Starting phenix.real_space_refine on Mon Feb 19 18:25:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhn_32000/02_2024/7vhn_32000.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 16196 2.51 5 N 4195 2.21 5 O 4895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25403 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.34, per 1000 atoms: 0.53 Number of scatterers: 25403 At special positions: 0 Unit cell: (154.08, 151.94, 201.16, 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 117 16.00 O 4895 8.00 N 4195 7.00 C 16196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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 C 15 " - pdb=" SG CYS C 136 " 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 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 A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 603 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A1074 " " NAG A1211 " - " ASN A 165 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 331 " " NAG B1205 " - " ASN B 343 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 709 " " NAG B1208 " - " ASN B1074 " " NAG B1209 " - " ASN B 165 " " NAG B1210 " - " ASN B 616 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 331 " " NAG C1203 " - " ASN C 343 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 657 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG C1208 " - " ASN C 61 " " NAG C1209 " - " ASN C 122 " " NAG C1210 " - " ASN C 165 " Time building additional restraints: 10.07 Conformation dependent library (CDL) restraints added in 4.9 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 47 sheets defined 23.8% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.655A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.624A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.636A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.798A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.903A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.900A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.652A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) 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 979 through 983 removed outlier: 3.507A pdb=" N ARG A 983 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1019 removed outlier: 3.930A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.519A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1148 removed outlier: 4.268A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (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 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.932A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.200A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.954A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.022A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.056A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.176A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 857' Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.027A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 898 through 907 removed outlier: 3.541A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.829A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) 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 989 through 1015 removed outlier: 3.543A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1026 removed outlier: 3.846A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.761A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.177A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.324A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.637A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.581A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.174A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.656A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.763A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.030A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.774A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.587A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 4.004A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1018 removed outlier: 3.516A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.532A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.708A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.501A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.703A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.891A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.338A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.687A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.058A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.655A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.036A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.951A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.131A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.664A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 4.147A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.767A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 removed outlier: 4.081A pdb=" N SER B 735 " --> pdb=" O ASN B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.364A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.612A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.745A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.790A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 11.636A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.302A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.600A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.080A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.803A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.130A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2283 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: 10.87 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5556 1.33 - 1.45: 6794 1.45 - 1.58: 13476 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 25973 Sorted by residual: bond pdb=" N ILE A 714 " pdb=" CA ILE A 714 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.70e-03 1.69e+04 1.55e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.43e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.41e+01 bond pdb=" N ASP B 578 " pdb=" CA ASP B 578 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N VAL B 126 " pdb=" CA VAL B 126 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.01e+01 ... (remaining 25968 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.46: 707 106.46 - 113.36: 14137 113.36 - 120.26: 9403 120.26 - 127.16: 10871 127.16 - 134.06: 205 Bond angle restraints: 35323 Sorted by residual: angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.57e+01 angle pdb=" CA PHE B 133 " pdb=" CB PHE B 133 " pdb=" CG PHE B 133 " ideal model delta sigma weight residual 113.80 118.38 -4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.73 119.29 -8.56 1.90e+00 2.77e-01 2.03e+01 angle pdb=" C PHE A 559 " pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " ideal model delta sigma weight residual 113.15 102.57 10.58 2.38e+00 1.77e-01 1.98e+01 angle pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" O THR B 124 " ideal model delta sigma weight residual 120.82 116.24 4.58 1.05e+00 9.07e-01 1.91e+01 ... (remaining 35318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14383 17.83 - 35.66: 1243 35.66 - 53.49: 212 53.49 - 71.32: 32 71.32 - 89.15: 18 Dihedral angle restraints: 15888 sinusoidal: 6603 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.13 -77.87 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 169.15 -76.15 1 1.00e+01 1.00e-02 7.30e+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 -23.81 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 15885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3780 0.104 - 0.208: 266 0.208 - 0.313: 33 0.313 - 0.417: 4 0.417 - 0.521: 5 Chirality restraints: 4088 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG B1203 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1203 " pdb=" O5 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1205 " 0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG B1205 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1205 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG B1205 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG B1205 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1208 " -0.326 2.00e-02 2.50e+03 2.82e-01 9.95e+02 pdb=" C7 NAG C1208 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1208 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG C1208 " 0.495 2.00e-02 2.50e+03 pdb=" O7 NAG C1208 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1208 " -0.316 2.00e-02 2.50e+03 2.76e-01 9.53e+02 pdb=" C7 NAG B1208 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B1208 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG B1208 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B1208 " -0.162 2.00e-02 2.50e+03 ... (remaining 4565 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 4 2.16 - 2.84: 9031 2.84 - 3.53: 33847 3.53 - 4.21: 55697 4.21 - 4.90: 95836 Nonbonded interactions: 194415 Sorted by model distance: nonbonded pdb=" ND2 ASN A 164 " pdb=" C1 NAG A1211 " model vdw 1.473 3.550 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.029 2.440 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 77 " model vdw 2.147 2.440 nonbonded pdb=" O ASP C 442 " pdb=" ND2 ASN C 448 " model vdw 2.172 2.520 ... (remaining 194410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1148 or resid 1201 through 1210)) selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.130 Check model and map are aligned: 0.370 Set scattering table: 0.250 Process input model: 68.890 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 0.066 25973 Z= 0.401 Angle : 0.846 11.419 35323 Z= 0.520 Chirality : 0.062 0.521 4088 Planarity : 0.015 0.300 4537 Dihedral : 13.367 89.150 9786 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.22 % Rotamer: Outliers : 0.72 % Allowed : 1.47 % Favored : 97.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.94 (0.13), residues: 3150 helix: -1.45 (0.19), residues: 639 sheet: -1.15 (0.19), residues: 646 loop : -2.54 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 PHE 0.029 0.002 PHE B 201 TYR 0.023 0.002 TYR A 453 ARG 0.006 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8205 (m-80) cc_final: 0.7616 (m-80) REVERT: A 374 PHE cc_start: 0.5230 (m-80) cc_final: 0.4898 (m-80) REVERT: A 855 PHE cc_start: 0.8341 (m-10) cc_final: 0.8104 (m-80) REVERT: B 118 LEU cc_start: 0.8960 (tt) cc_final: 0.8320 (mp) REVERT: B 129 LYS cc_start: 0.7421 (mttt) cc_final: 0.7039 (mttt) REVERT: B 177 MET cc_start: -0.0844 (tpp) cc_final: -0.1841 (ttp) REVERT: B 708 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 900 MET cc_start: 0.8416 (mtt) cc_final: 0.8215 (mtt) REVERT: B 1029 MET cc_start: 0.9359 (tpp) cc_final: 0.9047 (tpp) REVERT: C 904 TYR cc_start: 0.7625 (m-10) cc_final: 0.7285 (m-10) REVERT: C 1050 MET cc_start: 0.8370 (ptm) cc_final: 0.8137 (ptm) outliers start: 20 outliers final: 7 residues processed: 207 average time/residue: 0.3839 time to fit residues: 127.1998 Evaluate side-chains 132 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 0.0970 chunk 185 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 655 HIS B 774 GLN B 859 ASN B 901 GLN C 81 ASN C 872 GLN C 949 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25973 Z= 0.167 Angle : 0.622 10.791 35323 Z= 0.317 Chirality : 0.045 0.335 4088 Planarity : 0.004 0.050 4537 Dihedral : 5.850 57.761 4078 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.90 % Allowed : 7.18 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3150 helix: -0.32 (0.20), residues: 644 sheet: -0.85 (0.19), residues: 647 loop : -2.34 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 436 HIS 0.006 0.001 HIS C1118 PHE 0.032 0.001 PHE B 338 TYR 0.018 0.001 TYR C 204 ARG 0.005 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7509 (m-80) cc_final: 0.6336 (m-10) REVERT: A 135 PHE cc_start: 0.8075 (m-80) cc_final: 0.7300 (m-80) REVERT: A 529 LYS cc_start: 0.7923 (tppt) cc_final: 0.7590 (tppt) REVERT: A 570 ASP cc_start: 0.8087 (p0) cc_final: 0.7672 (p0) REVERT: B 118 LEU cc_start: 0.8826 (tt) cc_final: 0.8198 (mp) REVERT: B 129 LYS cc_start: 0.7152 (mttt) cc_final: 0.6824 (mttt) REVERT: B 153 MET cc_start: 0.1874 (tmm) cc_final: 0.1620 (tmm) REVERT: B 177 MET cc_start: -0.0337 (tpp) cc_final: -0.2225 (mtm) REVERT: B 745 ASP cc_start: 0.6897 (m-30) cc_final: 0.4285 (m-30) REVERT: B 1029 MET cc_start: 0.9302 (tpp) cc_final: 0.8989 (tpp) REVERT: C 238 PHE cc_start: 0.8387 (p90) cc_final: 0.7985 (p90) REVERT: C 327 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9042 (t) REVERT: C 529 LYS cc_start: 0.6662 (mmmt) cc_final: 0.6299 (mmmt) REVERT: C 773 GLU cc_start: 0.7412 (tp30) cc_final: 0.7201 (tp30) REVERT: C 904 TYR cc_start: 0.7466 (m-10) cc_final: 0.7141 (m-10) outliers start: 25 outliers final: 16 residues processed: 182 average time/residue: 0.3398 time to fit residues: 103.5609 Evaluate side-chains 146 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 312 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 286 optimal weight: 0.0570 chunk 98 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 859 ASN C 30 ASN C 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25973 Z= 0.211 Angle : 0.584 11.598 35323 Z= 0.297 Chirality : 0.044 0.280 4088 Planarity : 0.004 0.059 4537 Dihedral : 5.525 59.654 4075 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.69 % Allowed : 10.05 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.14), residues: 3150 helix: 0.02 (0.20), residues: 639 sheet: -0.86 (0.19), residues: 645 loop : -2.22 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 436 HIS 0.004 0.001 HIS C1048 PHE 0.023 0.002 PHE C 429 TYR 0.017 0.001 TYR C 204 ARG 0.004 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 2.966 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 133 PHE cc_start: 0.7625 (m-80) cc_final: 0.6750 (m-10) REVERT: A 529 LYS cc_start: 0.7957 (tppt) cc_final: 0.7627 (tppt) REVERT: A 570 ASP cc_start: 0.8208 (p0) cc_final: 0.7726 (p0) REVERT: B 118 LEU cc_start: 0.8819 (tt) cc_final: 0.8289 (mp) REVERT: B 129 LYS cc_start: 0.7215 (mttt) cc_final: 0.6893 (mttt) REVERT: B 177 MET cc_start: -0.0253 (tpp) cc_final: -0.1752 (ttm) REVERT: B 515 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7723 (p90) REVERT: B 1029 MET cc_start: 0.9314 (tpp) cc_final: 0.8970 (tpp) REVERT: C 238 PHE cc_start: 0.8416 (p90) cc_final: 0.8012 (p90) REVERT: C 342 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4574 (t80) REVERT: C 378 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (ttmt) REVERT: C 904 TYR cc_start: 0.7532 (m-10) cc_final: 0.7175 (m-10) outliers start: 47 outliers final: 27 residues processed: 173 average time/residue: 0.3479 time to fit residues: 100.5118 Evaluate side-chains 155 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 290 optimal weight: 0.0980 chunk 307 optimal weight: 0.0570 chunk 151 optimal weight: 0.8980 chunk 275 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN B 125 ASN C 81 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25973 Z= 0.136 Angle : 0.545 12.729 35323 Z= 0.274 Chirality : 0.043 0.274 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.200 57.755 4075 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.72 % Allowed : 11.45 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3150 helix: 0.33 (0.21), residues: 657 sheet: -0.66 (0.20), residues: 638 loop : -2.10 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS C1118 PHE 0.015 0.001 PHE C1052 TYR 0.017 0.001 TYR A 495 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 3.285 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 133 PHE cc_start: 0.7515 (m-80) cc_final: 0.6570 (m-10) REVERT: A 158 ARG cc_start: 0.7208 (mmt90) cc_final: 0.7007 (ttm110) REVERT: A 570 ASP cc_start: 0.8262 (p0) cc_final: 0.7768 (p0) REVERT: B 118 LEU cc_start: 0.8797 (tt) cc_final: 0.8321 (mp) REVERT: B 129 LYS cc_start: 0.7117 (mttt) cc_final: 0.6840 (mttt) REVERT: B 158 ARG cc_start: 0.5663 (mmt90) cc_final: 0.5395 (mmm-85) REVERT: B 177 MET cc_start: -0.0426 (tpp) cc_final: -0.1930 (ttm) REVERT: B 324 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: B 515 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7571 (p90) REVERT: B 565 PHE cc_start: 0.7555 (m-80) cc_final: 0.7329 (m-10) REVERT: B 1029 MET cc_start: 0.9264 (tpp) cc_final: 0.8914 (tpp) REVERT: C 21 ARG cc_start: 0.3454 (OUTLIER) cc_final: 0.3138 (mtt180) REVERT: C 238 PHE cc_start: 0.8387 (p90) cc_final: 0.8020 (p90) REVERT: C 342 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4353 (t80) REVERT: C 378 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7432 (ttmt) REVERT: C 904 TYR cc_start: 0.7326 (m-10) cc_final: 0.7067 (m-10) REVERT: C 974 SER cc_start: 0.8660 (m) cc_final: 0.8363 (m) outliers start: 48 outliers final: 29 residues processed: 197 average time/residue: 0.3411 time to fit residues: 111.1092 Evaluate side-chains 167 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 262 optimal weight: 0.0370 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 519 HIS C 872 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25973 Z= 0.291 Angle : 0.602 11.191 35323 Z= 0.306 Chirality : 0.044 0.265 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.414 59.559 4074 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.37 % Allowed : 12.85 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3150 helix: 0.17 (0.20), residues: 659 sheet: -0.79 (0.19), residues: 646 loop : -2.11 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 436 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.002 PHE A 456 TYR 0.032 0.001 TYR A 473 ARG 0.005 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 131 time to evaluate : 2.929 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 133 PHE cc_start: 0.7645 (m-80) cc_final: 0.6676 (m-10) REVERT: A 570 ASP cc_start: 0.8222 (p0) cc_final: 0.7779 (p0) REVERT: B 118 LEU cc_start: 0.8810 (tt) cc_final: 0.8277 (mp) REVERT: B 129 LYS cc_start: 0.7081 (mttt) cc_final: 0.6859 (mttt) REVERT: B 158 ARG cc_start: 0.5888 (mmt90) cc_final: 0.5563 (mmm-85) REVERT: B 177 MET cc_start: -0.0376 (tpp) cc_final: -0.2584 (mtm) REVERT: B 515 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7836 (p90) REVERT: B 1029 MET cc_start: 0.9330 (tpp) cc_final: 0.9035 (tpp) REVERT: C 21 ARG cc_start: 0.3658 (OUTLIER) cc_final: 0.3350 (mtt180) REVERT: C 238 PHE cc_start: 0.8450 (p90) cc_final: 0.8028 (p90) REVERT: C 378 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7459 (ttmt) REVERT: C 904 TYR cc_start: 0.7623 (m-10) cc_final: 0.7280 (m-10) outliers start: 66 outliers final: 51 residues processed: 186 average time/residue: 0.3526 time to fit residues: 108.8574 Evaluate side-chains 177 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 123 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 872 GLN C 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25973 Z= 0.243 Angle : 0.579 13.804 35323 Z= 0.292 Chirality : 0.044 0.443 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.379 58.557 4074 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.30 % Allowed : 13.92 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3150 helix: 0.32 (0.21), residues: 650 sheet: -0.69 (0.20), residues: 636 loop : -2.10 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE A 456 TYR 0.033 0.001 TYR A 473 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 132 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7534 (m-80) cc_final: 0.6564 (m-10) REVERT: A 570 ASP cc_start: 0.8219 (p0) cc_final: 0.7748 (p0) REVERT: A 878 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9055 (mp) REVERT: B 118 LEU cc_start: 0.8784 (tt) cc_final: 0.8280 (mp) REVERT: B 129 LYS cc_start: 0.7074 (mttt) cc_final: 0.6787 (mttt) REVERT: B 158 ARG cc_start: 0.5842 (mmt90) cc_final: 0.5544 (mmm-85) REVERT: B 177 MET cc_start: -0.0545 (tpp) cc_final: -0.2663 (mtm) REVERT: B 324 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: B 396 TYR cc_start: 0.7889 (m-80) cc_final: 0.7384 (m-80) REVERT: B 515 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7801 (p90) REVERT: B 1029 MET cc_start: 0.9305 (tpp) cc_final: 0.9008 (tpp) REVERT: C 21 ARG cc_start: 0.3748 (OUTLIER) cc_final: 0.3441 (mtt180) REVERT: C 238 PHE cc_start: 0.8474 (p90) cc_final: 0.8057 (p90) REVERT: C 378 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7480 (ttmt) REVERT: C 904 TYR cc_start: 0.7583 (m-10) cc_final: 0.7219 (m-10) outliers start: 64 outliers final: 44 residues processed: 185 average time/residue: 0.3557 time to fit residues: 111.1572 Evaluate side-chains 171 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 122 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25973 Z= 0.162 Angle : 0.543 12.872 35323 Z= 0.274 Chirality : 0.043 0.261 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.219 58.179 4074 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.33 % Allowed : 14.28 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3150 helix: 0.57 (0.21), residues: 651 sheet: -0.57 (0.20), residues: 641 loop : -2.02 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 PHE 0.036 0.001 PHE C 429 TYR 0.017 0.001 TYR A 473 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 142 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7466 (m-80) cc_final: 0.6471 (m-10) REVERT: A 570 ASP cc_start: 0.8223 (p0) cc_final: 0.7786 (p0) REVERT: A 878 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9002 (mp) REVERT: A 1031 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 118 LEU cc_start: 0.8777 (tt) cc_final: 0.8282 (mp) REVERT: B 129 LYS cc_start: 0.7066 (mttt) cc_final: 0.6781 (mttt) REVERT: B 158 ARG cc_start: 0.5755 (mmt90) cc_final: 0.5481 (mmt90) REVERT: B 177 MET cc_start: -0.0736 (tpp) cc_final: -0.2583 (mtm) REVERT: B 324 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: B 396 TYR cc_start: 0.7865 (m-80) cc_final: 0.7354 (m-80) REVERT: B 515 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7704 (p90) REVERT: B 1029 MET cc_start: 0.9260 (tpp) cc_final: 0.8970 (tpp) REVERT: C 238 PHE cc_start: 0.8430 (p90) cc_final: 0.8071 (p90) REVERT: C 974 SER cc_start: 0.8623 (m) cc_final: 0.8352 (m) outliers start: 65 outliers final: 44 residues processed: 196 average time/residue: 0.3327 time to fit residues: 109.3843 Evaluate side-chains 173 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 151 optimal weight: 0.0020 chunk 28 optimal weight: 0.0000 chunk 240 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN C 954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25973 Z= 0.142 Angle : 0.539 12.245 35323 Z= 0.273 Chirality : 0.043 0.256 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.078 59.932 4074 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.15 % Allowed : 14.89 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3150 helix: 0.74 (0.21), residues: 657 sheet: -0.47 (0.20), residues: 647 loop : -1.94 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 PHE 0.026 0.001 PHE C 429 TYR 0.042 0.001 TYR A 473 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 141 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7435 (m-80) cc_final: 0.6456 (m-10) REVERT: A 421 TYR cc_start: 0.3758 (m-80) cc_final: 0.3440 (m-10) REVERT: A 570 ASP cc_start: 0.8232 (p0) cc_final: 0.7789 (p0) REVERT: A 878 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8956 (mp) REVERT: A 1031 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 118 LEU cc_start: 0.8804 (tt) cc_final: 0.8461 (mp) REVERT: B 129 LYS cc_start: 0.7019 (mttt) cc_final: 0.6728 (mttt) REVERT: B 158 ARG cc_start: 0.5705 (mmt90) cc_final: 0.5437 (mmt90) REVERT: B 177 MET cc_start: -0.0624 (tpp) cc_final: -0.2795 (mtm) REVERT: B 396 TYR cc_start: 0.7818 (m-80) cc_final: 0.7295 (m-80) REVERT: B 515 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7642 (p90) REVERT: B 1029 MET cc_start: 0.9261 (tpp) cc_final: 0.8976 (tpp) REVERT: C 974 SER cc_start: 0.8577 (m) cc_final: 0.8333 (m) outliers start: 60 outliers final: 40 residues processed: 191 average time/residue: 0.3249 time to fit residues: 103.1731 Evaluate side-chains 171 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 267 optimal weight: 0.5980 chunk 285 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25973 Z= 0.215 Angle : 0.574 11.238 35323 Z= 0.289 Chirality : 0.044 0.261 4088 Planarity : 0.004 0.062 4537 Dihedral : 5.119 58.816 4072 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.97 % Allowed : 15.00 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3150 helix: 0.71 (0.21), residues: 659 sheet: -0.50 (0.20), residues: 644 loop : -1.96 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP B 436 HIS 0.003 0.001 HIS C 66 PHE 0.023 0.001 PHE C 238 TYR 0.030 0.001 TYR A 473 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 133 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7516 (m-80) cc_final: 0.6499 (m-10) REVERT: A 570 ASP cc_start: 0.8225 (p0) cc_final: 0.7784 (p0) REVERT: A 878 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8998 (mp) REVERT: A 1031 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 118 LEU cc_start: 0.8843 (tt) cc_final: 0.8275 (mp) REVERT: B 129 LYS cc_start: 0.7000 (mttt) cc_final: 0.6599 (mttt) REVERT: B 158 ARG cc_start: 0.5650 (mmt90) cc_final: 0.5386 (mmt90) REVERT: B 177 MET cc_start: -0.0758 (tpp) cc_final: -0.2619 (mtm) REVERT: B 396 TYR cc_start: 0.7921 (m-80) cc_final: 0.7426 (m-80) REVERT: B 515 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7723 (p90) REVERT: B 1029 MET cc_start: 0.9328 (tpp) cc_final: 0.9077 (tpp) REVERT: C 974 SER cc_start: 0.8638 (m) cc_final: 0.8368 (m) outliers start: 55 outliers final: 46 residues processed: 181 average time/residue: 0.3393 time to fit residues: 103.4180 Evaluate side-chains 176 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25973 Z= 0.224 Angle : 0.578 11.381 35323 Z= 0.290 Chirality : 0.044 0.265 4088 Planarity : 0.004 0.062 4537 Dihedral : 5.176 58.713 4072 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.94 % Allowed : 15.21 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3150 helix: 0.70 (0.21), residues: 659 sheet: -0.45 (0.20), residues: 641 loop : -1.96 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 436 HIS 0.003 0.001 HIS C 66 PHE 0.034 0.001 PHE C 79 TYR 0.033 0.001 TYR A 473 ARG 0.004 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 126 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7558 (m-80) cc_final: 0.6263 (m-10) REVERT: A 135 PHE cc_start: 0.8199 (m-80) cc_final: 0.7502 (m-80) REVERT: A 570 ASP cc_start: 0.8230 (p0) cc_final: 0.7805 (p0) REVERT: A 878 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9009 (mp) REVERT: A 1031 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 129 LYS cc_start: 0.6979 (mttt) cc_final: 0.6709 (mttt) REVERT: B 177 MET cc_start: -0.0669 (tpp) cc_final: -0.2601 (mtm) REVERT: B 396 TYR cc_start: 0.7934 (m-80) cc_final: 0.7439 (m-80) REVERT: B 515 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7776 (p90) REVERT: B 1029 MET cc_start: 0.9341 (tpp) cc_final: 0.9061 (tpp) REVERT: C 974 SER cc_start: 0.8591 (m) cc_final: 0.8312 (m) outliers start: 54 outliers final: 47 residues processed: 174 average time/residue: 0.3418 time to fit residues: 99.5561 Evaluate side-chains 173 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 123 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 259 optimal weight: 0.0670 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076132 restraints weight = 66693.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075172 restraints weight = 44774.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075602 restraints weight = 53981.065| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25973 Z= 0.298 Angle : 0.615 11.152 35323 Z= 0.310 Chirality : 0.045 0.262 4088 Planarity : 0.004 0.062 4537 Dihedral : 5.356 59.442 4070 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.87 % Allowed : 15.61 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3150 helix: 0.53 (0.21), residues: 668 sheet: -0.54 (0.20), residues: 625 loop : -2.03 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 436 HIS 0.003 0.001 HIS A 655 PHE 0.023 0.002 PHE C 238 TYR 0.030 0.001 TYR A 473 ARG 0.010 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.96 seconds wall clock time: 73 minutes 49.98 seconds (4429.98 seconds total)