Starting phenix.real_space_refine on Wed Feb 21 09:01:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukm_26584/02_2024/7ukm_26584.pdb" } resolution = 3.03 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= 0.001 sd= 0.044 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 135 5.16 5 C 19174 2.51 5 N 4955 2.21 5 O 5881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 60": "OE1" <-> "OE2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y GLU 79": "OE1" <-> "OE2" Residue "Y TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 50": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N ASP 82": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30145 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "X" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "Y" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "H" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "C" Number of atoms: 7902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7902 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 51, 'TRANS': 960} Chain breaks: 8 Chain: "M" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 15.72, per 1000 atoms: 0.52 Number of scatterers: 30145 At special positions: 0 Unit cell: (176.79, 185.09, 172.64, 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 135 16.00 O 5881 8.00 N 4955 7.00 C 19174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG A1314 " - " ASN A 603 " " NAG A1315 " - " ASN A 122 " " NAG A1316 " - " ASN A 61 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 165 " " NAG B1314 " - " ASN B 331 " " NAG B1315 " - " ASN B 343 " " NAG B1316 " - " ASN B1074 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 165 " " NAG C1314 " - " ASN C 234 " " NAG C1315 " - " ASN C 343 " Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 5.7 seconds 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 64 sheets defined 22.9% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.571A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.414A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.988A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.732A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.507A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.725A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.690A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.909A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.282A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 30 No H-bonds generated for 'chain 'X' and resid 28 through 30' Processing helix chain 'X' and resid 61 through 64 removed outlier: 3.834A pdb=" N LYS X 64 " --> pdb=" O ASP X 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 64' Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.620A pdb=" N VAL Y 83 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.658A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.398A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.899A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.656A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.559A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.704A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.972A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.641A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100A through 100E Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.893A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.155A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.059A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.996A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.523A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.612A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.744A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.654A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.715A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.736A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.802A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.912A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100A through 100E Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.726A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.007A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.733A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.103A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.215A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.563A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.446A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.370A pdb=" N ASP X 33 " --> pdb=" O ASP X 95 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 10 through 12 removed outlier: 7.136A pdb=" N CYS X 92 " --> pdb=" O TRP X 103 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP X 103 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG X 94 " --> pdb=" O ASP X 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 4.595A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU Y 50 " --> pdb=" O ASN Y 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.166A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.958A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.778A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.323A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.178A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.275A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.531A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.955A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.900A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.316A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.237A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.185A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.745A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.867A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.867A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.896A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.010A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.849A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.175A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.045A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.161A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.866A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.957A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.195A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.437A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.585A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.101A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.635A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.829A pdb=" N ALA N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 75 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.987A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 10 through 13 removed outlier: 4.289A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3267 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: 15.82 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5026 1.32 - 1.46: 9957 1.46 - 1.59: 15669 1.59 - 1.72: 0 1.72 - 1.85: 177 Bond restraints: 30829 Sorted by residual: bond pdb=" C LYS L 24 " pdb=" O LYS L 24 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.19e-02 7.06e+03 1.39e+01 bond pdb=" N LEU L 46 " pdb=" CA LEU L 46 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.22e-02 6.72e+03 1.15e+01 bond pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" N ILE Y 92 " pdb=" CA ILE Y 92 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.07e+00 ... (remaining 30824 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.43: 662 105.43 - 113.02: 16494 113.02 - 120.61: 12867 120.61 - 128.20: 11623 128.20 - 135.78: 299 Bond angle restraints: 41945 Sorted by residual: angle pdb=" CA MET M 82 " pdb=" C MET M 82 " pdb=" O MET M 82 " ideal model delta sigma weight residual 121.46 115.20 6.26 1.17e+00 7.31e-01 2.86e+01 angle pdb=" CA GLY B 744 " pdb=" C GLY B 744 " pdb=" O GLY B 744 " ideal model delta sigma weight residual 121.18 116.70 4.48 8.80e-01 1.29e+00 2.59e+01 angle pdb=" CA TYR C 160 " pdb=" C TYR C 160 " pdb=" O TYR C 160 " ideal model delta sigma weight residual 121.23 116.18 5.05 1.07e+00 8.73e-01 2.23e+01 angle pdb=" N LYS M 57 " pdb=" CA LYS M 57 " pdb=" C LYS M 57 " ideal model delta sigma weight residual 109.59 117.04 -7.45 1.61e+00 3.86e-01 2.14e+01 angle pdb=" CA LYS M 57 " pdb=" C LYS M 57 " pdb=" O LYS M 57 " ideal model delta sigma weight residual 120.71 115.83 4.88 1.06e+00 8.90e-01 2.12e+01 ... (remaining 41940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17534 17.96 - 35.92: 1133 35.92 - 53.89: 199 53.89 - 71.85: 51 71.85 - 89.81: 25 Dihedral angle restraints: 18942 sinusoidal: 7998 harmonic: 10944 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 42.90 50.10 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -37.01 -48.99 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 ... (remaining 18939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4428 0.088 - 0.176: 418 0.176 - 0.264: 11 0.264 - 0.352: 0 0.352 - 0.440: 1 Chirality restraints: 4858 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA PHE M 58 " pdb=" N PHE M 58 " pdb=" C PHE M 58 " pdb=" CB PHE M 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS C 166 " pdb=" N CYS C 166 " pdb=" C CYS C 166 " pdb=" CB CYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 4855 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.048 2.00e-02 2.50e+03 3.39e-02 2.88e+01 pdb=" CG TRP B 886 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 67 " 0.024 2.00e-02 2.50e+03 2.99e-02 1.57e+01 pdb=" CG PHE M 67 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE M 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE M 67 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE M 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE M 67 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE M 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 14 " -0.062 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO N 15 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO N 15 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO N 15 " -0.051 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4334 2.76 - 3.29: 29420 3.29 - 3.83: 48664 3.83 - 4.36: 60064 4.36 - 4.90: 105030 Nonbonded interactions: 247512 Sorted by model distance: nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.223 2.440 nonbonded pdb=" OE2 GLU C 773 " pdb=" NE ARG C1019 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR A 108 " pdb=" O6 NAG A1305 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.260 2.440 ... (remaining 247507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1147 or resid 1301 through 1315)) selection = (chain 'B' and (resid 27 through 1147 or resid 1301 through 1315)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Y' } 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: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 19.690 Check model and map are aligned: 0.460 Set scattering table: 0.650 Process input model: 84.070 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.200 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30829 Z= 0.298 Angle : 0.759 10.784 41945 Z= 0.428 Chirality : 0.048 0.440 4858 Planarity : 0.005 0.119 5369 Dihedral : 12.649 89.809 11781 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3705 helix: 1.79 (0.21), residues: 645 sheet: -0.13 (0.16), residues: 1050 loop : -0.22 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.002 TRP B 886 HIS 0.012 0.001 HIS A1083 PHE 0.068 0.001 PHE M 67 TYR 0.053 0.001 TYR C 904 ARG 0.017 0.001 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 68 THR cc_start: 0.9401 (m) cc_final: 0.9178 (p) REVERT: X 77 THR cc_start: 0.9064 (p) cc_final: 0.8798 (p) REVERT: X 82 MET cc_start: 0.8919 (mmm) cc_final: 0.8713 (mmt) REVERT: X 101 ASP cc_start: 0.8778 (t0) cc_final: 0.8439 (t0) REVERT: Y 2 ASN cc_start: 0.8285 (t0) cc_final: 0.8009 (t0) REVERT: Y 11 LEU cc_start: 0.8123 (tp) cc_final: 0.7498 (tp) REVERT: Y 30 LYS cc_start: 0.8995 (mttm) cc_final: 0.8793 (mttt) REVERT: Y 73 LEU cc_start: 0.8991 (tt) cc_final: 0.8382 (tt) REVERT: Y 77 ARG cc_start: 0.7623 (ptm160) cc_final: 0.7311 (ptm160) REVERT: Y 79 GLU cc_start: 0.7863 (mp0) cc_final: 0.7539 (mp0) REVERT: Y 97 THR cc_start: 0.7927 (p) cc_final: 0.7271 (p) REVERT: Y 105 GLU cc_start: 0.7555 (pt0) cc_final: 0.7012 (pm20) REVERT: H 6 GLU cc_start: 0.7696 (mp0) cc_final: 0.7472 (mp0) REVERT: H 23 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7404 (tm-30) REVERT: H 32 TYR cc_start: 0.9145 (m-80) cc_final: 0.8872 (m-80) REVERT: H 64 LYS cc_start: 0.9278 (tptt) cc_final: 0.8739 (mmmt) REVERT: H 100 ASP cc_start: 0.8637 (t0) cc_final: 0.8343 (t0) REVERT: L 45 GLN cc_start: 0.7007 (pm20) cc_final: 0.6500 (pm20) REVERT: L 61 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7443 (ptp90) REVERT: L 79 GLU cc_start: 0.7960 (mp0) cc_final: 0.7328 (mp0) REVERT: L 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8402 (m-30) REVERT: L 103 LYS cc_start: 0.8192 (tmtt) cc_final: 0.7992 (tptp) REVERT: L 104 LEU cc_start: 0.8329 (tt) cc_final: 0.8013 (tt) REVERT: M 72 ASP cc_start: 0.8878 (t0) cc_final: 0.8515 (t0) REVERT: N 11 LEU cc_start: 0.8599 (pt) cc_final: 0.8391 (pt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.4396 time to fit residues: 239.8353 Evaluate side-chains 278 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 340 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 394 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN L 27 GLN C 121 ASN M 13 GLN ** M 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30829 Z= 0.219 Angle : 0.553 11.529 41945 Z= 0.283 Chirality : 0.044 0.226 4858 Planarity : 0.004 0.064 5369 Dihedral : 5.682 54.588 5046 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.76 % Allowed : 4.22 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3705 helix: 2.11 (0.21), residues: 624 sheet: 0.09 (0.16), residues: 1041 loop : -0.27 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Y 35 HIS 0.006 0.001 HIS A1083 PHE 0.020 0.001 PHE N 55 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 317 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7453 (ttp80) REVERT: B 869 MET cc_start: 0.9085 (mtt) cc_final: 0.8881 (mtt) REVERT: X 23 GLU cc_start: 0.8807 (tp30) cc_final: 0.8582 (tp30) REVERT: X 64 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8590 (mmmt) REVERT: X 82 MET cc_start: 0.8844 (mmm) cc_final: 0.8591 (mmt) REVERT: X 101 ASP cc_start: 0.8787 (t0) cc_final: 0.8510 (t0) REVERT: Y 11 LEU cc_start: 0.8075 (tp) cc_final: 0.7373 (tp) REVERT: Y 34 TYR cc_start: 0.8834 (m-80) cc_final: 0.8250 (m-80) REVERT: Y 73 LEU cc_start: 0.9356 (tt) cc_final: 0.9077 (tt) REVERT: Y 81 GLU cc_start: 0.8858 (pm20) cc_final: 0.8531 (pm20) REVERT: Y 89 MET cc_start: 0.8961 (ttp) cc_final: 0.8222 (ttp) REVERT: Y 105 GLU cc_start: 0.7448 (pt0) cc_final: 0.6985 (pm20) REVERT: H 23 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7601 (tm-30) REVERT: H 32 TYR cc_start: 0.9016 (m-80) cc_final: 0.8726 (m-80) REVERT: L 79 GLU cc_start: 0.7957 (mp0) cc_final: 0.7595 (mp0) REVERT: L 82 ASP cc_start: 0.8484 (m-30) cc_final: 0.8058 (m-30) REVERT: L 104 LEU cc_start: 0.8126 (tt) cc_final: 0.7516 (tt) REVERT: C 140 PHE cc_start: 0.7983 (p90) cc_final: 0.7704 (p90) REVERT: C 904 TYR cc_start: 0.7291 (m-80) cc_final: 0.6939 (m-80) REVERT: M 72 ASP cc_start: 0.8713 (t0) cc_final: 0.8289 (t0) REVERT: N 4 MET cc_start: 0.8529 (tpt) cc_final: 0.8173 (mmm) REVERT: N 37 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8726 (pt) REVERT: N 55 PHE cc_start: 0.9051 (t80) cc_final: 0.8838 (t80) REVERT: N 61 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7894 (ptt-90) outliers start: 25 outliers final: 17 residues processed: 326 average time/residue: 0.4319 time to fit residues: 223.4614 Evaluate side-chains 296 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 75 ILE Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN X 39 GLN Y 38 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN M 82AASN N 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30829 Z= 0.314 Angle : 0.561 11.598 41945 Z= 0.285 Chirality : 0.045 0.234 4858 Planarity : 0.004 0.053 5369 Dihedral : 5.483 54.373 5046 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.34 % Allowed : 6.59 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3705 helix: 2.08 (0.21), residues: 624 sheet: 0.08 (0.15), residues: 1041 loop : -0.26 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Y 35 HIS 0.005 0.001 HIS A1083 PHE 0.016 0.001 PHE N 96 TYR 0.024 0.001 TYR Y 49 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 295 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8087 (pmm) cc_final: 0.7814 (pmm) REVERT: B 346 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7466 (ttp80) REVERT: X 23 GLU cc_start: 0.8776 (tp30) cc_final: 0.8552 (tp30) REVERT: X 64 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8549 (mmmm) REVERT: X 79 TYR cc_start: 0.8721 (m-80) cc_final: 0.8137 (m-10) REVERT: X 100 ASP cc_start: 0.8657 (t0) cc_final: 0.8424 (t0) REVERT: Y 2 ASN cc_start: 0.8277 (t0) cc_final: 0.7856 (t0) REVERT: Y 11 LEU cc_start: 0.8111 (tp) cc_final: 0.7394 (tp) REVERT: Y 34 TYR cc_start: 0.8835 (m-80) cc_final: 0.8401 (m-80) REVERT: Y 81 GLU cc_start: 0.8896 (pm20) cc_final: 0.8541 (pm20) REVERT: Y 89 MET cc_start: 0.8918 (ttp) cc_final: 0.8272 (ttp) REVERT: Y 105 GLU cc_start: 0.7407 (pt0) cc_final: 0.6907 (pm20) REVERT: H 6 GLU cc_start: 0.7524 (mp0) cc_final: 0.6814 (mp0) REVERT: H 23 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 34 MET cc_start: 0.9130 (mmt) cc_final: 0.8786 (mmt) REVERT: L 82 ASP cc_start: 0.8301 (m-30) cc_final: 0.8024 (m-30) REVERT: L 103 LYS cc_start: 0.8279 (tptp) cc_final: 0.8069 (tptp) REVERT: C 113 LYS cc_start: 0.8856 (tppt) cc_final: 0.8575 (tppt) REVERT: C 455 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7327 (mt) REVERT: C 904 TYR cc_start: 0.7403 (m-80) cc_final: 0.7120 (m-80) REVERT: M 16 ARG cc_start: 0.7384 (mtm180) cc_final: 0.7115 (ttp-110) REVERT: M 72 ASP cc_start: 0.8710 (t0) cc_final: 0.8274 (t0) REVERT: M 100 ASP cc_start: 0.8436 (t0) cc_final: 0.8147 (t0) REVERT: N 4 MET cc_start: 0.8290 (tpt) cc_final: 0.7854 (mmm) REVERT: N 55 PHE cc_start: 0.9053 (t80) cc_final: 0.8693 (t80) REVERT: N 61 ARG cc_start: 0.8331 (ptt-90) cc_final: 0.8099 (ptt-90) outliers start: 44 outliers final: 26 residues processed: 315 average time/residue: 0.4388 time to fit residues: 220.7506 Evaluate side-chains 304 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 342 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS M 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30829 Z= 0.214 Angle : 0.523 11.172 41945 Z= 0.265 Chirality : 0.044 0.236 4858 Planarity : 0.004 0.061 5369 Dihedral : 5.244 53.825 5046 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 7.53 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3705 helix: 2.33 (0.21), residues: 609 sheet: 0.22 (0.16), residues: 1014 loop : -0.25 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 35 HIS 0.004 0.001 HIS B 66 PHE 0.010 0.001 PHE N 96 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8060 (pmm) cc_final: 0.7793 (pmm) REVERT: B 394 ASN cc_start: 0.7341 (t0) cc_final: 0.7101 (t0) REVERT: X 64 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8640 (mmmm) REVERT: X 67 PHE cc_start: 0.8598 (m-10) cc_final: 0.8270 (m-80) REVERT: X 79 TYR cc_start: 0.8758 (m-80) cc_final: 0.8143 (m-10) REVERT: X 82 MET cc_start: 0.8626 (mmt) cc_final: 0.8370 (mmt) REVERT: X 100 ASP cc_start: 0.8665 (t0) cc_final: 0.8415 (t0) REVERT: Y 11 LEU cc_start: 0.8135 (tp) cc_final: 0.7407 (tp) REVERT: Y 45 GLN cc_start: 0.8854 (tt0) cc_final: 0.8461 (pt0) REVERT: Y 81 GLU cc_start: 0.8865 (pm20) cc_final: 0.8483 (pm20) REVERT: Y 105 GLU cc_start: 0.7229 (pt0) cc_final: 0.6798 (pm20) REVERT: H 6 GLU cc_start: 0.7535 (mp0) cc_final: 0.7006 (mp0) REVERT: H 23 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7688 (tm-30) REVERT: L 31 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8589 (t) REVERT: C 113 LYS cc_start: 0.8855 (tppt) cc_final: 0.8580 (tppt) REVERT: C 177 MET cc_start: 0.7708 (pmm) cc_final: 0.7495 (pmm) REVERT: C 455 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7236 (mt) REVERT: C 904 TYR cc_start: 0.7242 (m-80) cc_final: 0.7009 (m-10) REVERT: M 72 ASP cc_start: 0.8641 (t0) cc_final: 0.8187 (t0) REVERT: M 79 TYR cc_start: 0.9237 (m-10) cc_final: 0.8947 (m-10) REVERT: M 83 ARG cc_start: 0.8190 (mmt90) cc_final: 0.7963 (mmt90) REVERT: M 100 ASP cc_start: 0.8464 (t0) cc_final: 0.8161 (t0) REVERT: N 4 MET cc_start: 0.8257 (tpt) cc_final: 0.8055 (mmm) REVERT: N 55 PHE cc_start: 0.9045 (t80) cc_final: 0.8691 (t80) REVERT: N 61 ARG cc_start: 0.8345 (ptt-90) cc_final: 0.8124 (ptt-90) outliers start: 50 outliers final: 33 residues processed: 333 average time/residue: 0.4184 time to fit residues: 222.9433 Evaluate side-chains 317 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 309 optimal weight: 0.0770 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30829 Z= 0.291 Angle : 0.549 11.240 41945 Z= 0.277 Chirality : 0.044 0.232 4858 Planarity : 0.004 0.046 5369 Dihedral : 5.257 54.213 5046 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.73 % Allowed : 8.35 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3705 helix: 2.01 (0.21), residues: 645 sheet: 0.17 (0.15), residues: 1032 loop : -0.32 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP Y 35 HIS 0.004 0.001 HIS B 66 PHE 0.011 0.001 PHE B1121 TYR 0.028 0.001 TYR Y 49 ARG 0.005 0.000 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8063 (pmm) cc_final: 0.7780 (pmm) REVERT: B 394 ASN cc_start: 0.7351 (t0) cc_final: 0.7100 (t0) REVERT: X 64 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8693 (mmmm) REVERT: X 67 PHE cc_start: 0.8689 (m-10) cc_final: 0.8273 (m-80) REVERT: X 79 TYR cc_start: 0.8848 (m-80) cc_final: 0.8273 (m-10) REVERT: X 100 ASP cc_start: 0.8690 (t0) cc_final: 0.8434 (t0) REVERT: Y 11 LEU cc_start: 0.8168 (tp) cc_final: 0.7409 (tp) REVERT: Y 45 GLN cc_start: 0.8858 (tt0) cc_final: 0.8528 (pt0) REVERT: Y 81 GLU cc_start: 0.8902 (pm20) cc_final: 0.8499 (pm20) REVERT: Y 105 GLU cc_start: 0.7218 (pt0) cc_final: 0.6812 (pm20) REVERT: H 6 GLU cc_start: 0.7553 (mp0) cc_final: 0.6980 (mp0) REVERT: H 23 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7697 (tm-30) REVERT: H 64 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8275 (mmmm) REVERT: L 31 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8590 (t) REVERT: L 82 ASP cc_start: 0.7656 (m-30) cc_final: 0.7437 (m-30) REVERT: L 89 MET cc_start: 0.8131 (ttt) cc_final: 0.7804 (ttt) REVERT: C 113 LYS cc_start: 0.8884 (tppt) cc_final: 0.8622 (tppt) REVERT: C 177 MET cc_start: 0.7903 (pmm) cc_final: 0.7687 (pmm) REVERT: C 455 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7221 (mt) REVERT: C 904 TYR cc_start: 0.7389 (m-80) cc_final: 0.7187 (m-10) REVERT: M 64 LYS cc_start: 0.9093 (tppt) cc_final: 0.8549 (tppt) REVERT: M 72 ASP cc_start: 0.8643 (t0) cc_final: 0.8165 (t0) REVERT: M 82 LEU cc_start: 0.8653 (mp) cc_final: 0.7009 (mt) REVERT: M 100 ASP cc_start: 0.8495 (t0) cc_final: 0.8176 (t0) REVERT: N 4 MET cc_start: 0.8244 (tpt) cc_final: 0.7699 (mmm) REVERT: N 55 PHE cc_start: 0.9054 (t80) cc_final: 0.8758 (t80) REVERT: N 61 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.8106 (ptt-90) REVERT: N 79 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7868 (mm-30) outliers start: 57 outliers final: 45 residues processed: 323 average time/residue: 0.4311 time to fit residues: 221.3399 Evaluate side-chains 329 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 20.0000 chunk 326 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 362 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN N 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30829 Z= 0.155 Angle : 0.510 11.134 41945 Z= 0.255 Chirality : 0.043 0.218 4858 Planarity : 0.003 0.045 5369 Dihedral : 5.030 53.488 5046 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 9.14 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3705 helix: 2.37 (0.21), residues: 627 sheet: 0.23 (0.15), residues: 1020 loop : -0.27 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 PHE 0.014 0.001 PHE M 67 TYR 0.027 0.001 TYR Y 49 ARG 0.006 0.000 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 302 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8039 (pmm) cc_final: 0.7780 (pmm) REVERT: B 394 ASN cc_start: 0.7294 (t0) cc_final: 0.7028 (t0) REVERT: X 64 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8718 (mmmm) REVERT: X 67 PHE cc_start: 0.8555 (m-10) cc_final: 0.8256 (m-10) REVERT: X 79 TYR cc_start: 0.8875 (m-10) cc_final: 0.8343 (m-10) REVERT: X 83 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7357 (ptp90) REVERT: X 100 ASP cc_start: 0.8708 (t0) cc_final: 0.8458 (t0) REVERT: Y 11 LEU cc_start: 0.8117 (tp) cc_final: 0.7386 (tp) REVERT: Y 45 GLN cc_start: 0.8837 (tt0) cc_final: 0.8568 (pt0) REVERT: Y 81 GLU cc_start: 0.8872 (pm20) cc_final: 0.8449 (pm20) REVERT: Y 105 GLU cc_start: 0.7021 (pt0) cc_final: 0.6659 (pm20) REVERT: A 52 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8412 (tm-30) REVERT: H 6 GLU cc_start: 0.7415 (mp0) cc_final: 0.6856 (mp0) REVERT: H 23 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7657 (tm-30) REVERT: H 64 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8341 (mmmm) REVERT: L 31 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8595 (t) REVERT: L 89 MET cc_start: 0.8055 (ttt) cc_final: 0.7752 (ttt) REVERT: C 113 LYS cc_start: 0.8868 (tppt) cc_final: 0.8603 (tppt) REVERT: C 455 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7179 (mt) REVERT: C 904 TYR cc_start: 0.7273 (m-80) cc_final: 0.6996 (m-10) REVERT: M 59 TYR cc_start: 0.8028 (m-80) cc_final: 0.7530 (m-80) REVERT: M 64 LYS cc_start: 0.9098 (tppt) cc_final: 0.8541 (tppt) REVERT: M 72 ASP cc_start: 0.8606 (t0) cc_final: 0.8101 (t0) REVERT: M 100 ASP cc_start: 0.8485 (t0) cc_final: 0.8154 (t0) REVERT: N 4 MET cc_start: 0.8188 (tpt) cc_final: 0.7729 (mmm) REVERT: N 55 PHE cc_start: 0.9026 (t80) cc_final: 0.8697 (t80) REVERT: N 61 ARG cc_start: 0.8407 (ptt-90) cc_final: 0.8146 (ptt-90) REVERT: N 79 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7884 (mm-30) REVERT: N 98 PHE cc_start: 0.8028 (m-80) cc_final: 0.7805 (m-80) outliers start: 50 outliers final: 38 residues processed: 328 average time/residue: 0.4184 time to fit residues: 219.5519 Evaluate side-chains 328 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 287 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.1980 chunk 40 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Y 2 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 901 GLN C 914 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 0.005 0.059 30829 Z= 0.345 Angle : 0.568 11.447 41945 Z= 0.286 Chirality : 0.045 0.236 4858 Planarity : 0.004 0.045 5369 Dihedral : 5.224 54.330 5046 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 9.59 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3705 helix: 2.07 (0.21), residues: 645 sheet: 0.18 (0.15), residues: 1038 loop : -0.32 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 35 HIS 0.004 0.001 HIS B1058 PHE 0.019 0.001 PHE Y 96 TYR 0.027 0.001 TYR Y 49 ARG 0.007 0.000 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 283 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8056 (pmm) cc_final: 0.7642 (pmm) REVERT: B 394 ASN cc_start: 0.7391 (t0) cc_final: 0.7108 (t0) REVERT: B 902 MET cc_start: 0.8939 (tpt) cc_final: 0.8498 (tpt) REVERT: X 64 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8733 (mmmm) REVERT: X 67 PHE cc_start: 0.8670 (m-10) cc_final: 0.8307 (m-10) REVERT: X 79 TYR cc_start: 0.8839 (m-10) cc_final: 0.8265 (m-10) REVERT: X 85 GLU cc_start: 0.8953 (pm20) cc_final: 0.8741 (pm20) REVERT: X 100 ASP cc_start: 0.8691 (t0) cc_final: 0.8433 (t0) REVERT: Y 11 LEU cc_start: 0.8158 (tp) cc_final: 0.7456 (tp) REVERT: Y 45 GLN cc_start: 0.8867 (tt0) cc_final: 0.8612 (pt0) REVERT: Y 81 GLU cc_start: 0.8883 (pm20) cc_final: 0.8682 (pm20) REVERT: Y 105 GLU cc_start: 0.7037 (pt0) cc_final: 0.6637 (pm20) REVERT: A 52 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 1050 MET cc_start: 0.8774 (ptp) cc_final: 0.8468 (ptm) REVERT: H 6 GLU cc_start: 0.7485 (mp0) cc_final: 0.6892 (mp0) REVERT: H 23 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7707 (tm-30) REVERT: H 64 LYS cc_start: 0.9284 (mmmt) cc_final: 0.8381 (mmmm) REVERT: H 82 MET cc_start: 0.8214 (mtt) cc_final: 0.7777 (mtt) REVERT: L 24 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8835 (tppt) REVERT: L 31 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8615 (t) REVERT: L 79 GLU cc_start: 0.8029 (mp0) cc_final: 0.7806 (mp0) REVERT: C 113 LYS cc_start: 0.8900 (tppt) cc_final: 0.8648 (tppt) REVERT: C 455 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7311 (mt) REVERT: C 904 TYR cc_start: 0.7588 (m-80) cc_final: 0.7283 (m-10) REVERT: M 72 ASP cc_start: 0.8659 (t0) cc_final: 0.8245 (t0) REVERT: M 100 ASP cc_start: 0.8535 (t0) cc_final: 0.8171 (t0) REVERT: N 4 MET cc_start: 0.8200 (tpt) cc_final: 0.7747 (mmm) REVERT: N 37 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (pt) REVERT: N 55 PHE cc_start: 0.9030 (t80) cc_final: 0.8824 (t80) REVERT: N 61 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.8060 (ptt-90) outliers start: 60 outliers final: 45 residues processed: 316 average time/residue: 0.4154 time to fit residues: 211.1989 Evaluate side-chains 325 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN Y 2 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN H 56 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30829 Z= 0.153 Angle : 0.514 11.208 41945 Z= 0.257 Chirality : 0.043 0.220 4858 Planarity : 0.003 0.045 5369 Dihedral : 5.018 53.441 5046 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.67 % Allowed : 9.90 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3705 helix: 2.26 (0.21), residues: 645 sheet: 0.28 (0.16), residues: 1002 loop : -0.28 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 PHE 0.013 0.001 PHE Y 96 TYR 0.026 0.001 TYR Y 49 ARG 0.005 0.000 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8091 (pmm) cc_final: 0.7702 (pmm) REVERT: B 394 ASN cc_start: 0.7262 (t0) cc_final: 0.6997 (t0) REVERT: B 902 MET cc_start: 0.8731 (tpt) cc_final: 0.8137 (tpt) REVERT: X 64 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8719 (mmmm) REVERT: X 67 PHE cc_start: 0.8545 (m-10) cc_final: 0.8236 (m-10) REVERT: X 79 TYR cc_start: 0.8878 (m-10) cc_final: 0.8326 (m-10) REVERT: X 85 GLU cc_start: 0.8939 (pm20) cc_final: 0.8714 (pm20) REVERT: X 100 ASP cc_start: 0.8698 (t0) cc_final: 0.8447 (t0) REVERT: Y 11 LEU cc_start: 0.8158 (tp) cc_final: 0.7497 (tp) REVERT: Y 45 GLN cc_start: 0.8837 (tt0) cc_final: 0.8590 (pt0) REVERT: Y 81 GLU cc_start: 0.8834 (pm20) cc_final: 0.8623 (pm20) REVERT: Y 105 GLU cc_start: 0.7022 (pt0) cc_final: 0.6610 (pm20) REVERT: A 52 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 1108 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8690 (p0) REVERT: H 6 GLU cc_start: 0.7404 (mp0) cc_final: 0.6769 (mp0) REVERT: H 23 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7680 (tm-30) REVERT: H 64 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8428 (mmmm) REVERT: H 72 ASP cc_start: 0.8275 (t0) cc_final: 0.7977 (t0) REVERT: H 75 LYS cc_start: 0.9174 (mtmt) cc_final: 0.8773 (mtmt) REVERT: H 82 MET cc_start: 0.8104 (mtt) cc_final: 0.7724 (mtt) REVERT: L 24 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8884 (tppt) REVERT: L 31 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8552 (t) REVERT: L 79 GLU cc_start: 0.8036 (mp0) cc_final: 0.7798 (mp0) REVERT: C 113 LYS cc_start: 0.8862 (tppt) cc_final: 0.8609 (tppt) REVERT: C 455 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7186 (mt) REVERT: C 904 TYR cc_start: 0.7266 (m-80) cc_final: 0.7043 (m-10) REVERT: M 59 TYR cc_start: 0.8029 (m-80) cc_final: 0.7591 (m-80) REVERT: M 64 LYS cc_start: 0.9086 (tppt) cc_final: 0.8571 (tppt) REVERT: M 72 ASP cc_start: 0.8578 (t0) cc_final: 0.8154 (t0) REVERT: M 100 ASP cc_start: 0.8556 (t0) cc_final: 0.8229 (t0) REVERT: N 4 MET cc_start: 0.8058 (tpt) cc_final: 0.7634 (mmm) REVERT: N 37 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8709 (pt) REVERT: N 55 PHE cc_start: 0.9035 (t80) cc_final: 0.8724 (t80) REVERT: N 61 ARG cc_start: 0.8460 (ptt-90) cc_final: 0.8218 (ptt180) REVERT: N 93 GLN cc_start: 0.7988 (tp40) cc_final: 0.7502 (tp-100) outliers start: 55 outliers final: 47 residues processed: 323 average time/residue: 0.4504 time to fit residues: 235.7427 Evaluate side-chains 333 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 282 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 chunk 315 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 335 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 2 ASN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** L 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30829 Z= 0.285 Angle : 0.547 11.351 41945 Z= 0.274 Chirality : 0.044 0.230 4858 Planarity : 0.003 0.044 5369 Dihedral : 5.094 54.063 5046 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.85 % Allowed : 9.84 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3705 helix: 2.15 (0.21), residues: 645 sheet: 0.20 (0.15), residues: 1020 loop : -0.29 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 35 HIS 0.003 0.001 HIS B 66 PHE 0.025 0.001 PHE M 67 TYR 0.026 0.001 TYR N 49 ARG 0.005 0.000 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 286 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8051 (pmm) cc_final: 0.7634 (pmm) REVERT: B 394 ASN cc_start: 0.7268 (t0) cc_final: 0.6998 (t0) REVERT: X 64 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8734 (mmmm) REVERT: X 67 PHE cc_start: 0.8544 (m-10) cc_final: 0.8155 (m-10) REVERT: X 79 TYR cc_start: 0.8905 (m-10) cc_final: 0.8290 (m-10) REVERT: X 100 ASP cc_start: 0.8705 (t0) cc_final: 0.8453 (t0) REVERT: Y 2 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8088 (t0) REVERT: Y 11 LEU cc_start: 0.8207 (tp) cc_final: 0.7540 (tp) REVERT: Y 81 GLU cc_start: 0.8854 (pm20) cc_final: 0.8643 (pm20) REVERT: Y 105 GLU cc_start: 0.7046 (pt0) cc_final: 0.6617 (pm20) REVERT: A 52 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8432 (tm-30) REVERT: H 6 GLU cc_start: 0.7497 (mp0) cc_final: 0.6908 (mp0) REVERT: H 23 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 64 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8500 (mmmm) REVERT: H 72 ASP cc_start: 0.8289 (t0) cc_final: 0.7946 (t0) REVERT: H 75 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8800 (mtmt) REVERT: H 82 MET cc_start: 0.8207 (mtt) cc_final: 0.7797 (mtt) REVERT: L 31 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8491 (t) REVERT: L 61 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7474 (ptp90) REVERT: L 79 GLU cc_start: 0.7925 (mp0) cc_final: 0.7436 (mp0) REVERT: C 113 LYS cc_start: 0.8889 (tppt) cc_final: 0.8641 (tppt) REVERT: C 455 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7288 (mt) REVERT: C 904 TYR cc_start: 0.7536 (m-80) cc_final: 0.7235 (m-10) REVERT: M 64 LYS cc_start: 0.9110 (tppt) cc_final: 0.8593 (tppt) REVERT: M 72 ASP cc_start: 0.8613 (t0) cc_final: 0.8170 (t0) REVERT: M 100 ASP cc_start: 0.8577 (t0) cc_final: 0.8210 (t0) REVERT: N 37 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (pt) REVERT: N 42 GLN cc_start: 0.8464 (pt0) cc_final: 0.7681 (pm20) REVERT: N 55 PHE cc_start: 0.9040 (t80) cc_final: 0.8826 (t80) REVERT: N 61 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.8219 (ptt-90) REVERT: N 92 ILE cc_start: 0.9225 (tt) cc_final: 0.9018 (pt) REVERT: N 93 GLN cc_start: 0.8055 (tp40) cc_final: 0.7558 (tp-100) outliers start: 61 outliers final: 51 residues processed: 319 average time/residue: 0.4336 time to fit residues: 222.0021 Evaluate side-chains 339 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 100 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.8980 chunk 356 optimal weight: 0.0470 chunk 217 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 373 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 76 ASN Y 2 ASN Y 45 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN H 105 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30829 Z= 0.152 Angle : 0.522 11.242 41945 Z= 0.259 Chirality : 0.043 0.217 4858 Planarity : 0.003 0.045 5369 Dihedral : 4.936 53.315 5046 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.70 % Allowed : 10.08 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3705 helix: 2.30 (0.21), residues: 645 sheet: 0.32 (0.16), residues: 984 loop : -0.25 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 35 HIS 0.004 0.000 HIS B 66 PHE 0.012 0.001 PHE Y 96 TYR 0.024 0.001 TYR N 49 ARG 0.004 0.000 ARG M 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7410 Ramachandran restraints generated. 3705 Oldfield, 0 Emsley, 3705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 296 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.8039 (pmm) cc_final: 0.7608 (pmm) REVERT: B 394 ASN cc_start: 0.7249 (t0) cc_final: 0.6975 (t0) REVERT: X 64 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8712 (mmmm) REVERT: X 67 PHE cc_start: 0.8470 (m-10) cc_final: 0.8149 (m-10) REVERT: X 79 TYR cc_start: 0.8919 (m-10) cc_final: 0.8337 (m-10) REVERT: X 100 ASP cc_start: 0.8730 (t0) cc_final: 0.8494 (t0) REVERT: Y 11 LEU cc_start: 0.8179 (tp) cc_final: 0.7539 (tp) REVERT: Y 81 GLU cc_start: 0.8814 (pm20) cc_final: 0.8597 (pm20) REVERT: Y 105 GLU cc_start: 0.7023 (pt0) cc_final: 0.6581 (pm20) REVERT: A 52 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8378 (tm-30) REVERT: H 4 LEU cc_start: 0.9120 (mm) cc_final: 0.8754 (mm) REVERT: H 23 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 64 LYS cc_start: 0.9308 (mmmt) cc_final: 0.8432 (mmmm) REVERT: H 72 ASP cc_start: 0.8335 (t0) cc_final: 0.7981 (t0) REVERT: H 75 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8788 (mtmt) REVERT: H 82 MET cc_start: 0.8134 (mtt) cc_final: 0.7736 (mtt) REVERT: L 31 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8534 (t) REVERT: L 61 ARG cc_start: 0.7841 (ptp90) cc_final: 0.7476 (ptp90) REVERT: L 79 GLU cc_start: 0.7955 (mp0) cc_final: 0.7480 (mp0) REVERT: C 113 LYS cc_start: 0.8851 (tppt) cc_final: 0.8606 (tppt) REVERT: C 455 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7309 (mt) REVERT: C 904 TYR cc_start: 0.7234 (m-80) cc_final: 0.7033 (m-10) REVERT: M 59 TYR cc_start: 0.8013 (m-80) cc_final: 0.7578 (m-80) REVERT: M 64 LYS cc_start: 0.9098 (tppt) cc_final: 0.8564 (tppt) REVERT: M 72 ASP cc_start: 0.8545 (t0) cc_final: 0.8114 (t0) REVERT: M 100 ASP cc_start: 0.8526 (t0) cc_final: 0.8165 (t0) REVERT: N 4 MET cc_start: 0.7942 (mmm) cc_final: 0.7574 (tmm) REVERT: N 37 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8659 (pt) REVERT: N 55 PHE cc_start: 0.9052 (t80) cc_final: 0.8808 (t80) REVERT: N 61 ARG cc_start: 0.8505 (ptt-90) cc_final: 0.8248 (ptt-90) outliers start: 56 outliers final: 48 residues processed: 330 average time/residue: 0.4142 time to fit residues: 220.2308 Evaluate side-chains 334 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain X residue 33 ASP Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain Y residue 2 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 53 ASN Chi-restraints excluded: chain N residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 76 ASN Y 2 ASN Y 45 GLN ** Y 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN C 901 GLN N 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054218 restraints weight = 78160.007| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.98 r_work: 0.2754 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30829 Z= 0.386 Angle : 0.588 11.477 41945 Z= 0.296 Chirality : 0.045 0.237 4858 Planarity : 0.004 0.045 5369 Dihedral : 5.213 54.292 5046 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.79 % Allowed : 10.41 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3705 helix: 2.06 (0.21), residues: 645 sheet: 0.10 (0.15), residues: 1011 loop : -0.30 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP Y 35 HIS 0.004 0.001 HIS B1058 PHE 0.027 0.001 PHE M 67 TYR 0.028 0.001 TYR N 49 ARG 0.005 0.000 ARG M 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7321.82 seconds wall clock time: 133 minutes 44.63 seconds (8024.63 seconds total)