Starting phenix.real_space_refine on Fri Mar 22 05:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk8_16092/03_2024/8bk8_16092.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 20552 2.51 5 N 5760 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A ASP 954": "OD1" <-> "OD2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "B ASP 790": "OD1" <-> "OD2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B ASP 954": "OD1" <-> "OD2" Residue "B GLU 1006": "OE1" <-> "OE2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C ASP 509": "OD1" <-> "OD2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C GLU 681": "OE1" <-> "OE2" Residue "C ASP 782": "OD1" <-> "OD2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C GLU 808": "OE1" <-> "OE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C ASP 954": "OD1" <-> "OD2" Residue "C GLU 1006": "OE1" <-> "OE2" Residue "C TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 507": "OD1" <-> "OD2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D GLU 681": "OE1" <-> "OE2" Residue "D ASP 782": "OD1" <-> "OD2" Residue "D ASP 790": "OD1" <-> "OD2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 904": "OE1" <-> "OE2" Residue "D PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 943": "OE1" <-> "OE2" Residue "D ASP 954": "OD1" <-> "OD2" Residue "D GLU 1006": "OE1" <-> "OE2" Residue "D TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "B" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "C" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "D" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Time building chain proxies: 15.65, per 1000 atoms: 0.48 Number of scatterers: 32500 At special positions: 0 Unit cell: (195.825, 148.827, 101.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 6036 8.00 N 5760 7.00 C 20552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 5.7 seconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 52 sheets defined 16.9% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.907A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.906A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.906A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS C 754 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.907A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS D 754 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1216 hydrogen bonds defined for protein. 3180 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: 14.55 Time building geometry restraints manager: 11.54 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: 10030 1.33 - 1.45: 5842 1.45 - 1.57: 17356 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 33468 Sorted by residual: bond pdb=" C LEU C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU A 433 " pdb=" N PRO A 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU D 433 " pdb=" N PRO D 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU B 433 " pdb=" N PRO B 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" CB TYR A 472 " pdb=" CG TYR A 472 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.20e-02 2.07e+03 2.17e+00 ... (remaining 33463 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.23: 1190 106.23 - 113.19: 17416 113.19 - 120.15: 11580 120.15 - 127.11: 14778 127.11 - 134.07: 696 Bond angle restraints: 45660 Sorted by residual: angle pdb=" C ASN A 394 " pdb=" N HIS A 395 " pdb=" CA HIS A 395 " ideal model delta sigma weight residual 120.65 127.91 -7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" C ASN D 394 " pdb=" N HIS D 395 " pdb=" CA HIS D 395 " ideal model delta sigma weight residual 120.65 127.91 -7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" C ASN B 394 " pdb=" N HIS B 395 " pdb=" CA HIS B 395 " ideal model delta sigma weight residual 120.65 127.90 -7.25 1.36e+00 5.41e-01 2.84e+01 angle pdb=" C ASN C 394 " pdb=" N HIS C 395 " pdb=" CA HIS C 395 " ideal model delta sigma weight residual 120.65 127.90 -7.25 1.36e+00 5.41e-01 2.84e+01 angle pdb=" C SER D 545 " pdb=" N LEU D 546 " pdb=" CA LEU D 546 " ideal model delta sigma weight residual 122.36 127.49 -5.13 1.47e+00 4.63e-01 1.22e+01 ... (remaining 45655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 17960 17.74 - 35.47: 1360 35.47 - 53.21: 184 53.21 - 70.95: 68 70.95 - 88.69: 24 Dihedral angle restraints: 19596 sinusoidal: 7912 harmonic: 11684 Sorted by residual: dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ARG B 599 " pdb=" CA ARG B 599 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASP A 598 " pdb=" C ASP A 598 " pdb=" N ARG A 599 " pdb=" CA ARG A 599 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASP D 598 " pdb=" C ASP D 598 " pdb=" N ARG D 599 " pdb=" CA ARG D 599 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3680 0.051 - 0.101: 810 0.101 - 0.152: 250 0.152 - 0.203: 8 0.203 - 0.253: 4 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA ARG C 599 " pdb=" N ARG C 599 " pdb=" C ARG C 599 " pdb=" CB ARG C 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG A 599 " pdb=" N ARG A 599 " pdb=" C ARG A 599 " pdb=" CB ARG A 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG B 599 " pdb=" N ARG B 599 " pdb=" C ARG B 599 " pdb=" CB ARG B 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4749 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 403 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" CG ASP D 403 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP D 403 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP D 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 403 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" CG ASP A 403 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 403 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 403 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" CG ASP B 403 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP B 403 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP B 403 " -0.017 2.00e-02 2.50e+03 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6422 2.78 - 3.31: 27788 3.31 - 3.84: 58261 3.84 - 4.37: 70107 4.37 - 4.90: 119448 Nonbonded interactions: 282026 Sorted by model distance: nonbonded pdb=" O PRO A 434 " pdb=" OG SER A 437 " model vdw 2.252 2.440 nonbonded pdb=" O PRO C 434 " pdb=" OG SER C 437 " model vdw 2.252 2.440 nonbonded pdb=" O PRO B 434 " pdb=" OG SER B 437 " model vdw 2.252 2.440 nonbonded pdb=" O PRO D 434 " pdb=" OG SER D 437 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR A 105 " pdb=" O TYR A 196 " model vdw 2.260 2.440 ... (remaining 282021 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.970 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 81.720 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.003 0.034 33468 Z= 0.206 Angle : 0.657 7.262 45660 Z= 0.369 Chirality : 0.047 0.253 4752 Planarity : 0.005 0.046 6036 Dihedral : 13.276 88.687 12076 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 4036 helix: -0.98 (0.21), residues: 496 sheet: 0.74 (0.14), residues: 1300 loop : -0.55 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 523 HIS 0.006 0.001 HIS C 395 PHE 0.019 0.001 PHE B 549 TYR 0.022 0.002 TYR B 100 ARG 0.008 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 3.458 Fit side-chains REVERT: A 46 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6874 (mtt180) REVERT: A 102 ASN cc_start: 0.7754 (t0) cc_final: 0.7370 (t0) REVERT: A 221 GLN cc_start: 0.8002 (mt0) cc_final: 0.7770 (mt0) REVERT: A 281 GLU cc_start: 0.7913 (mp0) cc_final: 0.7609 (mp0) REVERT: A 584 PRO cc_start: 0.7550 (Cg_endo) cc_final: 0.7066 (Cg_exo) REVERT: A 782 ASP cc_start: 0.8059 (m-30) cc_final: 0.7722 (m-30) REVERT: A 925 MET cc_start: 0.8214 (mmm) cc_final: 0.7812 (mmm) REVERT: B 46 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6871 (mtt180) REVERT: B 102 ASN cc_start: 0.7760 (t0) cc_final: 0.7378 (t0) REVERT: B 221 GLN cc_start: 0.7998 (mt0) cc_final: 0.7763 (mt0) REVERT: B 245 GLN cc_start: 0.7042 (mt0) cc_final: 0.6838 (mt0) REVERT: B 281 GLU cc_start: 0.7913 (mp0) cc_final: 0.7607 (mp0) REVERT: B 584 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7061 (Cg_exo) REVERT: B 782 ASP cc_start: 0.8066 (m-30) cc_final: 0.7729 (m-30) REVERT: B 925 MET cc_start: 0.8213 (mmm) cc_final: 0.7812 (mmm) REVERT: C 46 ARG cc_start: 0.7088 (mtt90) cc_final: 0.6870 (mtt180) REVERT: C 102 ASN cc_start: 0.7759 (t0) cc_final: 0.7375 (t0) REVERT: C 221 GLN cc_start: 0.8001 (mt0) cc_final: 0.7765 (mt0) REVERT: C 245 GLN cc_start: 0.7042 (mt0) cc_final: 0.6838 (mt0) REVERT: C 281 GLU cc_start: 0.7914 (mp0) cc_final: 0.7612 (mp0) REVERT: C 584 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7058 (Cg_exo) REVERT: C 782 ASP cc_start: 0.8058 (m-30) cc_final: 0.7723 (m-30) REVERT: C 925 MET cc_start: 0.8210 (mmm) cc_final: 0.7814 (mmm) REVERT: D 46 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6873 (mtt180) REVERT: D 102 ASN cc_start: 0.7763 (t0) cc_final: 0.7377 (t0) REVERT: D 221 GLN cc_start: 0.8002 (mt0) cc_final: 0.7772 (mt0) REVERT: D 245 GLN cc_start: 0.7041 (mt0) cc_final: 0.6840 (mt0) REVERT: D 281 GLU cc_start: 0.7915 (mp0) cc_final: 0.7609 (mp0) REVERT: D 584 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7060 (Cg_exo) REVERT: D 782 ASP cc_start: 0.8058 (m-30) cc_final: 0.7721 (m-30) REVERT: D 925 MET cc_start: 0.8213 (mmm) cc_final: 0.7811 (mmm) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 1.7309 time to fit residues: 1358.5527 Evaluate side-chains 538 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 510 GLN A 739 HIS A 761 GLN A 903 GLN B 89 ASN B 395 HIS B 510 GLN B 739 HIS B 761 GLN B 903 GLN C 395 HIS C 510 GLN C 739 HIS C 761 GLN C 903 GLN D 395 HIS D 510 GLN D 739 HIS D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33468 Z= 0.410 Angle : 0.663 7.677 45660 Z= 0.349 Chirality : 0.049 0.159 4752 Planarity : 0.006 0.042 6036 Dihedral : 5.259 30.352 4428 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 9.40 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.11 (0.13), residues: 4036 helix: -0.58 (0.22), residues: 488 sheet: 0.48 (0.14), residues: 1352 loop : -0.22 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 553 HIS 0.009 0.001 HIS B 395 PHE 0.013 0.002 PHE A 143 TYR 0.025 0.003 TYR A 100 ARG 0.005 0.001 ARG D 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 529 time to evaluate : 3.659 Fit side-chains REVERT: A 77 ASP cc_start: 0.6086 (p0) cc_final: 0.5877 (p0) REVERT: A 102 ASN cc_start: 0.7914 (t0) cc_final: 0.7442 (t0) REVERT: A 170 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: A 280 ASP cc_start: 0.6448 (m-30) cc_final: 0.6184 (m-30) REVERT: A 296 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6386 (mm-30) REVERT: A 502 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8141 (ptm) REVERT: A 584 PRO cc_start: 0.7798 (Cg_endo) cc_final: 0.7302 (Cg_exo) REVERT: A 693 GLN cc_start: 0.8210 (tp40) cc_final: 0.7996 (tm-30) REVERT: A 724 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 925 MET cc_start: 0.8084 (mmm) cc_final: 0.7695 (mmm) REVERT: B 77 ASP cc_start: 0.6082 (p0) cc_final: 0.5873 (p0) REVERT: B 102 ASN cc_start: 0.7922 (t0) cc_final: 0.7450 (t0) REVERT: B 170 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: B 245 GLN cc_start: 0.7245 (mt0) cc_final: 0.6950 (mt0) REVERT: B 280 ASP cc_start: 0.6451 (m-30) cc_final: 0.6187 (m-30) REVERT: B 296 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6375 (mm-30) REVERT: B 502 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8138 (ptm) REVERT: B 584 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: B 693 GLN cc_start: 0.8213 (tp40) cc_final: 0.7998 (tm-30) REVERT: B 724 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: B 925 MET cc_start: 0.8088 (mmm) cc_final: 0.7698 (mmm) REVERT: C 77 ASP cc_start: 0.6084 (p0) cc_final: 0.5872 (p0) REVERT: C 102 ASN cc_start: 0.7918 (t0) cc_final: 0.7445 (t0) REVERT: C 170 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: C 245 GLN cc_start: 0.7244 (mt0) cc_final: 0.6949 (mt0) REVERT: C 280 ASP cc_start: 0.6452 (m-30) cc_final: 0.6188 (m-30) REVERT: C 296 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6377 (mm-30) REVERT: C 502 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8146 (ptm) REVERT: C 584 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7299 (Cg_exo) REVERT: C 693 GLN cc_start: 0.8211 (tp40) cc_final: 0.7998 (tm-30) REVERT: C 724 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: C 925 MET cc_start: 0.8080 (mmm) cc_final: 0.7694 (mmm) REVERT: D 77 ASP cc_start: 0.6089 (p0) cc_final: 0.5876 (p0) REVERT: D 102 ASN cc_start: 0.7922 (t0) cc_final: 0.7447 (t0) REVERT: D 170 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: D 245 GLN cc_start: 0.7251 (mt0) cc_final: 0.6909 (mt0) REVERT: D 280 ASP cc_start: 0.6454 (m-30) cc_final: 0.6189 (m-30) REVERT: D 296 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6384 (mm-30) REVERT: D 502 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8154 (ptm) REVERT: D 584 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7303 (Cg_exo) REVERT: D 693 GLN cc_start: 0.8215 (tp40) cc_final: 0.8001 (tm-30) REVERT: D 724 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: D 925 MET cc_start: 0.8089 (mmm) cc_final: 0.7700 (mmm) outliers start: 126 outliers final: 40 residues processed: 589 average time/residue: 1.6241 time to fit residues: 1113.9454 Evaluate side-chains 564 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 512 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 397 optimal weight: 0.9990 chunk 327 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 739 HIS A 903 GLN B 395 HIS B 739 HIS B 903 GLN B 945 ASN C 395 HIS C 739 HIS C 903 GLN C 945 ASN D 395 HIS D 739 HIS D 903 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33468 Z= 0.250 Angle : 0.551 6.407 45660 Z= 0.290 Chirality : 0.045 0.153 4752 Planarity : 0.004 0.043 6036 Dihedral : 4.993 28.524 4428 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 11.92 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.03 (0.14), residues: 4036 helix: -0.38 (0.22), residues: 520 sheet: 0.52 (0.14), residues: 1384 loop : -0.12 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 553 HIS 0.009 0.001 HIS D 395 PHE 0.012 0.001 PHE C 143 TYR 0.024 0.002 TYR A 100 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 522 time to evaluate : 3.907 Fit side-chains REVERT: A 18 ASN cc_start: 0.7866 (t0) cc_final: 0.7386 (t0) REVERT: A 77 ASP cc_start: 0.6206 (p0) cc_final: 0.5960 (p0) REVERT: A 102 ASN cc_start: 0.7889 (t0) cc_final: 0.7430 (t0) REVERT: A 170 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: A 336 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7428 (ptt-90) REVERT: A 479 ASP cc_start: 0.7941 (t0) cc_final: 0.7616 (t70) REVERT: A 584 PRO cc_start: 0.7706 (Cg_endo) cc_final: 0.7200 (Cg_exo) REVERT: A 693 GLN cc_start: 0.8213 (tp40) cc_final: 0.7999 (tm-30) REVERT: A 724 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: A 770 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 925 MET cc_start: 0.7957 (mmm) cc_final: 0.7531 (mmm) REVERT: A 1006 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6996 (pt0) REVERT: B 18 ASN cc_start: 0.7871 (t0) cc_final: 0.7363 (t0) REVERT: B 77 ASP cc_start: 0.6208 (p0) cc_final: 0.5963 (p0) REVERT: B 102 ASN cc_start: 0.7895 (t0) cc_final: 0.7435 (t0) REVERT: B 170 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 245 GLN cc_start: 0.7113 (mt0) cc_final: 0.6792 (mt0) REVERT: B 336 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7430 (ptt-90) REVERT: B 479 ASP cc_start: 0.7938 (t0) cc_final: 0.7611 (t70) REVERT: B 584 PRO cc_start: 0.7704 (Cg_endo) cc_final: 0.7196 (Cg_exo) REVERT: B 693 GLN cc_start: 0.8216 (tp40) cc_final: 0.7999 (tm-30) REVERT: B 724 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: B 770 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 925 MET cc_start: 0.7956 (mmm) cc_final: 0.7534 (mmm) REVERT: B 1006 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: C 18 ASN cc_start: 0.7859 (t0) cc_final: 0.7348 (t0) REVERT: C 77 ASP cc_start: 0.6211 (p0) cc_final: 0.5961 (p0) REVERT: C 102 ASN cc_start: 0.7894 (t0) cc_final: 0.7434 (t0) REVERT: C 170 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: C 245 GLN cc_start: 0.7110 (mt0) cc_final: 0.6792 (mt0) REVERT: C 278 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (mm) REVERT: C 336 ARG cc_start: 0.7739 (ptt-90) cc_final: 0.7428 (ptt-90) REVERT: C 479 ASP cc_start: 0.7948 (t0) cc_final: 0.7619 (t70) REVERT: C 584 PRO cc_start: 0.7700 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: C 693 GLN cc_start: 0.8214 (tp40) cc_final: 0.7997 (tm-30) REVERT: C 724 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: C 770 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7950 (mp) REVERT: C 925 MET cc_start: 0.7955 (mmm) cc_final: 0.7534 (mmm) REVERT: C 1006 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7002 (pt0) REVERT: D 18 ASN cc_start: 0.7869 (t0) cc_final: 0.7361 (t0) REVERT: D 77 ASP cc_start: 0.6210 (p0) cc_final: 0.5962 (p0) REVERT: D 102 ASN cc_start: 0.7897 (t0) cc_final: 0.7432 (t0) REVERT: D 170 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: D 245 GLN cc_start: 0.7125 (mt0) cc_final: 0.6803 (mt0) REVERT: D 336 ARG cc_start: 0.7736 (ptt-90) cc_final: 0.7427 (ptt-90) REVERT: D 479 ASP cc_start: 0.7953 (t0) cc_final: 0.7619 (t70) REVERT: D 584 PRO cc_start: 0.7704 (Cg_endo) cc_final: 0.7198 (Cg_exo) REVERT: D 693 GLN cc_start: 0.8219 (tp40) cc_final: 0.8001 (tm-30) REVERT: D 724 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: D 770 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7948 (mp) REVERT: D 925 MET cc_start: 0.7960 (mmm) cc_final: 0.7535 (mmm) REVERT: D 1006 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6995 (pt0) outliers start: 114 outliers final: 64 residues processed: 574 average time/residue: 1.5644 time to fit residues: 1049.1478 Evaluate side-chains 589 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 508 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 754 LYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 89 ASN A 395 HIS A 604 ASN A 739 HIS A 878 HIS A 903 GLN A 945 ASN B 50 GLN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 739 HIS B 878 HIS B 903 GLN B 945 ASN C 50 GLN C 89 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 739 HIS C 878 HIS C 903 GLN C 945 ASN D 50 GLN D 89 ASN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 739 HIS D 878 HIS D 903 GLN D 945 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 33468 Z= 0.462 Angle : 0.677 7.970 45660 Z= 0.354 Chirality : 0.050 0.160 4752 Planarity : 0.006 0.046 6036 Dihedral : 5.471 30.743 4428 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.12 % Allowed : 12.12 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4036 helix: -0.65 (0.22), residues: 488 sheet: 0.29 (0.14), residues: 1344 loop : -0.22 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 553 HIS 0.009 0.001 HIS A 395 PHE 0.015 0.002 PHE A 143 TYR 0.024 0.003 TYR C 100 ARG 0.005 0.001 ARG B 699 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 495 time to evaluate : 3.836 Fit side-chains REVERT: A 71 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: A 77 ASP cc_start: 0.6249 (p0) cc_final: 0.5926 (p0) REVERT: A 102 ASN cc_start: 0.7938 (t0) cc_final: 0.7464 (t0) REVERT: A 170 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: A 278 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7758 (mp) REVERT: A 296 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6176 (mm-30) REVERT: A 336 ARG cc_start: 0.7763 (ptt-90) cc_final: 0.7416 (ptt-90) REVERT: A 479 ASP cc_start: 0.8017 (t0) cc_final: 0.7696 (t70) REVERT: A 584 PRO cc_start: 0.7801 (Cg_endo) cc_final: 0.7289 (Cg_exo) REVERT: A 693 GLN cc_start: 0.8192 (tp40) cc_final: 0.7939 (tm-30) REVERT: A 724 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: A 770 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 1006 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: B 71 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: B 77 ASP cc_start: 0.6245 (p0) cc_final: 0.5921 (p0) REVERT: B 102 ASN cc_start: 0.7943 (t0) cc_final: 0.7467 (t0) REVERT: B 170 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: B 245 GLN cc_start: 0.7269 (mt0) cc_final: 0.6890 (mt0) REVERT: B 278 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7760 (mp) REVERT: B 296 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6107 (mm-30) REVERT: B 336 ARG cc_start: 0.7767 (ptt-90) cc_final: 0.7428 (ptt-90) REVERT: B 479 ASP cc_start: 0.8016 (t0) cc_final: 0.7693 (t70) REVERT: B 584 PRO cc_start: 0.7799 (Cg_endo) cc_final: 0.7284 (Cg_exo) REVERT: B 693 GLN cc_start: 0.8192 (tp40) cc_final: 0.7941 (tm-30) REVERT: B 724 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: B 770 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 1006 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: C 71 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: C 77 ASP cc_start: 0.6249 (p0) cc_final: 0.5924 (p0) REVERT: C 102 ASN cc_start: 0.7936 (t0) cc_final: 0.7462 (t0) REVERT: C 170 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: C 245 GLN cc_start: 0.7270 (mt0) cc_final: 0.6889 (mt0) REVERT: C 278 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8015 (mm) REVERT: C 291 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 296 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6115 (mm-30) REVERT: C 336 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7428 (ptt-90) REVERT: C 479 ASP cc_start: 0.8024 (t0) cc_final: 0.7702 (t70) REVERT: C 584 PRO cc_start: 0.7798 (Cg_endo) cc_final: 0.7284 (Cg_exo) REVERT: C 693 GLN cc_start: 0.8190 (tp40) cc_final: 0.7940 (tm-30) REVERT: C 724 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: C 770 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7957 (mp) REVERT: C 1006 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: D 71 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: D 77 ASP cc_start: 0.6249 (p0) cc_final: 0.5924 (p0) REVERT: D 102 ASN cc_start: 0.7940 (t0) cc_final: 0.7465 (t0) REVERT: D 170 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: D 245 GLN cc_start: 0.7274 (mt0) cc_final: 0.6895 (mt0) REVERT: D 278 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7755 (mp) REVERT: D 296 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6176 (mm-30) REVERT: D 336 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7426 (ptt-90) REVERT: D 479 ASP cc_start: 0.8029 (t0) cc_final: 0.7697 (t70) REVERT: D 584 PRO cc_start: 0.7802 (Cg_endo) cc_final: 0.7289 (Cg_exo) REVERT: D 693 GLN cc_start: 0.8193 (tp40) cc_final: 0.7942 (tm-30) REVERT: D 724 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: D 770 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7953 (mp) REVERT: D 1006 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7171 (pt0) outliers start: 177 outliers final: 92 residues processed: 583 average time/residue: 1.6048 time to fit residues: 1090.7576 Evaluate side-chains 610 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 493 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 754 LYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 739 HIS B 903 GLN B 945 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 GLN C 739 HIS C 903 GLN C 945 ASN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN D 739 HIS D 903 GLN D 945 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33468 Z= 0.302 Angle : 0.582 6.924 45660 Z= 0.306 Chirality : 0.046 0.154 4752 Planarity : 0.005 0.045 6036 Dihedral : 5.228 29.608 4428 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.37 % Allowed : 14.00 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4036 helix: -0.38 (0.22), residues: 488 sheet: 0.35 (0.14), residues: 1344 loop : -0.15 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 553 HIS 0.008 0.001 HIS D 395 PHE 0.013 0.002 PHE A 143 TYR 0.025 0.002 TYR D 100 ARG 0.003 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 489 time to evaluate : 3.735 Fit side-chains REVERT: A 77 ASP cc_start: 0.6181 (p0) cc_final: 0.5792 (p0) REVERT: A 102 ASN cc_start: 0.7891 (t0) cc_final: 0.7405 (t0) REVERT: A 170 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: A 277 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6444 (pp20) REVERT: A 278 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 296 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6094 (mm-30) REVERT: A 336 ARG cc_start: 0.7704 (ptt-90) cc_final: 0.7294 (ptt-90) REVERT: A 479 ASP cc_start: 0.7977 (t0) cc_final: 0.7661 (t70) REVERT: A 502 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8125 (ptm) REVERT: A 584 PRO cc_start: 0.7774 (Cg_endo) cc_final: 0.7260 (Cg_exo) REVERT: A 693 GLN cc_start: 0.8166 (tp40) cc_final: 0.7933 (tm-30) REVERT: A 724 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: A 770 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 1006 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: B 77 ASP cc_start: 0.6179 (p0) cc_final: 0.5787 (p0) REVERT: B 102 ASN cc_start: 0.7893 (t0) cc_final: 0.7405 (t0) REVERT: B 170 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: B 245 GLN cc_start: 0.7077 (mt0) cc_final: 0.6722 (mt0) REVERT: B 277 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6453 (pp20) REVERT: B 278 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7709 (mp) REVERT: B 296 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6072 (mm-30) REVERT: B 336 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7304 (ptt-90) REVERT: B 479 ASP cc_start: 0.7973 (t0) cc_final: 0.7655 (t70) REVERT: B 502 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8119 (ptm) REVERT: B 584 PRO cc_start: 0.7771 (Cg_endo) cc_final: 0.7254 (Cg_exo) REVERT: B 693 GLN cc_start: 0.8166 (tp40) cc_final: 0.7933 (tm-30) REVERT: B 724 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: B 770 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7886 (mp) REVERT: B 1006 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: C 77 ASP cc_start: 0.6184 (p0) cc_final: 0.5791 (p0) REVERT: C 102 ASN cc_start: 0.7890 (t0) cc_final: 0.7405 (t0) REVERT: C 170 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: C 245 GLN cc_start: 0.7078 (mt0) cc_final: 0.6724 (mt0) REVERT: C 277 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6447 (pp20) REVERT: C 278 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7942 (mm) REVERT: C 296 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6090 (mm-30) REVERT: C 336 ARG cc_start: 0.7709 (ptt-90) cc_final: 0.7308 (ptt-90) REVERT: C 479 ASP cc_start: 0.7984 (t0) cc_final: 0.7665 (t70) REVERT: C 502 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8126 (ptm) REVERT: C 584 PRO cc_start: 0.7770 (Cg_endo) cc_final: 0.7254 (Cg_exo) REVERT: C 693 GLN cc_start: 0.8162 (tp40) cc_final: 0.7929 (tm-30) REVERT: C 724 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: C 770 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7890 (mp) REVERT: C 1006 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: D 77 ASP cc_start: 0.6181 (p0) cc_final: 0.5790 (p0) REVERT: D 102 ASN cc_start: 0.7894 (t0) cc_final: 0.7408 (t0) REVERT: D 170 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: D 245 GLN cc_start: 0.7082 (mt0) cc_final: 0.6735 (mt0) REVERT: D 277 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6457 (pp20) REVERT: D 278 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7674 (mp) REVERT: D 296 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6099 (mm-30) REVERT: D 336 ARG cc_start: 0.7709 (ptt-90) cc_final: 0.7304 (ptt-90) REVERT: D 479 ASP cc_start: 0.7987 (t0) cc_final: 0.7662 (t70) REVERT: D 502 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8125 (ptm) REVERT: D 584 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7258 (Cg_exo) REVERT: D 693 GLN cc_start: 0.8167 (tp40) cc_final: 0.7934 (tm-30) REVERT: D 724 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 770 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7886 (mp) REVERT: D 1006 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7157 (pt0) outliers start: 151 outliers final: 90 residues processed: 567 average time/residue: 1.6662 time to fit residues: 1094.8613 Evaluate side-chains 605 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 491 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 754 LYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 390 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 33468 Z= 0.375 Angle : 0.628 7.496 45660 Z= 0.329 Chirality : 0.048 0.160 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.365 29.582 4428 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.63 % Allowed : 13.86 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.14 (0.13), residues: 4036 helix: -0.52 (0.22), residues: 488 sheet: 0.44 (0.14), residues: 1284 loop : -0.23 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 553 HIS 0.008 0.001 HIS D 395 PHE 0.014 0.002 PHE A 143 TYR 0.025 0.002 TYR A 100 ARG 0.004 0.001 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 496 time to evaluate : 4.001 Fit side-chains REVERT: A 46 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6700 (mtt180) REVERT: A 77 ASP cc_start: 0.6286 (p0) cc_final: 0.5868 (p0) REVERT: A 102 ASN cc_start: 0.7919 (t0) cc_final: 0.7440 (t0) REVERT: A 170 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: A 187 MET cc_start: 0.8737 (ttm) cc_final: 0.8456 (ttm) REVERT: A 277 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6445 (pp20) REVERT: A 278 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 296 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6205 (mm-30) REVERT: A 336 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7370 (ptt-90) REVERT: A 479 ASP cc_start: 0.8011 (t0) cc_final: 0.7691 (t70) REVERT: A 584 PRO cc_start: 0.7807 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: A 693 GLN cc_start: 0.8189 (tp40) cc_final: 0.7956 (tm-30) REVERT: A 724 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: A 753 ASN cc_start: 0.6957 (t0) cc_final: 0.6596 (m-40) REVERT: A 770 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7958 (mp) REVERT: A 1006 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: B 46 ARG cc_start: 0.6946 (mtt180) cc_final: 0.6694 (mtt180) REVERT: B 77 ASP cc_start: 0.6287 (p0) cc_final: 0.5866 (p0) REVERT: B 102 ASN cc_start: 0.7922 (t0) cc_final: 0.7441 (t0) REVERT: B 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: B 187 MET cc_start: 0.8737 (ttm) cc_final: 0.8456 (ttm) REVERT: B 245 GLN cc_start: 0.7069 (mt0) cc_final: 0.6750 (mt0) REVERT: B 277 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6452 (pp20) REVERT: B 278 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 296 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6206 (mm-30) REVERT: B 336 ARG cc_start: 0.7746 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: B 479 ASP cc_start: 0.8006 (t0) cc_final: 0.7685 (t70) REVERT: B 584 PRO cc_start: 0.7804 (Cg_endo) cc_final: 0.7282 (Cg_exo) REVERT: B 693 GLN cc_start: 0.8187 (tp40) cc_final: 0.7956 (tm-30) REVERT: B 724 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: B 753 ASN cc_start: 0.6961 (t0) cc_final: 0.6599 (m-40) REVERT: B 770 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 1006 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: C 46 ARG cc_start: 0.6946 (mtt180) cc_final: 0.6693 (mtt180) REVERT: C 77 ASP cc_start: 0.6289 (p0) cc_final: 0.5866 (p0) REVERT: C 102 ASN cc_start: 0.7916 (t0) cc_final: 0.7441 (t0) REVERT: C 170 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: C 187 MET cc_start: 0.8742 (ttm) cc_final: 0.8458 (ttm) REVERT: C 245 GLN cc_start: 0.7074 (mt0) cc_final: 0.6756 (mt0) REVERT: C 277 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6442 (pp20) REVERT: C 278 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7707 (mp) REVERT: C 296 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6203 (mm-30) REVERT: C 336 ARG cc_start: 0.7744 (ptt-90) cc_final: 0.7379 (ptt-90) REVERT: C 479 ASP cc_start: 0.8018 (t0) cc_final: 0.7692 (t70) REVERT: C 584 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7283 (Cg_exo) REVERT: C 693 GLN cc_start: 0.8186 (tp40) cc_final: 0.7953 (tm-30) REVERT: C 724 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: C 753 ASN cc_start: 0.6961 (t0) cc_final: 0.6601 (m-40) REVERT: C 770 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7954 (mp) REVERT: C 1006 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: D 46 ARG cc_start: 0.6951 (mtt180) cc_final: 0.6698 (mtt180) REVERT: D 77 ASP cc_start: 0.6286 (p0) cc_final: 0.5868 (p0) REVERT: D 102 ASN cc_start: 0.7921 (t0) cc_final: 0.7440 (t0) REVERT: D 170 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: D 187 MET cc_start: 0.8740 (ttm) cc_final: 0.8457 (ttm) REVERT: D 245 GLN cc_start: 0.7073 (mt0) cc_final: 0.6768 (mt0) REVERT: D 277 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6445 (pp20) REVERT: D 278 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7706 (mp) REVERT: D 296 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6208 (mm-30) REVERT: D 336 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.7378 (ptt-90) REVERT: D 479 ASP cc_start: 0.8020 (t0) cc_final: 0.7690 (t70) REVERT: D 584 PRO cc_start: 0.7805 (Cg_endo) cc_final: 0.7288 (Cg_exo) REVERT: D 693 GLN cc_start: 0.8192 (tp40) cc_final: 0.7959 (tm-30) REVERT: D 724 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: D 753 ASN cc_start: 0.6965 (t0) cc_final: 0.6601 (m-40) REVERT: D 770 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 1006 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7162 (pt0) outliers start: 160 outliers final: 96 residues processed: 580 average time/residue: 1.6404 time to fit residues: 1108.0104 Evaluate side-chains 612 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 496 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 754 LYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 389 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 739 HIS A 903 GLN A 945 ASN A 956 GLN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN B 956 GLN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 739 HIS C 903 GLN C 945 ASN C 956 GLN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 739 HIS D 903 GLN D 945 ASN D 956 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33468 Z= 0.205 Angle : 0.528 5.889 45660 Z= 0.277 Chirality : 0.044 0.154 4752 Planarity : 0.004 0.043 6036 Dihedral : 4.960 27.317 4428 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.62 % Allowed : 15.60 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.12 (0.14), residues: 4036 helix: -0.07 (0.23), residues: 496 sheet: 0.39 (0.14), residues: 1392 loop : 0.03 (0.15), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 553 HIS 0.007 0.001 HIS D 395 PHE 0.012 0.001 PHE C 143 TYR 0.024 0.002 TYR C 100 ARG 0.004 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 535 time to evaluate : 3.442 Fit side-chains REVERT: A 77 ASP cc_start: 0.6229 (p0) cc_final: 0.5790 (p0) REVERT: A 102 ASN cc_start: 0.7850 (t0) cc_final: 0.7392 (t0) REVERT: A 170 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: A 187 MET cc_start: 0.8779 (ttm) cc_final: 0.8495 (ttm) REVERT: A 278 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7953 (mm) REVERT: A 296 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 336 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7326 (ptt-90) REVERT: A 479 ASP cc_start: 0.7976 (t0) cc_final: 0.7644 (t70) REVERT: A 530 THR cc_start: 0.7888 (t) cc_final: 0.7458 (p) REVERT: A 584 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.7150 (Cg_exo) REVERT: A 724 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: A 753 ASN cc_start: 0.6851 (t0) cc_final: 0.6529 (m-40) REVERT: A 770 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (mp) REVERT: A 1006 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: B 77 ASP cc_start: 0.6230 (p0) cc_final: 0.5788 (p0) REVERT: B 102 ASN cc_start: 0.7860 (t0) cc_final: 0.7392 (t0) REVERT: B 170 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: B 187 MET cc_start: 0.8777 (ttm) cc_final: 0.8495 (ttm) REVERT: B 245 GLN cc_start: 0.6932 (mt0) cc_final: 0.6633 (mt0) REVERT: B 277 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6207 (mm-30) REVERT: B 278 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7922 (mm) REVERT: B 296 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6326 (mm-30) REVERT: B 336 ARG cc_start: 0.7708 (ptt-90) cc_final: 0.7331 (ptt-90) REVERT: B 479 ASP cc_start: 0.7956 (t0) cc_final: 0.7647 (t70) REVERT: B 530 THR cc_start: 0.7720 (t) cc_final: 0.7286 (p) REVERT: B 584 PRO cc_start: 0.7683 (Cg_endo) cc_final: 0.7142 (Cg_exo) REVERT: B 724 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: B 753 ASN cc_start: 0.6851 (t0) cc_final: 0.6532 (m-40) REVERT: B 770 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7811 (mp) REVERT: B 1006 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: C 77 ASP cc_start: 0.6233 (p0) cc_final: 0.5787 (p0) REVERT: C 102 ASN cc_start: 0.7854 (t0) cc_final: 0.7390 (t0) REVERT: C 170 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: C 187 MET cc_start: 0.8780 (ttm) cc_final: 0.8497 (ttm) REVERT: C 245 GLN cc_start: 0.6933 (mt0) cc_final: 0.6637 (mt0) REVERT: C 277 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6198 (mm-30) REVERT: C 296 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6378 (mm-30) REVERT: C 336 ARG cc_start: 0.7706 (ptt-90) cc_final: 0.7335 (ptt-90) REVERT: C 479 ASP cc_start: 0.7982 (t0) cc_final: 0.7647 (t70) REVERT: C 530 THR cc_start: 0.7715 (t) cc_final: 0.7277 (p) REVERT: C 584 PRO cc_start: 0.7680 (Cg_endo) cc_final: 0.7136 (Cg_exo) REVERT: C 724 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: C 753 ASN cc_start: 0.6850 (t0) cc_final: 0.6531 (m-40) REVERT: C 770 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7900 (mp) REVERT: C 1006 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: D 77 ASP cc_start: 0.6232 (p0) cc_final: 0.5790 (p0) REVERT: D 102 ASN cc_start: 0.7857 (t0) cc_final: 0.7395 (t0) REVERT: D 170 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: D 187 MET cc_start: 0.8777 (ttm) cc_final: 0.8493 (ttm) REVERT: D 245 GLN cc_start: 0.6940 (mt0) cc_final: 0.6637 (mt0) REVERT: D 278 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7948 (mm) REVERT: D 296 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6385 (mm-30) REVERT: D 336 ARG cc_start: 0.7708 (ptt-90) cc_final: 0.7333 (ptt-90) REVERT: D 479 ASP cc_start: 0.7985 (t0) cc_final: 0.7647 (t70) REVERT: D 530 THR cc_start: 0.7888 (t) cc_final: 0.7454 (p) REVERT: D 584 PRO cc_start: 0.7685 (Cg_endo) cc_final: 0.7148 (Cg_exo) REVERT: D 724 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: D 753 ASN cc_start: 0.6855 (t0) cc_final: 0.6533 (m-40) REVERT: D 770 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7814 (mp) REVERT: D 1006 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7125 (pt0) outliers start: 125 outliers final: 70 residues processed: 600 average time/residue: 1.6098 time to fit residues: 1126.1079 Evaluate side-chains 595 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 506 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 265 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN D 990 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33468 Z= 0.256 Angle : 0.559 6.322 45660 Z= 0.293 Chirality : 0.045 0.159 4752 Planarity : 0.004 0.045 6036 Dihedral : 5.016 26.828 4428 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.31 % Allowed : 15.10 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.15 (0.14), residues: 4036 helix: -0.07 (0.23), residues: 496 sheet: 0.41 (0.14), residues: 1392 loop : 0.06 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 553 HIS 0.007 0.001 HIS C 395 PHE 0.012 0.001 PHE B 143 TYR 0.023 0.002 TYR B 100 ARG 0.004 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 497 time to evaluate : 3.666 Fit side-chains REVERT: A 18 ASN cc_start: 0.7808 (t0) cc_final: 0.7383 (t0) REVERT: A 46 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6725 (mtt180) REVERT: A 77 ASP cc_start: 0.6257 (p0) cc_final: 0.5805 (p0) REVERT: A 102 ASN cc_start: 0.7883 (t0) cc_final: 0.7419 (t0) REVERT: A 170 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 278 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 296 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6307 (mm-30) REVERT: A 336 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7360 (ptt-90) REVERT: A 479 ASP cc_start: 0.7968 (t0) cc_final: 0.7638 (t70) REVERT: A 530 THR cc_start: 0.7909 (t) cc_final: 0.7470 (p) REVERT: A 542 MET cc_start: 0.8341 (ttt) cc_final: 0.7934 (ttt) REVERT: A 584 PRO cc_start: 0.7756 (Cg_endo) cc_final: 0.7226 (Cg_exo) REVERT: A 724 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: A 753 ASN cc_start: 0.6818 (t0) cc_final: 0.6518 (m-40) REVERT: A 770 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 1006 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: B 18 ASN cc_start: 0.7811 (t0) cc_final: 0.7387 (t0) REVERT: B 46 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6721 (mtt180) REVERT: B 77 ASP cc_start: 0.6257 (p0) cc_final: 0.5801 (p0) REVERT: B 102 ASN cc_start: 0.7881 (t0) cc_final: 0.7419 (t0) REVERT: B 170 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: B 245 GLN cc_start: 0.6981 (mt0) cc_final: 0.6720 (mt0) REVERT: B 277 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6203 (mm-30) REVERT: B 278 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 296 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6296 (mm-30) REVERT: B 336 ARG cc_start: 0.7715 (ptt-90) cc_final: 0.7368 (ptt-90) REVERT: B 479 ASP cc_start: 0.7967 (t0) cc_final: 0.7636 (t70) REVERT: B 530 THR cc_start: 0.7868 (t) cc_final: 0.7421 (p) REVERT: B 584 PRO cc_start: 0.7751 (Cg_endo) cc_final: 0.7217 (Cg_exo) REVERT: B 724 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: B 753 ASN cc_start: 0.6820 (t0) cc_final: 0.6522 (m-40) REVERT: B 770 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 1006 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: C 18 ASN cc_start: 0.7801 (t0) cc_final: 0.7376 (t0) REVERT: C 46 ARG cc_start: 0.6960 (mtt180) cc_final: 0.6719 (mtt180) REVERT: C 77 ASP cc_start: 0.6258 (p0) cc_final: 0.5802 (p0) REVERT: C 102 ASN cc_start: 0.7874 (t0) cc_final: 0.7432 (t0) REVERT: C 170 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: C 245 GLN cc_start: 0.6980 (mt0) cc_final: 0.6723 (mt0) REVERT: C 277 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6195 (mm-30) REVERT: C 296 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6300 (mm-30) REVERT: C 336 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.7371 (ptt-90) REVERT: C 479 ASP cc_start: 0.7977 (t0) cc_final: 0.7647 (t70) REVERT: C 530 THR cc_start: 0.7869 (t) cc_final: 0.7417 (p) REVERT: C 542 MET cc_start: 0.8401 (ttt) cc_final: 0.7988 (ttt) REVERT: C 584 PRO cc_start: 0.7748 (Cg_endo) cc_final: 0.7208 (Cg_exo) REVERT: C 724 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: C 753 ASN cc_start: 0.6817 (t0) cc_final: 0.6520 (m-40) REVERT: C 770 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7895 (mp) REVERT: C 1006 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: D 18 ASN cc_start: 0.7810 (t0) cc_final: 0.7384 (t0) REVERT: D 46 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6723 (mtt180) REVERT: D 77 ASP cc_start: 0.6257 (p0) cc_final: 0.5801 (p0) REVERT: D 102 ASN cc_start: 0.7887 (t0) cc_final: 0.7442 (t0) REVERT: D 170 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 245 GLN cc_start: 0.6976 (mt0) cc_final: 0.6722 (mt0) REVERT: D 278 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7684 (mp) REVERT: D 296 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6310 (mm-30) REVERT: D 336 ARG cc_start: 0.7715 (ptt-90) cc_final: 0.7368 (ptt-90) REVERT: D 479 ASP cc_start: 0.7979 (t0) cc_final: 0.7642 (t70) REVERT: D 530 THR cc_start: 0.7909 (t) cc_final: 0.7466 (p) REVERT: D 542 MET cc_start: 0.8336 (ttt) cc_final: 0.7934 (ttt) REVERT: D 584 PRO cc_start: 0.7754 (Cg_endo) cc_final: 0.7222 (Cg_exo) REVERT: D 724 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: D 753 ASN cc_start: 0.6824 (t0) cc_final: 0.6523 (m-40) REVERT: D 770 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7897 (mp) REVERT: D 1006 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7121 (pt0) outliers start: 149 outliers final: 95 residues processed: 581 average time/residue: 1.5870 time to fit residues: 1075.6016 Evaluate side-chains 603 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 489 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 372 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 327 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN D 990 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33468 Z= 0.362 Angle : 0.626 7.242 45660 Z= 0.328 Chirality : 0.047 0.161 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.289 28.399 4428 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.37 % Allowed : 15.62 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 0.00 (0.13), residues: 4036 helix: -0.29 (0.22), residues: 488 sheet: 0.33 (0.14), residues: 1392 loop : -0.03 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 553 HIS 0.008 0.001 HIS B 395 PHE 0.013 0.002 PHE B 143 TYR 0.024 0.002 TYR B 100 ARG 0.004 0.001 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 489 time to evaluate : 3.822 Fit side-chains REVERT: A 77 ASP cc_start: 0.6332 (p0) cc_final: 0.5896 (p0) REVERT: A 102 ASN cc_start: 0.7920 (t0) cc_final: 0.7446 (t0) REVERT: A 170 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 278 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 296 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6271 (mm-30) REVERT: A 336 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7389 (ptt-90) REVERT: A 479 ASP cc_start: 0.8001 (t0) cc_final: 0.7670 (t70) REVERT: A 542 MET cc_start: 0.8463 (ttt) cc_final: 0.8085 (ttt) REVERT: A 584 PRO cc_start: 0.7810 (Cg_endo) cc_final: 0.7275 (Cg_exo) REVERT: A 724 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: A 753 ASN cc_start: 0.6837 (t0) cc_final: 0.6539 (m-40) REVERT: A 770 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 1006 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7146 (pt0) REVERT: B 77 ASP cc_start: 0.6332 (p0) cc_final: 0.5890 (p0) REVERT: B 102 ASN cc_start: 0.7917 (t0) cc_final: 0.7449 (t0) REVERT: B 170 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: B 245 GLN cc_start: 0.7086 (mt0) cc_final: 0.6856 (mt0) REVERT: B 278 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7712 (mp) REVERT: B 296 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6226 (mm-30) REVERT: B 336 ARG cc_start: 0.7736 (ptt-90) cc_final: 0.7398 (ptt-90) REVERT: B 479 ASP cc_start: 0.7973 (t0) cc_final: 0.7621 (t70) REVERT: B 584 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: B 724 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: B 753 ASN cc_start: 0.6834 (t0) cc_final: 0.6541 (m-40) REVERT: B 770 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 1006 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: C 77 ASP cc_start: 0.6335 (p0) cc_final: 0.5894 (p0) REVERT: C 102 ASN cc_start: 0.7916 (t0) cc_final: 0.7442 (t0) REVERT: C 170 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: C 245 GLN cc_start: 0.7089 (mt0) cc_final: 0.6858 (mt0) REVERT: C 278 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7743 (mp) REVERT: C 296 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6226 (mm-30) REVERT: C 336 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.7398 (ptt-90) REVERT: C 479 ASP cc_start: 0.7983 (t0) cc_final: 0.7630 (t70) REVERT: C 542 MET cc_start: 0.8460 (ttt) cc_final: 0.8074 (ttt) REVERT: C 584 PRO cc_start: 0.7805 (Cg_endo) cc_final: 0.7267 (Cg_exo) REVERT: C 724 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: C 753 ASN cc_start: 0.6835 (t0) cc_final: 0.6541 (m-40) REVERT: C 770 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7937 (mp) REVERT: C 1006 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: D 77 ASP cc_start: 0.6331 (p0) cc_final: 0.5893 (p0) REVERT: D 102 ASN cc_start: 0.7926 (t0) cc_final: 0.7448 (t0) REVERT: D 170 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: D 245 GLN cc_start: 0.7162 (mt0) cc_final: 0.6883 (mt0) REVERT: D 278 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7722 (mp) REVERT: D 296 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6275 (mm-30) REVERT: D 336 ARG cc_start: 0.7736 (ptt-90) cc_final: 0.7397 (ptt-90) REVERT: D 479 ASP cc_start: 0.7986 (t0) cc_final: 0.7628 (t70) REVERT: D 542 MET cc_start: 0.8458 (ttt) cc_final: 0.8082 (ttt) REVERT: D 584 PRO cc_start: 0.7808 (Cg_endo) cc_final: 0.7273 (Cg_exo) REVERT: D 724 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: D 753 ASN cc_start: 0.6840 (t0) cc_final: 0.6545 (m-40) REVERT: D 770 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7939 (mp) REVERT: D 1006 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7149 (pt0) outliers start: 151 outliers final: 99 residues processed: 583 average time/residue: 1.6336 time to fit residues: 1120.9986 Evaluate side-chains 599 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 480 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 234 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 402 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 chunk 320 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 945 ASN A 990 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN C 990 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN D 990 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33468 Z= 0.206 Angle : 0.540 6.850 45660 Z= 0.283 Chirality : 0.044 0.181 4752 Planarity : 0.004 0.043 6036 Dihedral : 4.954 26.434 4428 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.70 % Allowed : 16.03 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: 4036 helix: 0.05 (0.23), residues: 496 sheet: 0.42 (0.14), residues: 1392 loop : 0.09 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 553 HIS 0.008 0.001 HIS B 395 PHE 0.011 0.001 PHE D 143 TYR 0.023 0.002 TYR B 100 ARG 0.005 0.000 ARG D 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 509 time to evaluate : 3.784 Fit side-chains REVERT: A 77 ASP cc_start: 0.6249 (p0) cc_final: 0.5802 (p0) REVERT: A 102 ASN cc_start: 0.7860 (t0) cc_final: 0.7409 (t0) REVERT: A 170 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 277 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6207 (mm-30) REVERT: A 296 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6141 (mm-30) REVERT: A 336 ARG cc_start: 0.7810 (ptt-90) cc_final: 0.7446 (ptt-90) REVERT: A 479 ASP cc_start: 0.7978 (t0) cc_final: 0.7637 (t70) REVERT: A 542 MET cc_start: 0.8362 (ttt) cc_final: 0.7969 (ttt) REVERT: A 584 PRO cc_start: 0.7691 (Cg_endo) cc_final: 0.7142 (Cg_exo) REVERT: A 724 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: A 753 ASN cc_start: 0.6947 (t0) cc_final: 0.6617 (m-40) REVERT: A 770 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1006 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: B 77 ASP cc_start: 0.6251 (p0) cc_final: 0.5800 (p0) REVERT: B 102 ASN cc_start: 0.7856 (t0) cc_final: 0.7414 (t0) REVERT: B 170 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 245 GLN cc_start: 0.6948 (mt0) cc_final: 0.6734 (mt0) REVERT: B 277 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6232 (mm-30) REVERT: B 296 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6137 (mm-30) REVERT: B 336 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7470 (ptt-90) REVERT: B 479 ASP cc_start: 0.7970 (t0) cc_final: 0.7632 (t70) REVERT: B 584 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.7138 (Cg_exo) REVERT: B 724 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: B 753 ASN cc_start: 0.6944 (t0) cc_final: 0.6616 (m-40) REVERT: B 770 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 1006 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: C 46 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6797 (mtt180) REVERT: C 77 ASP cc_start: 0.6251 (p0) cc_final: 0.5801 (p0) REVERT: C 102 ASN cc_start: 0.7856 (t0) cc_final: 0.7405 (t0) REVERT: C 170 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 245 GLN cc_start: 0.6954 (mt0) cc_final: 0.6740 (mt0) REVERT: C 277 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6211 (mm-30) REVERT: C 296 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6139 (mm-30) REVERT: C 336 ARG cc_start: 0.7817 (ptt-90) cc_final: 0.7470 (ptt-90) REVERT: C 479 ASP cc_start: 0.7985 (t0) cc_final: 0.7643 (t70) REVERT: C 542 MET cc_start: 0.8368 (ttt) cc_final: 0.7974 (ttt) REVERT: C 584 PRO cc_start: 0.7698 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: C 724 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: C 753 ASN cc_start: 0.6941 (t0) cc_final: 0.6615 (m-40) REVERT: C 770 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7901 (mp) REVERT: C 1006 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: D 46 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6801 (mtt180) REVERT: D 77 ASP cc_start: 0.6252 (p0) cc_final: 0.5801 (p0) REVERT: D 102 ASN cc_start: 0.7865 (t0) cc_final: 0.7412 (t0) REVERT: D 170 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: D 245 GLN cc_start: 0.6945 (mt0) cc_final: 0.6734 (mt0) REVERT: D 277 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6214 (mm-30) REVERT: D 296 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6149 (mm-30) REVERT: D 336 ARG cc_start: 0.7822 (ptt-90) cc_final: 0.7472 (ptt-90) REVERT: D 479 ASP cc_start: 0.7987 (t0) cc_final: 0.7638 (t70) REVERT: D 542 MET cc_start: 0.8360 (ttt) cc_final: 0.7968 (ttt) REVERT: D 584 PRO cc_start: 0.7690 (Cg_endo) cc_final: 0.7140 (Cg_exo) REVERT: D 724 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: D 753 ASN cc_start: 0.6873 (t0) cc_final: 0.6550 (m-40) REVERT: D 770 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 1006 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7116 (pm20) outliers start: 128 outliers final: 82 residues processed: 582 average time/residue: 1.5698 time to fit residues: 1068.1055 Evaluate side-chains 609 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 511 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 828 ASP Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 341 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 945 ASN A 990 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN D 990 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.122575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104926 restraints weight = 39199.241| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.38 r_work: 0.2940 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33468 Z= 0.261 Angle : 0.570 6.358 45660 Z= 0.298 Chirality : 0.045 0.155 4752 Planarity : 0.004 0.045 6036 Dihedral : 5.051 26.331 4428 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.44 % Allowed : 16.32 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 4036 helix: -0.02 (0.23), residues: 496 sheet: 0.43 (0.14), residues: 1392 loop : 0.07 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 553 HIS 0.007 0.001 HIS A 395 PHE 0.013 0.001 PHE C 143 TYR 0.023 0.002 TYR D 100 ARG 0.004 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14838.52 seconds wall clock time: 261 minutes 18.32 seconds (15678.32 seconds total)