Starting phenix.real_space_refine on Wed Feb 21 01:49:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_25008/02_2024/7sc1_25008.pdb" } resolution = 3.2 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= 0.025 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 126 5.16 5 C 18711 2.51 5 N 4851 2.21 5 O 5727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 29415 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "P" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" 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 Chain: "B" 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 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: 14.95, per 1000 atoms: 0.51 Number of scatterers: 29415 At special positions: 0 Unit cell: (142.272, 143.936, 212.992, 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 126 16.00 O 5727 8.00 N 4851 7.00 C 18711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.03 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 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 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=2.03 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 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=2.02 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=2.03 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 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 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 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A1074 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " Time building additional restraints: 10.63 Conformation dependent library (CDL) restraints added in 5.0 seconds 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 64 sheets defined 21.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.395A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.948A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.642A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 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 912 through 919 removed outlier: 4.359A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.800A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.755A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.387A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.960A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.596A 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 removed outlier: 3.643A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.329A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.747A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.736A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.381A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.921A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.137A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.871A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.737A pdb=" N THR P 87 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.206A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.611A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.860A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.849A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.565A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.592A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.852A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.833A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.346A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.588A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.463A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 7 removed outlier: 4.054A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.866A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.668A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.164A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.172A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.682A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.578A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.590A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.590A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 58 through 59 removed outlier: 5.466A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 6 through 7 removed outlier: 4.061A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.860A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.149A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.625A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.869A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.522A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.585A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.870A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.066A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.651A 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 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.799A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AG4, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.331A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.586A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 58 through 59 removed outlier: 5.467A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 107 " --> pdb=" O TYR P 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 6 through 7 removed outlier: 4.045A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.874A pdb=" N GLU Q 105 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.42 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9361 1.34 - 1.46: 6074 1.46 - 1.58: 14469 1.58 - 1.70: 0 1.70 - 1.81: 159 Bond restraints: 30063 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C LEU C 223 " pdb=" N GLU C 224 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.07e-02 2.33e+03 5.91e+00 bond pdb=" CB ASN B 777 " pdb=" CG ASN B 777 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.58e+00 ... (remaining 30058 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.64: 611 105.64 - 112.75: 16248 112.75 - 119.87: 9328 119.87 - 126.98: 14421 126.98 - 134.09: 282 Bond angle restraints: 40890 Sorted by residual: angle pdb=" N GLY C 857 " pdb=" CA GLY C 857 " pdb=" C GLY C 857 " ideal model delta sigma weight residual 114.48 109.15 5.33 1.19e+00 7.06e-01 2.00e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.17 -3.47 1.22e+00 6.72e-01 8.11e+00 angle pdb=" CB MET P 34 " pdb=" CG MET P 34 " pdb=" SD MET P 34 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.64e+00 ... (remaining 40885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 17289 24.65 - 49.30: 870 49.30 - 73.94: 147 73.94 - 98.59: 44 98.59 - 123.24: 109 Dihedral angle restraints: 18459 sinusoidal: 7731 harmonic: 10728 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+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 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -157.70 71.70 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 18456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4386 0.090 - 0.180: 371 0.180 - 0.270: 13 0.270 - 0.360: 0 0.360 - 0.450: 3 Chirality restraints: 4773 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 4770 not shown) Planarity restraints: 5271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 527 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 85 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR C 881 " 0.032 2.00e-02 2.50e+03 pdb=" O THR C 881 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 882 " -0.011 2.00e-02 2.50e+03 ... (remaining 5268 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1260 2.72 - 3.26: 29537 3.26 - 3.81: 47622 3.81 - 4.35: 57909 4.35 - 4.90: 100555 Nonbonded interactions: 236883 Sorted by model distance: nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 2.440 nonbonded pdb=" OG SER N 9 " pdb=" O GLY N 101 " model vdw 2.184 2.440 nonbonded pdb=" OG SER Q 9 " pdb=" O GLY Q 101 " model vdw 2.185 2.440 nonbonded pdb=" OG SER L 9 " pdb=" O GLY L 101 " model vdw 2.188 2.440 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.193 2.440 ... (remaining 236878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.710 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 79.850 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.240 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.006 0.077 30063 Z= 0.391 Angle : 0.634 8.764 40890 Z= 0.328 Chirality : 0.048 0.450 4773 Planarity : 0.004 0.054 5226 Dihedral : 18.119 123.238 11454 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.55 (0.13), residues: 3645 helix: 1.29 (0.19), residues: 693 sheet: -0.52 (0.17), residues: 960 loop : -0.85 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.032 0.002 PHE A 906 TYR 0.023 0.001 TYR C 873 ARG 0.005 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6173 (tp40) REVERT: A 987 PRO cc_start: 0.7980 (Cg_exo) cc_final: 0.7748 (Cg_endo) REVERT: B 917 TYR cc_start: 0.8118 (m-10) cc_final: 0.7827 (m-10) REVERT: C 104 TRP cc_start: 0.7660 (m-90) cc_final: 0.7327 (m-90) REVERT: C 239 GLN cc_start: 0.6732 (tp-100) cc_final: 0.6054 (tp40) REVERT: P 34 MET cc_start: 0.1282 (mmm) cc_final: 0.1073 (mmm) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.3555 time to fit residues: 117.8698 Evaluate side-chains 151 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 675 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 1.9990 chunk 277 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 94 optimal weight: 0.2980 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 111 optimal weight: 50.0000 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 332 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN B 52 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 804 GLN B 935 GLN B1002 GLN N 37 GLN C 52 GLN C 239 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1088 HIS Q 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30063 Z= 0.211 Angle : 0.579 9.898 40890 Z= 0.288 Chirality : 0.048 0.432 4773 Planarity : 0.004 0.047 5226 Dihedral : 15.354 110.412 4920 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.37 % Allowed : 5.42 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3645 helix: 1.66 (0.19), residues: 690 sheet: -0.45 (0.16), residues: 990 loop : -0.90 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 PHE 0.017 0.001 PHE A 192 TYR 0.025 0.001 TYR A1067 ARG 0.002 0.000 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8039 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: A 1050 MET cc_start: 0.7637 (mtp) cc_final: 0.7400 (mtp) REVERT: B 663 ASP cc_start: 0.8126 (m-30) cc_final: 0.7924 (m-30) REVERT: C 675 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7055 (pp30) REVERT: C 987 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7760 (Cg_endo) REVERT: C 1050 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7667 (mtp) outliers start: 12 outliers final: 10 residues processed: 177 average time/residue: 0.3526 time to fit residues: 108.3062 Evaluate side-chains 155 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 226 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 359 optimal weight: 50.0000 chunk 296 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30063 Z= 0.337 Angle : 0.596 8.502 40890 Z= 0.296 Chirality : 0.048 0.413 4773 Planarity : 0.004 0.049 5226 Dihedral : 12.082 111.309 4920 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.93 % Allowed : 8.31 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 3645 helix: 1.64 (0.19), residues: 684 sheet: -0.59 (0.15), residues: 1056 loop : -0.93 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 PHE 0.022 0.002 PHE A1121 TYR 0.024 0.001 TYR A1067 ARG 0.004 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8089 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: B 663 ASP cc_start: 0.8318 (m-30) cc_final: 0.8113 (m-30) REVERT: M 100 MET cc_start: 0.1247 (OUTLIER) cc_final: -0.0786 (tpt) REVERT: C 987 PRO cc_start: 0.8128 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: P 100 MET cc_start: 0.1104 (ptm) cc_final: -0.0633 (tpp) outliers start: 30 outliers final: 19 residues processed: 173 average time/residue: 0.3507 time to fit residues: 104.3332 Evaluate side-chains 160 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 158 optimal weight: 40.0000 chunk 223 optimal weight: 40.0000 chunk 334 optimal weight: 0.5980 chunk 353 optimal weight: 50.0000 chunk 174 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30063 Z= 0.388 Angle : 0.604 9.130 40890 Z= 0.302 Chirality : 0.048 0.406 4773 Planarity : 0.004 0.049 5226 Dihedral : 9.965 108.075 4917 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.56 % Allowed : 9.87 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.62 (0.13), residues: 3645 helix: 1.50 (0.19), residues: 684 sheet: -0.62 (0.15), residues: 1056 loop : -0.97 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.003 0.001 HIS C1064 PHE 0.023 0.002 PHE A1121 TYR 0.024 0.001 TYR A1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 158 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.7863 (mtp) cc_final: 0.7579 (mtp) REVERT: B 470 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.5377 (p) REVERT: B 663 ASP cc_start: 0.8416 (m-30) cc_final: 0.8209 (m-30) REVERT: C 470 THR cc_start: 0.5656 (OUTLIER) cc_final: 0.5406 (p) REVERT: C 675 GLN cc_start: 0.7494 (pp30) cc_final: 0.7054 (pp30) outliers start: 50 outliers final: 30 residues processed: 197 average time/residue: 0.3618 time to fit residues: 123.0893 Evaluate side-chains 180 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS M 39 GLN C 580 GLN P 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30063 Z= 0.209 Angle : 0.536 8.750 40890 Z= 0.265 Chirality : 0.046 0.653 4773 Planarity : 0.004 0.045 5226 Dihedral : 9.233 106.482 4917 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.24 % Allowed : 11.14 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.41 (0.13), residues: 3645 helix: 2.04 (0.20), residues: 648 sheet: -0.54 (0.16), residues: 1026 loop : -0.90 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS A1048 PHE 0.015 0.001 PHE C 106 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 3.136 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 563 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 663 ASP cc_start: 0.8322 (m-30) cc_final: 0.8109 (m-30) REVERT: M 34 MET cc_start: 0.1348 (mmm) cc_final: 0.1089 (mmm) REVERT: M 100 MET cc_start: 0.1077 (OUTLIER) cc_final: 0.0473 (ptm) REVERT: C 663 ASP cc_start: 0.8056 (m-30) cc_final: 0.7727 (m-30) REVERT: P 100 MET cc_start: 0.1130 (ptm) cc_final: -0.0574 (tpp) outliers start: 40 outliers final: 23 residues processed: 190 average time/residue: 0.3566 time to fit residues: 117.9385 Evaluate side-chains 163 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 40.0000 chunk 318 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 chunk 207 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 354 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 117 optimal weight: 0.0060 chunk 185 optimal weight: 0.0370 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 239 GLN C 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30063 Z= 0.139 Angle : 0.504 8.674 40890 Z= 0.250 Chirality : 0.045 0.398 4773 Planarity : 0.004 0.046 5226 Dihedral : 8.679 104.658 4917 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 11.95 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3645 helix: 2.28 (0.20), residues: 648 sheet: -0.43 (0.16), residues: 1041 loop : -0.82 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.001 PHE B 759 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 3.152 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: H 100 MET cc_start: 0.1339 (OUTLIER) cc_final: 0.0925 (mtp) REVERT: B 470 THR cc_start: 0.5607 (OUTLIER) cc_final: 0.5350 (p) REVERT: B 563 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: B 663 ASP cc_start: 0.8250 (m-30) cc_final: 0.8033 (m-30) REVERT: B 987 PRO cc_start: 0.8351 (Cg_exo) cc_final: 0.8099 (Cg_endo) REVERT: C 470 THR cc_start: 0.5713 (OUTLIER) cc_final: 0.5482 (p) REVERT: C 643 PHE cc_start: 0.8204 (t80) cc_final: 0.7491 (t80) REVERT: C 663 ASP cc_start: 0.8011 (m-30) cc_final: 0.7687 (m-30) REVERT: P 100 MET cc_start: 0.1090 (ptm) cc_final: -0.0626 (tpp) outliers start: 42 outliers final: 24 residues processed: 194 average time/residue: 0.3554 time to fit residues: 120.6957 Evaluate side-chains 170 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 298 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 352 optimal weight: 30.0000 chunk 220 optimal weight: 3.9990 chunk 215 optimal weight: 0.0270 chunk 162 optimal weight: 40.0000 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.003 0.052 30063 Z= 0.223 Angle : 0.523 8.532 40890 Z= 0.258 Chirality : 0.045 0.384 4773 Planarity : 0.004 0.046 5226 Dihedral : 8.498 102.927 4917 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 12.39 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.26 (0.14), residues: 3645 helix: 2.08 (0.20), residues: 666 sheet: -0.40 (0.16), residues: 1041 loop : -0.83 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS A1048 PHE 0.019 0.001 PHE C 592 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8138 (Cg_exo) cc_final: 0.7847 (Cg_endo) REVERT: H 100 MET cc_start: 0.1352 (OUTLIER) cc_final: 0.1019 (mtp) REVERT: B 470 THR cc_start: 0.5602 (OUTLIER) cc_final: 0.5342 (p) REVERT: B 563 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: B 663 ASP cc_start: 0.8349 (m-30) cc_final: 0.8141 (m-30) REVERT: B 873 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: B 987 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8111 (Cg_endo) REVERT: C 470 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5488 (p) REVERT: C 643 PHE cc_start: 0.8286 (t80) cc_final: 0.7613 (t80) REVERT: P 100 MET cc_start: 0.1102 (ptm) cc_final: -0.0664 (tpp) outliers start: 41 outliers final: 29 residues processed: 189 average time/residue: 0.3495 time to fit residues: 114.8269 Evaluate side-chains 181 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 69 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 240 optimal weight: 50.0000 chunk 174 optimal weight: 4.9990 chunk 32 optimal weight: 0.0050 chunk 277 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30063 Z= 0.145 Angle : 0.501 8.501 40890 Z= 0.248 Chirality : 0.044 0.383 4773 Planarity : 0.004 0.045 5226 Dihedral : 8.196 100.998 4917 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.24 % Allowed : 12.79 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.12 (0.14), residues: 3645 helix: 2.41 (0.20), residues: 648 sheet: -0.31 (0.16), residues: 1026 loop : -0.79 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.004 0.000 HIS A1048 PHE 0.013 0.001 PHE B 106 TYR 0.018 0.001 TYR B1067 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 LYS cc_start: 0.8190 (mttt) cc_final: 0.7666 (tttm) REVERT: A 987 PRO cc_start: 0.8167 (Cg_exo) cc_final: 0.7871 (Cg_endo) REVERT: H 100 MET cc_start: 0.1317 (OUTLIER) cc_final: 0.1014 (mtp) REVERT: B 470 THR cc_start: 0.5666 (OUTLIER) cc_final: 0.5400 (p) REVERT: B 563 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: B 663 ASP cc_start: 0.8227 (m-30) cc_final: 0.8000 (m-30) REVERT: B 987 PRO cc_start: 0.8362 (Cg_exo) cc_final: 0.8122 (Cg_endo) REVERT: M 100 MET cc_start: 0.0840 (ptm) cc_final: -0.0693 (tpp) REVERT: C 470 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5466 (p) REVERT: C 643 PHE cc_start: 0.8161 (t80) cc_final: 0.7517 (t80) REVERT: P 100 MET cc_start: 0.1113 (ptm) cc_final: -0.0612 (tpt) outliers start: 40 outliers final: 28 residues processed: 195 average time/residue: 0.3440 time to fit residues: 117.4523 Evaluate side-chains 176 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.6980 chunk 337 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 327 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30063 Z= 0.178 Angle : 0.512 8.655 40890 Z= 0.253 Chirality : 0.045 0.376 4773 Planarity : 0.004 0.046 5226 Dihedral : 7.998 99.342 4917 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.06 % Allowed : 13.07 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.12 (0.14), residues: 3645 helix: 2.14 (0.19), residues: 684 sheet: -0.25 (0.16), residues: 1026 loop : -0.78 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.003 0.000 HIS A1048 PHE 0.021 0.001 PHE C 592 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 811 LYS cc_start: 0.8237 (mttt) cc_final: 0.7712 (tttm) REVERT: A 987 PRO cc_start: 0.8145 (Cg_exo) cc_final: 0.7854 (Cg_endo) REVERT: H 100 MET cc_start: 0.1269 (OUTLIER) cc_final: 0.0996 (mtp) REVERT: B 470 THR cc_start: 0.5660 (OUTLIER) cc_final: 0.5390 (p) REVERT: B 563 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: B 663 ASP cc_start: 0.8276 (m-30) cc_final: 0.8033 (m-30) REVERT: B 987 PRO cc_start: 0.8369 (Cg_exo) cc_final: 0.8117 (Cg_endo) REVERT: M 100 MET cc_start: 0.0656 (ptm) cc_final: -0.0826 (tpp) REVERT: C 470 THR cc_start: 0.5781 (OUTLIER) cc_final: 0.5554 (p) REVERT: C 563 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: C 643 PHE cc_start: 0.8195 (t80) cc_final: 0.7580 (t80) REVERT: P 100 MET cc_start: 0.0862 (ptm) cc_final: -0.0796 (tpt) outliers start: 34 outliers final: 27 residues processed: 183 average time/residue: 0.3597 time to fit residues: 114.4215 Evaluate side-chains 177 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 335 optimal weight: 1.9990 chunk 290 optimal weight: 0.3980 chunk 30 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 178 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30063 Z= 0.244 Angle : 0.533 8.801 40890 Z= 0.265 Chirality : 0.045 0.369 4773 Planarity : 0.004 0.047 5226 Dihedral : 7.851 97.034 4917 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.06 % Allowed : 13.23 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 3645 helix: 2.13 (0.20), residues: 663 sheet: -0.27 (0.16), residues: 1026 loop : -0.80 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.002 0.000 HIS A1048 PHE 0.018 0.001 PHE A1121 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG C1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 987 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7897 (Cg_endo) REVERT: H 100 MET cc_start: 0.1256 (OUTLIER) cc_final: 0.1007 (mtp) REVERT: B 470 THR cc_start: 0.5654 (OUTLIER) cc_final: 0.5383 (p) REVERT: B 563 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: B 987 PRO cc_start: 0.8381 (Cg_exo) cc_final: 0.8139 (Cg_endo) REVERT: C 470 THR cc_start: 0.5776 (OUTLIER) cc_final: 0.5522 (p) REVERT: C 643 PHE cc_start: 0.8272 (t80) cc_final: 0.7695 (t80) REVERT: P 100 MET cc_start: 0.0915 (ptm) cc_final: -0.0753 (tpt) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.3606 time to fit residues: 109.9130 Evaluate side-chains 172 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 121 optimal weight: 40.0000 chunk 298 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.222157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128440 restraints weight = 39723.867| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.09 r_work: 0.3299 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30063 Z= 0.240 Angle : 0.534 9.062 40890 Z= 0.265 Chirality : 0.045 0.364 4773 Planarity : 0.004 0.049 5226 Dihedral : 7.691 94.042 4917 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.09 % Allowed : 13.35 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 3645 helix: 2.24 (0.20), residues: 648 sheet: -0.28 (0.16), residues: 1026 loop : -0.81 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.003 0.000 HIS A1048 PHE 0.023 0.001 PHE C 592 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG C1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.79 seconds wall clock time: 102 minutes 14.26 seconds (6134.26 seconds total)