Starting phenix.real_space_refine on Fri Feb 23 06:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzh_33527/02_2024/7xzh_33527_neut_updated.pdb" } resolution = 2.78 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= 0.003 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 156 5.16 5 C 24296 2.51 5 N 6095 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B ARG 731": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 804": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C ARG 731": "NH1" <-> "NH2" Residue "C ARG 734": "NH1" <-> "NH2" Residue "C ARG 804": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ARG 496": "NH1" <-> "NH2" Residue "D ARG 666": "NH1" <-> "NH2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 734": "NH1" <-> "NH2" Residue "D ARG 804": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E ARG 666": "NH1" <-> "NH2" Residue "E ARG 719": "NH1" <-> "NH2" Residue "E ARG 731": "NH1" <-> "NH2" Residue "E ARG 734": "NH1" <-> "NH2" Residue "E ARG 804": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F ARG 496": "NH1" <-> "NH2" Residue "F ARG 666": "NH1" <-> "NH2" Residue "F ARG 719": "NH1" <-> "NH2" Residue "F ARG 731": "NH1" <-> "NH2" Residue "F ARG 734": "NH1" <-> "NH2" Residue "F ARG 804": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37073 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 6025 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 29, 'TRANS': 699} Chain breaks: 2 Chain: "B" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "C" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "D" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "E" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 18.60, per 1000 atoms: 0.50 Number of scatterers: 37073 At special positions: 0 Unit cell: (147.68, 143.52, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 12 15.00 O 6514 8.00 N 6095 7.00 C 24296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.02 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 6.0 seconds 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8518 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 18 sheets defined 45.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.89 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.414A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 145 Proline residue: A 126 - end of helix removed outlier: 5.306A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 4.287A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.721A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 344 Processing helix chain 'A' and resid 356 through 359 No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.029A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.763A pdb=" N GLN A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.957A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.101A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.749A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.620A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'B' and resid 4 through 9 removed outlier: 4.165A pdb=" N TYR B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.642A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 48 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.991A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.960A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 260 through 288 removed outlier: 4.510A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 315 through 344 Processing helix chain 'B' and resid 356 through 359 No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'B' and resid 373 through 382 removed outlier: 3.659A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 removed outlier: 3.880A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 4.168A pdb=" N ASN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.944A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 removed outlier: 5.088A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 4.744A pdb=" N VAL B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.790A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 788 through 793 removed outlier: 3.946A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.490A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 5.404A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 4.469A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 237 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.625A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 356 through 359 No H-bonds generated for 'chain 'C' and resid 356 through 359' Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.998A pdb=" N ILE C 379 " --> pdb=" O MET C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.924A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.541A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 510 through 514 removed outlier: 3.957A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 4.101A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'C' and resid 586 through 589 Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.749A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 679 through 683 Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 725 through 729 Processing helix chain 'C' and resid 748 through 752 Processing helix chain 'C' and resid 771 through 775 Processing helix chain 'C' and resid 788 through 793 removed outlier: 3.619A pdb=" N THR C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 Processing helix chain 'D' and resid 4 through 7 No H-bonds generated for 'chain 'D' and resid 4 through 7' Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 120 through 145 Proline residue: D 126 - end of helix removed outlier: 5.081A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.824A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.562A pdb=" N LYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 288 removed outlier: 3.540A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 313 through 344 removed outlier: 4.360A pdb=" N THR D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 360 Processing helix chain 'D' and resid 373 through 382 removed outlier: 3.754A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.850A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 410 removed outlier: 4.138A pdb=" N ASN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 removed outlier: 3.551A pdb=" N ARG D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 510 through 514 removed outlier: 3.945A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 542 removed outlier: 5.088A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 4.743A pdb=" N VAL D 567 " --> pdb=" O THR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 630 through 637 removed outlier: 3.790A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 748 through 752 Processing helix chain 'D' and resid 771 through 775 Processing helix chain 'D' and resid 788 through 793 removed outlier: 3.946A pdb=" N THR D 793 " --> pdb=" O ASP D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'E' and resid 7 through 9 No H-bonds generated for 'chain 'E' and resid 7 through 9' Processing helix chain 'E' and resid 15 through 20 removed outlier: 4.361A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 48 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 5.322A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 4.295A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.694A pdb=" N LYS E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 288 removed outlier: 4.555A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 344 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 373 through 380 Processing helix chain 'E' and resid 384 through 394 removed outlier: 3.978A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU E 394 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 485 through 493 Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 510 through 514 removed outlier: 3.958A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 4.102A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 Processing helix chain 'E' and resid 586 through 589 Processing helix chain 'E' and resid 608 through 612 Processing helix chain 'E' and resid 630 through 637 removed outlier: 3.751A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 660 Processing helix chain 'E' and resid 679 through 683 Processing helix chain 'E' and resid 702 through 706 Processing helix chain 'E' and resid 725 through 729 Processing helix chain 'E' and resid 748 through 752 Processing helix chain 'E' and resid 771 through 775 Processing helix chain 'E' and resid 788 through 793 removed outlier: 3.619A pdb=" N THR E 793 " --> pdb=" O ASP E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 806 Processing helix chain 'F' and resid 4 through 10 removed outlier: 4.273A pdb=" N TYR F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.660A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 48 Processing helix chain 'F' and resid 103 through 116 Processing helix chain 'F' and resid 120 through 145 Proline residue: F 126 - end of helix removed outlier: 4.994A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 165 removed outlier: 3.891A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 234 through 254 removed outlier: 3.739A pdb=" N LYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 288 removed outlier: 3.622A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 344 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 384 through 394 removed outlier: 3.854A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU F 394 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 410 Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.549A pdb=" N ARG F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 463 through 467 Processing helix chain 'F' and resid 485 through 493 Processing helix chain 'F' and resid 505 through 507 No H-bonds generated for 'chain 'F' and resid 505 through 507' Processing helix chain 'F' and resid 510 through 514 removed outlier: 3.945A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 542 removed outlier: 5.088A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 removed outlier: 4.742A pdb=" N VAL F 567 " --> pdb=" O THR F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 Processing helix chain 'F' and resid 609 through 612 Processing helix chain 'F' and resid 630 through 637 removed outlier: 3.790A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 660 Processing helix chain 'F' and resid 679 through 683 Processing helix chain 'F' and resid 702 through 706 Processing helix chain 'F' and resid 725 through 729 Processing helix chain 'F' and resid 748 through 752 Processing helix chain 'F' and resid 771 through 775 Processing helix chain 'F' and resid 788 through 793 removed outlier: 3.946A pdb=" N THR F 793 " --> pdb=" O ASP F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 806 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.551A pdb=" N VAL A 450 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 432 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS A 452 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A 473 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU A 453 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP A 475 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA A 497 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU A 476 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N HIS A 499 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU A 520 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE A 500 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 522 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 548 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU A 523 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 550 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 571 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU A 551 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 573 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU A 595 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE A 574 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 597 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU A 618 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A 598 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 620 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS A 643 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG A 666 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 689 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 712 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 735 " --> pdb=" O LEU A 713 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 459 through 461 Processing sheet with id= D, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= E, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.856A pdb=" N VAL B 450 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU B 432 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS B 452 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU B 473 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU B 453 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP B 475 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 497 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 476 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS B 499 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU B 520 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE B 500 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS B 522 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 548 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU B 523 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG B 550 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 571 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 551 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER B 573 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU B 595 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE B 574 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLU B 597 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 618 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU B 598 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP B 620 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 643 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG B 666 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR B 689 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN B 712 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 735 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN B 758 " --> pdb=" O LEU B 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 459 through 461 Processing sheet with id= G, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= H, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.552A pdb=" N VAL C 450 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU C 432 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS C 452 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 473 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LEU C 453 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP C 475 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 497 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU C 476 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS C 499 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C 520 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE C 500 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS C 522 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 548 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU C 523 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG C 550 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS C 571 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU C 551 " --> pdb=" O LYS C 571 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER C 573 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU C 595 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE C 574 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU C 597 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU C 618 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU C 598 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP C 620 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS C 643 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG C 666 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 689 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C 712 " --> pdb=" O LEU C 690 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA C 735 " --> pdb=" O LEU C 713 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 459 through 461 Processing sheet with id= J, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= K, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.856A pdb=" N VAL D 450 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU D 432 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS D 452 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU D 473 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU D 453 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP D 475 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 497 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU D 476 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS D 499 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU D 520 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE D 500 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS D 522 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 548 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU D 523 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG D 550 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS D 571 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 551 " --> pdb=" O LYS D 571 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER D 573 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU D 595 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE D 574 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU D 597 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU D 618 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU D 598 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 620 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS D 643 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG D 666 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR D 689 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN D 712 " --> pdb=" O LEU D 690 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA D 735 " --> pdb=" O LEU D 713 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN D 758 " --> pdb=" O LEU D 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= M, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= N, first strand: chain 'E' and resid 429 through 433 removed outlier: 6.551A pdb=" N VAL E 450 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 432 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS E 452 " --> pdb=" O LEU E 432 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 473 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LEU E 453 " --> pdb=" O GLU E 473 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP E 475 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA E 497 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU E 476 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS E 499 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU E 520 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE E 500 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS E 522 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 548 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU E 523 " --> pdb=" O VAL E 548 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG E 550 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS E 571 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU E 551 " --> pdb=" O LYS E 571 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER E 573 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU E 595 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE E 574 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU E 597 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU E 618 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU E 598 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP E 620 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS E 643 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG E 666 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN E 712 " --> pdb=" O LEU E 690 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA E 735 " --> pdb=" O LEU E 713 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 459 through 461 Processing sheet with id= P, first strand: chain 'F' and resid 53 through 56 Processing sheet with id= Q, first strand: chain 'F' and resid 429 through 433 removed outlier: 6.855A pdb=" N VAL F 450 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU F 432 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS F 452 " --> pdb=" O LEU F 432 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU F 473 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU F 453 " --> pdb=" O GLU F 473 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP F 475 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA F 497 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU F 476 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS F 499 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU F 520 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE F 500 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS F 522 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL F 548 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU F 523 " --> pdb=" O VAL F 548 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG F 550 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS F 571 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU F 551 " --> pdb=" O LYS F 571 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER F 573 " --> pdb=" O LEU F 551 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU F 595 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE F 574 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU F 597 " --> pdb=" O ILE F 574 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU F 618 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU F 598 " --> pdb=" O GLU F 618 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 620 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS F 643 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG F 666 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR F 689 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN F 712 " --> pdb=" O LEU F 690 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA F 735 " --> pdb=" O LEU F 713 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN F 758 " --> pdb=" O LEU F 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 459 through 461 1194 hydrogen bonds defined for protein. 3012 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: 13.65 Time building geometry restraints manager: 14.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8019 1.33 - 1.45: 7876 1.45 - 1.57: 21772 1.57 - 1.69: 30 1.69 - 1.81: 216 Bond restraints: 37913 Sorted by residual: bond pdb=" C38 P5S A 901 " pdb=" O37 P5S A 901 " ideal model delta sigma weight residual 1.331 1.462 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C31 POV E 902 " pdb=" O31 POV E 902 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C31 POV F 902 " pdb=" O31 POV F 902 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C31 POV B 904 " pdb=" O31 POV B 904 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C31 POV D 902 " pdb=" O31 POV D 902 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 37908 not shown) Histogram of bond angle deviations from ideal: 95.61 - 103.37: 315 103.37 - 111.13: 15452 111.13 - 118.89: 16027 118.89 - 126.64: 19013 126.64 - 134.40: 567 Bond angle restraints: 51374 Sorted by residual: angle pdb=" N LEU D 584 " pdb=" CA LEU D 584 " pdb=" C LEU D 584 " ideal model delta sigma weight residual 111.52 124.27 -12.75 1.40e+00 5.10e-01 8.29e+01 angle pdb=" N TYR B 683 " pdb=" CA TYR B 683 " pdb=" C TYR B 683 " ideal model delta sigma weight residual 113.28 102.85 10.43 1.22e+00 6.72e-01 7.31e+01 angle pdb=" N GLU C 767 " pdb=" CA GLU C 767 " pdb=" C GLU C 767 " ideal model delta sigma weight residual 113.55 103.34 10.21 1.26e+00 6.30e-01 6.57e+01 angle pdb=" N TYR A 683 " pdb=" CA TYR A 683 " pdb=" C TYR A 683 " ideal model delta sigma weight residual 113.28 103.93 9.35 1.22e+00 6.72e-01 5.87e+01 angle pdb=" N TYR E 683 " pdb=" CA TYR E 683 " pdb=" C TYR E 683 " ideal model delta sigma weight residual 113.18 104.26 8.92 1.21e+00 6.83e-01 5.44e+01 ... (remaining 51369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 23104 35.72 - 71.44: 502 71.44 - 107.16: 42 107.16 - 142.88: 22 142.88 - 178.61: 14 Dihedral angle restraints: 23684 sinusoidal: 10619 harmonic: 13065 Sorted by residual: dihedral pdb=" CA GLU D 6 " pdb=" C GLU D 6 " pdb=" N LEU D 7 " pdb=" CA LEU D 7 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL E 4 " pdb=" C VAL E 4 " pdb=" N THR E 5 " pdb=" CA THR E 5 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ARG D 8 " pdb=" C ARG D 8 " pdb=" N TYR D 9 " pdb=" CA TYR D 9 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 23681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5682 0.119 - 0.239: 199 0.239 - 0.358: 24 0.358 - 0.477: 1 0.477 - 0.596: 2 Chirality restraints: 5908 Sorted by residual: chirality pdb=" CA LEU D 584 " pdb=" N LEU D 584 " pdb=" C LEU D 584 " pdb=" CB LEU D 584 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA PHE F 682 " pdb=" N PHE F 682 " pdb=" C PHE F 682 " pdb=" CB PHE F 682 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CA ARG D 346 " pdb=" N ARG D 346 " pdb=" C ARG D 346 " pdb=" CB ARG D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 5905 not shown) Planarity restraints: 6251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 409 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ASN A 409 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN A 409 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 345 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ARG D 345 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG D 345 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG D 346 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 582 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C ILE D 582 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE D 582 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL D 583 " 0.018 2.00e-02 2.50e+03 ... (remaining 6248 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 481 2.63 - 3.20: 34472 3.20 - 3.77: 55805 3.77 - 4.33: 82156 4.33 - 4.90: 131760 Nonbonded interactions: 304674 Sorted by model distance: nonbonded pdb=" OG1 THR F 48 " pdb=" OE1 GLN F 49 " model vdw 2.064 2.440 nonbonded pdb=" O LEU A 584 " pdb=" CB ASN A 585 " model vdw 2.182 3.440 nonbonded pdb=" OE2 GLU E 577 " pdb=" NZ LYS F 516 " model vdw 2.223 2.520 nonbonded pdb=" OG1 THR D 303 " pdb=" OH TYR D 308 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR F 303 " pdb=" OH TYR F 308 " model vdw 2.232 2.440 ... (remaining 304669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 807) selection = (chain 'B' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'C' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'D' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'E' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'F' and (resid 1 through 175 or resid 231 through 807)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 8.270 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 91.110 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 0.131 37913 Z= 0.538 Angle : 0.985 12.749 51374 Z= 0.503 Chirality : 0.056 0.596 5908 Planarity : 0.005 0.078 6251 Dihedral : 15.726 178.605 15112 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 1.23 % Allowed : 7.73 % Favored : 91.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4343 helix: -0.56 (0.12), residues: 2042 sheet: -1.68 (0.21), residues: 576 loop : -0.71 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 143 HIS 0.011 0.002 HIS B 694 PHE 0.023 0.002 PHE E 728 TYR 0.019 0.002 TYR E 281 ARG 0.012 0.001 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 458 time to evaluate : 4.140 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: A 245 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 371 ASP cc_start: 0.8885 (t0) cc_final: 0.8654 (t0) REVERT: A 526 ASN cc_start: 0.6391 (t0) cc_final: 0.6086 (t0) REVERT: B 476 LEU cc_start: 0.8949 (mt) cc_final: 0.8625 (pp) REVERT: B 500 ILE cc_start: 0.8314 (mt) cc_final: 0.7700 (mt) REVERT: B 692 LEU cc_start: 0.8902 (mt) cc_final: 0.8153 (tt) REVERT: C 410 GLU cc_start: 0.8306 (pt0) cc_final: 0.8008 (tm-30) REVERT: C 413 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6017 (tp) REVERT: C 414 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7777 (t0) REVERT: C 444 ASP cc_start: 0.7632 (m-30) cc_final: 0.7349 (m-30) REVERT: C 451 LEU cc_start: 0.8528 (tp) cc_final: 0.8316 (tm) REVERT: C 501 LYS cc_start: 0.8580 (tttm) cc_final: 0.8330 (tptp) REVERT: C 691 ASP cc_start: 0.7805 (t0) cc_final: 0.7567 (p0) REVERT: C 692 LEU cc_start: 0.9073 (mt) cc_final: 0.8746 (pp) REVERT: D 500 ILE cc_start: 0.8180 (mt) cc_final: 0.7522 (mt) REVERT: E 154 GLU cc_start: 0.8796 (tt0) cc_final: 0.8496 (mm-30) REVERT: E 409 ASN cc_start: 0.8388 (m110) cc_final: 0.7428 (t0) REVERT: E 451 LEU cc_start: 0.8650 (tp) cc_final: 0.8408 (tm) REVERT: E 499 HIS cc_start: 0.6438 (m90) cc_final: 0.6182 (m90) REVERT: E 510 LEU cc_start: 0.7868 (mt) cc_final: 0.7493 (pp) REVERT: E 692 LEU cc_start: 0.9090 (mt) cc_final: 0.8802 (pp) REVERT: E 713 LEU cc_start: 0.8568 (tp) cc_final: 0.8319 (mt) REVERT: F 63 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7412 (t0) REVERT: F 476 LEU cc_start: 0.8652 (mt) cc_final: 0.8292 (pp) REVERT: F 692 LEU cc_start: 0.8934 (mt) cc_final: 0.8698 (pt) outliers start: 50 outliers final: 5 residues processed: 497 average time/residue: 1.4763 time to fit residues: 886.2374 Evaluate side-chains 251 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain F residue 63 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 0.5980 chunk 331 optimal weight: 5.9990 chunk 183 optimal weight: 0.0570 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 342 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 254 optimal weight: 0.0670 chunk 396 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS C 718 ASN D 404 GLN D 409 ASN D 418 GLN ** D 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37913 Z= 0.183 Angle : 0.679 15.653 51374 Z= 0.325 Chirality : 0.043 0.178 5908 Planarity : 0.004 0.048 6251 Dihedral : 15.386 176.559 6046 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.09 % Allowed : 11.86 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4343 helix: -0.15 (0.12), residues: 2008 sheet: -1.43 (0.22), residues: 572 loop : -0.42 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 411 HIS 0.006 0.001 HIS F 694 PHE 0.016 0.001 PHE F 433 TYR 0.012 0.001 TYR C 338 ARG 0.009 0.001 ARG C 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 273 time to evaluate : 4.493 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: A 371 ASP cc_start: 0.8660 (t0) cc_final: 0.8194 (t0) REVERT: A 399 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: A 433 PHE cc_start: 0.6685 (t80) cc_final: 0.6464 (t80) REVERT: A 526 ASN cc_start: 0.6380 (t0) cc_final: 0.6151 (t0) REVERT: A 550 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7975 (mtm-85) REVERT: B 238 GLU cc_start: 0.9044 (tp30) cc_final: 0.8044 (tm-30) REVERT: B 692 LEU cc_start: 0.8876 (mt) cc_final: 0.8269 (tt) REVERT: C 410 GLU cc_start: 0.8205 (pt0) cc_final: 0.7959 (tm-30) REVERT: C 434 MET cc_start: 0.8477 (mmm) cc_final: 0.8251 (mmp) REVERT: C 590 MET cc_start: 0.3195 (mpm) cc_final: 0.2975 (mpm) REVERT: C 691 ASP cc_start: 0.7984 (t0) cc_final: 0.7466 (p0) REVERT: C 692 LEU cc_start: 0.9067 (mt) cc_final: 0.8856 (pp) REVERT: C 736 LEU cc_start: 0.8972 (tp) cc_final: 0.8449 (mm) REVERT: D 238 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 17 TYR cc_start: 0.8780 (m-10) cc_final: 0.8117 (m-10) REVERT: E 154 GLU cc_start: 0.8772 (tt0) cc_final: 0.8491 (mm-30) REVERT: E 165 ASP cc_start: 0.8936 (t0) cc_final: 0.8562 (t0) REVERT: E 245 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8453 (mm-30) REVERT: E 692 LEU cc_start: 0.9088 (mt) cc_final: 0.8839 (pp) REVERT: F 63 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7375 (t0) REVERT: F 238 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8735 (tm-30) REVERT: F 346 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7352 (ttm110) REVERT: F 440 ASP cc_start: 0.8056 (m-30) cc_final: 0.7508 (m-30) REVERT: F 581 LEU cc_start: 0.5677 (tm) cc_final: 0.5400 (mt) REVERT: F 692 LEU cc_start: 0.8795 (mt) cc_final: 0.8578 (pt) outliers start: 85 outliers final: 21 residues processed: 345 average time/residue: 1.4207 time to fit residues: 599.2254 Evaluate side-chains 231 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 442 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 220 optimal weight: 0.0470 chunk 123 optimal weight: 20.0000 chunk 330 optimal weight: 30.0000 chunk 270 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 397 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 394 optimal weight: 0.5980 chunk 135 optimal weight: 20.0000 chunk 318 optimal weight: 0.4980 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS B 624 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS C 554 ASN C 608 HIS D 408 ASN D 608 HIS D 624 ASN D 729 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS E 554 ASN E 617 GLN F 608 HIS F 737 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 37913 Z= 0.362 Angle : 0.691 13.187 51374 Z= 0.334 Chirality : 0.044 0.236 5908 Planarity : 0.004 0.046 6251 Dihedral : 14.337 178.772 6036 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.90 % Allowed : 12.57 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4343 helix: -0.18 (0.12), residues: 2005 sheet: -1.41 (0.22), residues: 582 loop : -0.22 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 411 HIS 0.005 0.001 HIS A 155 PHE 0.016 0.002 PHE A 433 TYR 0.016 0.002 TYR A 281 ARG 0.012 0.000 ARG C 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 230 time to evaluate : 4.086 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: A 245 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 371 ASP cc_start: 0.8755 (t0) cc_final: 0.8316 (t0) REVERT: A 399 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: A 434 MET cc_start: 0.6804 (mmt) cc_final: 0.6526 (mmm) REVERT: A 507 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: A 526 ASN cc_start: 0.6335 (t0) cc_final: 0.6085 (t0) REVERT: B 238 GLU cc_start: 0.9061 (tp30) cc_final: 0.8140 (tm-30) REVERT: B 488 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8597 (mt) REVERT: B 581 LEU cc_start: 0.6383 (tm) cc_final: 0.6068 (mt) REVERT: B 692 LEU cc_start: 0.8769 (mt) cc_final: 0.8136 (tt) REVERT: C 245 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 370 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8118 (p0) REVERT: C 399 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: C 590 MET cc_start: 0.3388 (mpm) cc_final: 0.3053 (mpm) REVERT: C 692 LEU cc_start: 0.9218 (mt) cc_final: 0.8921 (pp) REVERT: D 238 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8521 (tm-30) REVERT: D 433 PHE cc_start: 0.6992 (p90) cc_final: 0.6120 (p90) REVERT: D 551 LEU cc_start: 0.8692 (mp) cc_final: 0.8235 (tt) REVERT: D 581 LEU cc_start: 0.4949 (tm) cc_final: 0.4666 (mt) REVERT: E 154 GLU cc_start: 0.8752 (tt0) cc_final: 0.8472 (mm-30) REVERT: E 165 ASP cc_start: 0.9023 (t0) cc_final: 0.8636 (t0) REVERT: E 399 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: E 409 ASN cc_start: 0.8331 (m110) cc_final: 0.7436 (t0) REVERT: E 692 LEU cc_start: 0.9132 (mt) cc_final: 0.8902 (pp) REVERT: E 738 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6983 (tp) REVERT: F 238 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8761 (tm-30) REVERT: F 520 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: F 581 LEU cc_start: 0.5924 (tm) cc_final: 0.5641 (mt) REVERT: F 692 LEU cc_start: 0.8799 (mt) cc_final: 0.8596 (pt) outliers start: 118 outliers final: 43 residues processed: 327 average time/residue: 1.2367 time to fit residues: 507.3413 Evaluate side-chains 239 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 520 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 392 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 189 optimal weight: 50.0000 chunk 266 optimal weight: 4.9990 chunk 398 optimal weight: 8.9990 chunk 422 optimal weight: 30.0000 chunk 208 optimal weight: 0.9990 chunk 378 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS B 431 HIS C 409 ASN C 617 GLN C 694 HIS ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 HIS F 624 ASN F 737 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 37913 Z= 0.401 Angle : 0.672 10.810 51374 Z= 0.328 Chirality : 0.045 0.209 5908 Planarity : 0.004 0.100 6251 Dihedral : 13.657 176.092 6032 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.14 % Allowed : 13.33 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4343 helix: -0.19 (0.12), residues: 1991 sheet: -1.40 (0.22), residues: 576 loop : -0.11 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 411 HIS 0.006 0.001 HIS A 155 PHE 0.016 0.002 PHE C 156 TYR 0.021 0.002 TYR D 362 ARG 0.013 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 208 time to evaluate : 4.766 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: A 165 ASP cc_start: 0.9060 (t0) cc_final: 0.8686 (t0) REVERT: A 254 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8236 (t) REVERT: A 371 ASP cc_start: 0.8847 (t0) cc_final: 0.8364 (t0) REVERT: A 471 LEU cc_start: 0.8727 (tm) cc_final: 0.8284 (pt) REVERT: A 526 ASN cc_start: 0.6366 (t0) cc_final: 0.6151 (t0) REVERT: A 550 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8030 (mtm-85) REVERT: A 590 MET cc_start: 0.4250 (mpm) cc_final: 0.3855 (mpm) REVERT: A 755 ASN cc_start: 0.4852 (OUTLIER) cc_final: 0.4610 (p0) REVERT: B 238 GLU cc_start: 0.9084 (tp30) cc_final: 0.8213 (tm-30) REVERT: B 482 LYS cc_start: 0.6613 (tptp) cc_final: 0.6404 (tptp) REVERT: B 488 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 527 LEU cc_start: 0.6428 (mt) cc_final: 0.6165 (tt) REVERT: B 692 LEU cc_start: 0.8706 (mt) cc_final: 0.8263 (pt) REVERT: C 245 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8288 (mm-30) REVERT: C 399 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: C 590 MET cc_start: 0.3194 (mpm) cc_final: 0.2861 (mpm) REVERT: C 692 LEU cc_start: 0.9187 (mt) cc_final: 0.8951 (pp) REVERT: C 765 ARG cc_start: 0.3762 (OUTLIER) cc_final: 0.2120 (ptm160) REVERT: D 238 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8567 (tm-30) REVERT: E 154 GLU cc_start: 0.8755 (tt0) cc_final: 0.8391 (mm-30) REVERT: E 165 ASP cc_start: 0.9106 (t0) cc_final: 0.8783 (t0) REVERT: E 399 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: E 671 ARG cc_start: 0.9023 (tpm170) cc_final: 0.8058 (ptm-80) REVERT: E 681 LEU cc_start: 0.8379 (mp) cc_final: 0.8116 (pt) REVERT: E 692 LEU cc_start: 0.9161 (mt) cc_final: 0.8913 (pp) REVERT: E 738 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6650 (tp) REVERT: E 752 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5272 (pp20) REVERT: F 238 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8709 (tm-30) REVERT: F 430 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8578 (tp) REVERT: F 491 LEU cc_start: 0.8280 (mm) cc_final: 0.7790 (mm) REVERT: F 520 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: F 572 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7921 (tt) REVERT: F 581 LEU cc_start: 0.6012 (tm) cc_final: 0.5713 (mt) REVERT: F 692 LEU cc_start: 0.8819 (mt) cc_final: 0.8530 (pp) outliers start: 128 outliers final: 39 residues processed: 315 average time/residue: 1.2969 time to fit residues: 509.3855 Evaluate side-chains 237 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 572 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 360 optimal weight: 20.0000 chunk 291 optimal weight: 0.0010 chunk 0 optimal weight: 8.9990 chunk 215 optimal weight: 0.0980 chunk 379 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37913 Z= 0.169 Angle : 0.600 12.037 51374 Z= 0.287 Chirality : 0.041 0.237 5908 Planarity : 0.003 0.053 6251 Dihedral : 13.136 172.470 6032 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.58 % Allowed : 14.53 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4343 helix: -0.03 (0.12), residues: 2004 sheet: -1.29 (0.22), residues: 570 loop : 0.02 (0.16), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 411 HIS 0.004 0.001 HIS A 253 PHE 0.030 0.001 PHE F 490 TYR 0.013 0.001 TYR A 477 ARG 0.008 0.000 ARG B 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 222 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9001 (t0) cc_final: 0.8622 (t0) REVERT: A 371 ASP cc_start: 0.8678 (t0) cc_final: 0.8227 (t0) REVERT: A 471 LEU cc_start: 0.8620 (tm) cc_final: 0.8273 (pt) REVERT: A 526 ASN cc_start: 0.6393 (t0) cc_final: 0.6163 (t0) REVERT: A 550 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8050 (mtm-85) REVERT: A 755 ASN cc_start: 0.4828 (OUTLIER) cc_final: 0.4565 (p0) REVERT: B 1 MET cc_start: 0.5623 (ptm) cc_final: 0.5372 (ttt) REVERT: B 104 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.7980 (t70) REVERT: B 238 GLU cc_start: 0.9026 (tp30) cc_final: 0.8097 (tm-30) REVERT: B 488 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8745 (mt) REVERT: B 692 LEU cc_start: 0.8676 (mt) cc_final: 0.8024 (tt) REVERT: C 245 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 590 MET cc_start: 0.3079 (mpm) cc_final: 0.2794 (mpm) REVERT: C 687 LEU cc_start: 0.8391 (tm) cc_final: 0.8188 (mm) REVERT: C 692 LEU cc_start: 0.9167 (mt) cc_final: 0.8944 (pp) REVERT: D 238 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 482 LYS cc_start: 0.6281 (tptt) cc_final: 0.5458 (tptp) REVERT: D 669 LEU cc_start: 0.8925 (mm) cc_final: 0.8651 (mt) REVERT: E 17 TYR cc_start: 0.8772 (m-10) cc_final: 0.8289 (m-10) REVERT: E 154 GLU cc_start: 0.8742 (tt0) cc_final: 0.8437 (mm-30) REVERT: E 165 ASP cc_start: 0.9085 (t0) cc_final: 0.8713 (t0) REVERT: E 245 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8461 (mm-30) REVERT: E 399 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: E 692 LEU cc_start: 0.9131 (mt) cc_final: 0.8898 (pp) REVERT: E 738 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6746 (tp) REVERT: E 765 ARG cc_start: 0.4828 (OUTLIER) cc_final: 0.3633 (ptt-90) REVERT: F 238 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8657 (tm-30) REVERT: F 263 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8537 (tp) REVERT: F 413 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7835 (tm) REVERT: F 491 LEU cc_start: 0.8117 (mm) cc_final: 0.7889 (mm) REVERT: F 520 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: F 551 LEU cc_start: 0.8740 (mp) cc_final: 0.8363 (tt) REVERT: F 572 LEU cc_start: 0.8510 (mt) cc_final: 0.8021 (tm) REVERT: F 581 LEU cc_start: 0.5992 (tm) cc_final: 0.5722 (mt) REVERT: F 692 LEU cc_start: 0.8808 (mt) cc_final: 0.8521 (pp) outliers start: 105 outliers final: 31 residues processed: 315 average time/residue: 1.2247 time to fit residues: 487.8294 Evaluate side-chains 236 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 520 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 30.0000 chunk 380 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 422 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 HIS F 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 37913 Z= 0.460 Angle : 0.698 16.706 51374 Z= 0.336 Chirality : 0.045 0.173 5908 Planarity : 0.004 0.051 6251 Dihedral : 12.992 175.047 6032 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.63 % Allowed : 14.71 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4343 helix: -0.13 (0.12), residues: 1978 sheet: -1.34 (0.23), residues: 571 loop : -0.02 (0.16), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 411 HIS 0.005 0.001 HIS A 155 PHE 0.034 0.002 PHE B 490 TYR 0.017 0.002 TYR D 281 ARG 0.007 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 197 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9109 (t0) cc_final: 0.8762 (t0) REVERT: A 254 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8274 (t) REVERT: A 371 ASP cc_start: 0.8828 (t0) cc_final: 0.8411 (t0) REVERT: A 471 LEU cc_start: 0.8612 (tm) cc_final: 0.8288 (pt) REVERT: A 526 ASN cc_start: 0.6188 (t0) cc_final: 0.5961 (t0) REVERT: A 550 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8081 (mtm-85) REVERT: A 590 MET cc_start: 0.3938 (mpm) cc_final: 0.3672 (mpm) REVERT: A 755 ASN cc_start: 0.4817 (OUTLIER) cc_final: 0.4523 (p0) REVERT: B 238 GLU cc_start: 0.9085 (tp30) cc_final: 0.8232 (tm-30) REVERT: B 488 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8776 (mt) REVERT: B 692 LEU cc_start: 0.8692 (mt) cc_final: 0.8188 (pt) REVERT: C 165 ASP cc_start: 0.9085 (t0) cc_final: 0.8629 (t0) REVERT: C 245 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8319 (mm-30) REVERT: C 370 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.7982 (p0) REVERT: C 399 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: C 471 LEU cc_start: 0.8589 (tm) cc_final: 0.8059 (pt) REVERT: C 590 MET cc_start: 0.3095 (mpm) cc_final: 0.2764 (mpm) REVERT: C 692 LEU cc_start: 0.9210 (mt) cc_final: 0.8968 (pp) REVERT: C 765 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.2292 (ptm160) REVERT: D 238 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 572 LEU cc_start: 0.8107 (mt) cc_final: 0.7604 (tm) REVERT: D 669 LEU cc_start: 0.8857 (mm) cc_final: 0.8536 (mt) REVERT: E 154 GLU cc_start: 0.8760 (tt0) cc_final: 0.8406 (mm-30) REVERT: E 165 ASP cc_start: 0.9097 (t0) cc_final: 0.8756 (t0) REVERT: E 236 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7277 (pp20) REVERT: E 245 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8467 (mm-30) REVERT: E 399 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: E 590 MET cc_start: 0.4425 (mpm) cc_final: 0.4158 (mpm) REVERT: E 681 LEU cc_start: 0.8500 (mp) cc_final: 0.8264 (pp) REVERT: E 692 LEU cc_start: 0.9161 (mt) cc_final: 0.8941 (pp) REVERT: E 765 ARG cc_start: 0.4842 (OUTLIER) cc_final: 0.3589 (ptt-90) REVERT: F 238 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 520 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: F 551 LEU cc_start: 0.8717 (mp) cc_final: 0.8333 (tt) REVERT: F 572 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8214 (tm) REVERT: F 581 LEU cc_start: 0.6093 (tm) cc_final: 0.5818 (mt) REVERT: F 692 LEU cc_start: 0.8761 (mt) cc_final: 0.8546 (pp) outliers start: 107 outliers final: 42 residues processed: 286 average time/residue: 1.1776 time to fit residues: 433.8748 Evaluate side-chains 238 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 10.0000 chunk 47 optimal weight: 50.0000 chunk 240 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 421 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 256 optimal weight: 0.0970 chunk 194 optimal weight: 40.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37913 Z= 0.164 Angle : 0.608 14.529 51374 Z= 0.287 Chirality : 0.041 0.246 5908 Planarity : 0.003 0.053 6251 Dihedral : 12.454 176.508 6032 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.09 % Allowed : 15.59 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 4343 helix: 0.01 (0.12), residues: 1981 sheet: -1.23 (0.23), residues: 556 loop : 0.11 (0.16), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 411 HIS 0.005 0.001 HIS A 253 PHE 0.029 0.001 PHE B 490 TYR 0.012 0.001 TYR E 338 ARG 0.003 0.000 ARG F 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 202 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9021 (t0) cc_final: 0.8670 (t0) REVERT: A 254 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8235 (t) REVERT: A 371 ASP cc_start: 0.8737 (t0) cc_final: 0.8322 (t0) REVERT: A 399 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: A 433 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7292 (t80) REVERT: A 471 LEU cc_start: 0.8656 (tm) cc_final: 0.8277 (pt) REVERT: A 526 ASN cc_start: 0.6354 (t0) cc_final: 0.6132 (t0) REVERT: A 590 MET cc_start: 0.4182 (mpm) cc_final: 0.3860 (mpm) REVERT: A 755 ASN cc_start: 0.4871 (OUTLIER) cc_final: 0.4597 (p0) REVERT: B 1 MET cc_start: 0.5603 (ptm) cc_final: 0.5292 (ttt) REVERT: B 238 GLU cc_start: 0.9030 (tp30) cc_final: 0.8179 (tm-30) REVERT: B 472 LYS cc_start: 0.8598 (mmpt) cc_final: 0.8353 (mmmt) REVERT: B 482 LYS cc_start: 0.7243 (tptp) cc_final: 0.6703 (tptp) REVERT: B 692 LEU cc_start: 0.8661 (mt) cc_final: 0.8169 (pt) REVERT: C 165 ASP cc_start: 0.9046 (t0) cc_final: 0.8557 (t0) REVERT: C 245 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8292 (mm-30) REVERT: C 399 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: C 590 MET cc_start: 0.3213 (mpm) cc_final: 0.2855 (mpm) REVERT: C 692 LEU cc_start: 0.9170 (mt) cc_final: 0.8943 (pp) REVERT: C 765 ARG cc_start: 0.3928 (OUTLIER) cc_final: 0.2410 (ptm160) REVERT: D 238 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 572 LEU cc_start: 0.8320 (mt) cc_final: 0.7884 (tm) REVERT: D 669 LEU cc_start: 0.8910 (mm) cc_final: 0.8566 (mt) REVERT: E 17 TYR cc_start: 0.8785 (m-10) cc_final: 0.8294 (m-10) REVERT: E 154 GLU cc_start: 0.8724 (tt0) cc_final: 0.8423 (mm-30) REVERT: E 165 ASP cc_start: 0.9105 (t0) cc_final: 0.8730 (t0) REVERT: E 236 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: E 245 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8436 (mm-30) REVERT: E 399 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: E 681 LEU cc_start: 0.8479 (mp) cc_final: 0.8270 (pp) REVERT: E 738 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6656 (tp) REVERT: E 765 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.3539 (ptt-90) REVERT: F 238 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8683 (tm-30) REVERT: F 440 ASP cc_start: 0.8319 (m-30) cc_final: 0.8046 (m-30) REVERT: F 491 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7915 (mm) REVERT: F 520 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: F 551 LEU cc_start: 0.8691 (mp) cc_final: 0.8344 (tt) REVERT: F 572 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8182 (tm) REVERT: F 581 LEU cc_start: 0.6072 (tm) cc_final: 0.5803 (mt) REVERT: F 692 LEU cc_start: 0.8713 (mt) cc_final: 0.8510 (pp) outliers start: 85 outliers final: 31 residues processed: 274 average time/residue: 1.2064 time to fit residues: 417.8524 Evaluate side-chains 226 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 756 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 260 optimal weight: 20.0000 chunk 168 optimal weight: 0.8980 chunk 251 optimal weight: 0.1980 chunk 126 optimal weight: 50.0000 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37913 Z= 0.244 Angle : 0.613 14.673 51374 Z= 0.292 Chirality : 0.042 0.169 5908 Planarity : 0.003 0.111 6251 Dihedral : 12.125 177.903 6032 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.06 % Allowed : 15.89 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4343 helix: 0.00 (0.12), residues: 1986 sheet: -1.17 (0.23), residues: 556 loop : 0.14 (0.16), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 411 HIS 0.004 0.001 HIS A 253 PHE 0.024 0.001 PHE B 490 TYR 0.017 0.001 TYR A 477 ARG 0.018 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 186 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9036 (t0) cc_final: 0.8678 (t0) REVERT: A 254 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8295 (t) REVERT: A 371 ASP cc_start: 0.8777 (t0) cc_final: 0.8421 (t0) REVERT: A 399 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: A 433 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7339 (t80) REVERT: A 471 LEU cc_start: 0.8664 (tm) cc_final: 0.8260 (pt) REVERT: A 501 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8495 (tptp) REVERT: A 526 ASN cc_start: 0.6241 (t0) cc_final: 0.6015 (t0) REVERT: A 590 MET cc_start: 0.4083 (mpm) cc_final: 0.3854 (mpm) REVERT: A 755 ASN cc_start: 0.4808 (OUTLIER) cc_final: 0.4520 (p0) REVERT: B 1 MET cc_start: 0.5611 (ptm) cc_final: 0.5307 (ttt) REVERT: B 238 GLU cc_start: 0.9075 (tp30) cc_final: 0.8207 (tm-30) REVERT: B 692 LEU cc_start: 0.8670 (mt) cc_final: 0.8184 (pt) REVERT: C 165 ASP cc_start: 0.9055 (t0) cc_final: 0.8576 (t0) REVERT: C 245 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 399 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: C 590 MET cc_start: 0.3169 (mpm) cc_final: 0.2826 (mpm) REVERT: C 692 LEU cc_start: 0.9158 (mt) cc_final: 0.8938 (pp) REVERT: C 765 ARG cc_start: 0.3790 (OUTLIER) cc_final: 0.2340 (ptm160) REVERT: D 238 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8516 (tm-30) REVERT: D 572 LEU cc_start: 0.8232 (mt) cc_final: 0.7799 (tm) REVERT: D 669 LEU cc_start: 0.8910 (mm) cc_final: 0.8542 (mt) REVERT: E 154 GLU cc_start: 0.8741 (tt0) cc_final: 0.8416 (mm-30) REVERT: E 165 ASP cc_start: 0.9102 (t0) cc_final: 0.8727 (t0) REVERT: E 236 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: E 245 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8465 (mm-30) REVERT: E 399 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: E 590 MET cc_start: 0.4726 (mpm) cc_final: 0.4412 (mpm) REVERT: E 681 LEU cc_start: 0.8494 (mp) cc_final: 0.8272 (pp) REVERT: E 692 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8547 (tp) REVERT: E 738 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6862 (tp) REVERT: E 765 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.3453 (ptt-90) REVERT: F 238 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8659 (tm-30) REVERT: F 440 ASP cc_start: 0.8398 (m-30) cc_final: 0.8115 (m-30) REVERT: F 491 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7908 (mm) REVERT: F 520 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: F 551 LEU cc_start: 0.8725 (mp) cc_final: 0.8328 (tt) REVERT: F 572 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8224 (tt) REVERT: F 581 LEU cc_start: 0.6066 (tm) cc_final: 0.5811 (mt) REVERT: F 692 LEU cc_start: 0.8711 (mt) cc_final: 0.8505 (pp) outliers start: 84 outliers final: 37 residues processed: 258 average time/residue: 1.2232 time to fit residues: 401.1677 Evaluate side-chains 235 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 4.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 685 ARG Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 756 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 2.9990 chunk 403 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 392 optimal weight: 7.9990 chunk 236 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 308 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 391 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN E 66 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37913 Z= 0.173 Angle : 0.604 15.523 51374 Z= 0.285 Chirality : 0.041 0.175 5908 Planarity : 0.003 0.053 6251 Dihedral : 11.703 178.740 6029 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 16.13 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 4343 helix: 0.08 (0.12), residues: 1986 sheet: -1.11 (0.23), residues: 556 loop : 0.21 (0.16), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 411 HIS 0.005 0.001 HIS A 253 PHE 0.023 0.001 PHE B 490 TYR 0.015 0.001 TYR A 477 ARG 0.005 0.000 ARG B 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9067 (t0) cc_final: 0.8807 (t0) REVERT: A 254 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8260 (t) REVERT: A 371 ASP cc_start: 0.8588 (t0) cc_final: 0.8126 (t0) REVERT: A 433 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 471 LEU cc_start: 0.8681 (tm) cc_final: 0.8238 (pt) REVERT: A 501 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8493 (tptp) REVERT: A 526 ASN cc_start: 0.6274 (t0) cc_final: 0.6033 (t0) REVERT: A 590 MET cc_start: 0.4005 (mpm) cc_final: 0.3774 (mpm) REVERT: A 755 ASN cc_start: 0.4803 (OUTLIER) cc_final: 0.4507 (p0) REVERT: B 1 MET cc_start: 0.5493 (ptm) cc_final: 0.5257 (ttt) REVERT: B 238 GLU cc_start: 0.9067 (tp30) cc_final: 0.8193 (tm-30) REVERT: B 482 LYS cc_start: 0.7351 (tptp) cc_final: 0.6960 (tptp) REVERT: B 692 LEU cc_start: 0.8658 (mt) cc_final: 0.8177 (pt) REVERT: C 165 ASP cc_start: 0.9028 (t0) cc_final: 0.8545 (t0) REVERT: C 245 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8308 (mm-30) REVERT: C 399 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: C 590 MET cc_start: 0.3322 (mpm) cc_final: 0.2943 (mpm) REVERT: C 692 LEU cc_start: 0.9170 (mt) cc_final: 0.8948 (pp) REVERT: C 765 ARG cc_start: 0.3762 (OUTLIER) cc_final: 0.2345 (ptm160) REVERT: D 238 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8500 (tm-30) REVERT: D 669 LEU cc_start: 0.8900 (mm) cc_final: 0.8532 (mt) REVERT: E 17 TYR cc_start: 0.8759 (m-10) cc_final: 0.8261 (m-10) REVERT: E 154 GLU cc_start: 0.8731 (tt0) cc_final: 0.8409 (mm-30) REVERT: E 165 ASP cc_start: 0.9070 (t0) cc_final: 0.8681 (t0) REVERT: E 236 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: E 245 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8520 (mm-30) REVERT: E 399 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: E 590 MET cc_start: 0.4683 (mpm) cc_final: 0.4363 (mpm) REVERT: E 681 LEU cc_start: 0.8506 (mp) cc_final: 0.8260 (pp) REVERT: E 692 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8604 (mm) REVERT: E 738 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6856 (tp) REVERT: E 765 ARG cc_start: 0.4683 (OUTLIER) cc_final: 0.3362 (ptt180) REVERT: F 238 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 440 ASP cc_start: 0.8439 (m-30) cc_final: 0.8007 (m-30) REVERT: F 491 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7932 (mm) REVERT: F 551 LEU cc_start: 0.8695 (mp) cc_final: 0.8330 (tt) REVERT: F 572 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8184 (tm) REVERT: F 581 LEU cc_start: 0.6060 (tm) cc_final: 0.5815 (mt) outliers start: 76 outliers final: 34 residues processed: 267 average time/residue: 1.1943 time to fit residues: 404.7028 Evaluate side-chains 231 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 572 LEU Chi-restraints excluded: chain F residue 756 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 5.9990 chunk 415 optimal weight: 50.0000 chunk 253 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 435 optimal weight: 7.9990 chunk 400 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 37913 Z= 0.383 Angle : 0.673 15.718 51374 Z= 0.322 Chirality : 0.044 0.172 5908 Planarity : 0.004 0.054 6251 Dihedral : 11.793 176.587 6029 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.60 % Allowed : 16.70 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4343 helix: 0.04 (0.12), residues: 1940 sheet: -1.25 (0.23), residues: 559 loop : 0.29 (0.16), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 411 HIS 0.005 0.001 HIS F 694 PHE 0.023 0.002 PHE B 490 TYR 0.016 0.002 TYR C 281 ARG 0.004 0.000 ARG B 640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 178 time to evaluate : 3.931 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: A 165 ASP cc_start: 0.9083 (t0) cc_final: 0.8809 (t0) REVERT: A 254 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8292 (t) REVERT: A 371 ASP cc_start: 0.8796 (t0) cc_final: 0.8412 (t0) REVERT: A 471 LEU cc_start: 0.8723 (tm) cc_final: 0.8281 (pt) REVERT: A 501 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8622 (tmtt) REVERT: A 526 ASN cc_start: 0.6090 (t0) cc_final: 0.5872 (t0) REVERT: A 590 MET cc_start: 0.4160 (mpm) cc_final: 0.3880 (mpm) REVERT: A 755 ASN cc_start: 0.4705 (OUTLIER) cc_final: 0.4392 (p0) REVERT: B 1 MET cc_start: 0.5554 (ptm) cc_final: 0.5235 (ttt) REVERT: B 238 GLU cc_start: 0.9093 (tp30) cc_final: 0.8233 (tm-30) REVERT: B 572 LEU cc_start: 0.8756 (tm) cc_final: 0.8067 (pt) REVERT: B 692 LEU cc_start: 0.8664 (mt) cc_final: 0.8172 (pt) REVERT: C 165 ASP cc_start: 0.9106 (t0) cc_final: 0.8454 (p0) REVERT: C 245 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8269 (mm-30) REVERT: C 399 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: C 590 MET cc_start: 0.3267 (mpm) cc_final: 0.2833 (mpm) REVERT: C 765 ARG cc_start: 0.3840 (OUTLIER) cc_final: 0.2410 (ptm160) REVERT: D 238 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 434 MET cc_start: 0.7126 (pmt) cc_final: 0.6918 (pmm) REVERT: D 551 LEU cc_start: 0.8620 (mp) cc_final: 0.8258 (tt) REVERT: E 154 GLU cc_start: 0.8748 (tt0) cc_final: 0.8433 (mm-30) REVERT: E 165 ASP cc_start: 0.9121 (t0) cc_final: 0.8765 (t0) REVERT: E 245 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 399 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: E 590 MET cc_start: 0.4690 (mpm) cc_final: 0.4364 (mpm) REVERT: E 692 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8526 (mm) REVERT: E 738 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6800 (tp) REVERT: E 765 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.3461 (ptt180) REVERT: F 238 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8684 (tm-30) REVERT: F 491 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7934 (mm) REVERT: F 520 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: F 572 LEU cc_start: 0.8661 (mt) cc_final: 0.8210 (tm) REVERT: F 581 LEU cc_start: 0.6078 (tm) cc_final: 0.5820 (mt) outliers start: 65 outliers final: 35 residues processed: 237 average time/residue: 1.1662 time to fit residues: 354.0858 Evaluate side-chains 219 residues out of total 4073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 755 ASN Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain E residue 765 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 520 GLU Chi-restraints excluded: chain F residue 756 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 51 optimal weight: 40.0000 chunk 96 optimal weight: 0.6980 chunk 347 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 356 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS C 478 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN F 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.164211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096523 restraints weight = 73892.111| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.52 r_work: 0.3217 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 37913 Z= 0.367 Angle : 0.670 15.823 51374 Z= 0.318 Chirality : 0.044 0.168 5908 Planarity : 0.003 0.052 6251 Dihedral : 11.711 172.785 6029 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.42 % Allowed : 17.09 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 4343 helix: 0.00 (0.12), residues: 1939 sheet: -1.28 (0.23), residues: 559 loop : 0.30 (0.16), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 411 HIS 0.008 0.001 HIS D 694 PHE 0.021 0.002 PHE D 433 TYR 0.015 0.002 TYR E 338 ARG 0.004 0.000 ARG B 640 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11769.86 seconds wall clock time: 213 minutes 2.49 seconds (12782.49 seconds total)