: x 561 MET cc_start: 0.8742 (tpp) cc_final: 0.8018 (ttt) outliers start: 127 outliers final: 88 residues processed: 535 average time/residue: 0.4890 time to fit residues: 429.7518 Evaluate side-chains 505 residues out of total 4122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 402 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 717 ASP Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 792 SER Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 190 ASN Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 415 ILE Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 542 HIS Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 687 THR Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 138 THR Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 415 ILE Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 717 ASP Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 131 ASN Chi-restraints excluded: chain v residue 214 ASN Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 414 LEU Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 438 ASN Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 332 CYS Chi-restraints excluded: chain w residue 385 LEU Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 486 GLU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 542 HIS Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 656 LEU Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 332 CYS Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 438 ASN Chi-restraints excluded: chain x residue 495 TYR Chi-restraints excluded: chain x residue 656 LEU Chi-restraints excluded: chain x residue 666 MET Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 717 ASP Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 346 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 0.0010 chunk 376 optimal weight: 0.2980 chunk 157 optimal weight: 1.9990 chunk 386 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 567 ASN ** t 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 10 ASN ** v 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN v 672 ASN w 10 ASN ** w 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 726 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086506 restraints weight = 75778.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088680 restraints weight = 42129.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090079 restraints weight = 28431.380| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 38748 Z= 0.237 Angle : 0.880 15.784 52692 Z= 0.441 Chirality : 0.052 0.223 5640 Planarity : 0.005 0.060 6918 Dihedral : 7.685 54.760 5214 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.77 % Favored : 82.97 % Rotamer: Outliers : 2.50 % Allowed : 23.87 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 1.33 % Twisted Proline : 0.46 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.11), residues: 4716 helix: -1.80 (0.35), residues: 204 sheet: -2.48 (0.13), residues: 1440 loop : -2.69 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP v 416 HIS 0.005 0.001 HIS x 542 PHE 0.037 0.002 PHE x 50 TYR 0.040 0.002 TYR w 405 ARG 0.009 0.001 ARG u 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9345.28 seconds wall clock time: 170 minutes 7.51 seconds (10207.51 seconds total)