Starting phenix.real_space_refine on Sat Mar 23 23:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdk_33150/03_2024/7xdk_33150.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.089 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 168 5.16 5 C 24699 2.51 5 N 6477 2.21 5 O 7656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C GLU 644": "OE1" <-> "OE2" Residue "C GLU 1075": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 214": "OE1" <-> "OE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 82": "OD1" <-> "OD2" Residue "O PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39000 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "K" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "O" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 20.39, per 1000 atoms: 0.52 Number of scatterers: 39000 At special positions: 0 Unit cell: (183.312, 183.312, 241.2, 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 168 16.00 O 7656 8.00 N 6477 7.00 C 24699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.04 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.05 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 141 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 362 " - pdb=" SG CYS B 415 " distance=2.04 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 645 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 141 " - pdb=" SG CYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 508 " distance=2.04 Simple disulfide: pdb=" SG CYS C 463 " - pdb=" SG CYS C 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 521 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 600 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 645 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 141 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1201 " - " ASN A1117 " " NAG A1202 " - " ASN A 692 " " NAG A1203 " - " ASN A1057 " " NAG A1204 " - " ASN A 640 " " NAG B1201 " - " ASN B1117 " " NAG B1202 " - " ASN B 692 " " NAG B1203 " - " ASN B1057 " " NAG B1204 " - " ASN B 640 " " NAG C1201 " - " ASN C1117 " " NAG C1202 " - " ASN C 692 " " NAG C1203 " - " ASN C1057 " " NAG C1204 " - " ASN C 640 " " NAG P 1 " - " ASN A1081 " " NAG Q 1 " - " ASN A 700 " " NAG R 1 " - " ASN A 784 " " NAG S 1 " - " ASN A 314 " " NAG T 1 " - " ASN B1081 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B 314 " " NAG X 1 " - " ASN C1081 " " NAG Y 1 " - " ASN C 700 " " NAG Z 1 " - " ASN C 784 " " NAG a 1 " - " ASN C 314 " Time building additional restraints: 14.50 Conformation dependent library (CDL) restraints added in 6.4 seconds 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9270 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 94 sheets defined 16.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.607A pdb=" N GLU A 389 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.619A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.893A pdb=" N ASN A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.252A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.910A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.871A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.857A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.687A pdb=" N GLY F 191 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.668A pdb=" N SER G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.884A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.597A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.664A pdb=" N TYR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.534A pdb=" N VAL B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 388 through 393 removed outlier: 4.063A pdb=" N ARG B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.603A pdb=" N SER B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 766 removed outlier: 4.080A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 747 " --> pdb=" O CYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.706A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 873 " --> pdb=" O THR B 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 869 through 873' Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.039A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 928 through 950 removed outlier: 4.090A pdb=" N SER B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 4.097A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.823A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 186 through 193 Processing helix chain 'J' and resid 80 through 84 removed outlier: 4.022A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.519A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.991A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.877A pdb=" N TYR C 143 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 144 " --> pdb=" O GLY C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 144' Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.908A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.779A pdb=" N LEU C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 removed outlier: 4.668A pdb=" N ARG C 391 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 392 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 720 through 727 Processing helix chain 'C' and resid 729 through 738 removed outlier: 3.776A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 766 Processing helix chain 'C' and resid 799 through 809 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.138A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 924 Processing helix chain 'C' and resid 928 through 949 Processing helix chain 'C' and resid 959 through 966 removed outlier: 4.046A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1015 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.889A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 159 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'M' and resid 29 through 32 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.029A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 129 removed outlier: 3.701A pdb=" N GLY M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR N 91 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.624A pdb=" N ALA A 12 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASN A 46 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR A 252 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 184 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A 211 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 186 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.766A pdb=" N ALA B 558 " --> pdb=" O GLY B 549 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP B 557 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 533 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.951A pdb=" N LYS A 261 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.652A pdb=" N GLY A 92 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 88 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.048A pdb=" N VAL A 115 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 302 removed outlier: 6.756A pdb=" N VAL A 578 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 300 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 576 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 577 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.740A pdb=" N GLY A 533 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP A 557 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 558 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 548 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 378 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 337 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.461A pdb=" N CYS A 344 " --> pdb=" O CYS A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AB5, first strand: chain 'A' and resid 642 through 643 removed outlier: 3.979A pdb=" N TYR A 643 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.549A pdb=" N SER A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A1059 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1053 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.630A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 3.535A pdb=" N SER A1106 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.558A pdb=" N TYR F 93 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP F 34 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 181 " --> pdb=" O CYS F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR F 177 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 22 removed outlier: 4.031A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.740A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.811A pdb=" N VAL G 151 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS G 195 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS G 208 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 197 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL G 206 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.511A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.870A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 69 through 73 Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.510A pdb=" N ASP E 105 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA E 13 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'E' and resid 45 through 49 removed outlier: 5.699A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 13 through 15 removed outlier: 8.071A pdb=" N ASN B 46 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 252 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 250 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 184 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 211 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE B 186 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.568A pdb=" N ALA C 558 " --> pdb=" O GLY C 549 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP C 557 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 533 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 33 through 40 removed outlier: 3.931A pdb=" N ASP B 270 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.563A pdb=" N GLY B 92 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 115 through 116 removed outlier: 7.217A pdb=" N VAL B 115 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 294 through 302 removed outlier: 5.405A pdb=" N ILE B 295 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR B 582 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN B 297 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 580 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 299 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 577 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.902A pdb=" N ASN B 337 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AE9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AF1, first strand: chain 'B' and resid 642 through 643 removed outlier: 3.933A pdb=" N TYR B 643 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.647A pdb=" N SER B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B1059 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 704 " --> pdb=" O THR B1049 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 716 through 717 removed outlier: 4.568A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 770 through 772 removed outlier: 5.619A pdb=" N ILE B 771 " --> pdb=" O ASN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.274A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 removed outlier: 5.924A pdb=" N GLU K 16 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.310A pdb=" N TRP K 34 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN K 50 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.378A pdb=" N LYS K 210 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR J 98 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.753A pdb=" N ASP J 71 " --> pdb=" O SER J 68 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 117 through 119 removed outlier: 4.164A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA J 131 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 146 through 151 removed outlier: 3.747A pdb=" N LYS J 146 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 198 " --> pdb=" O LYS J 146 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.621A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.549A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.932A pdb=" N ALA I 13 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.535A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.649A pdb=" N ALA C 12 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASN C 46 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 252 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE C 184 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 211 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE C 186 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS C 190 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ALA C 205 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 21 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.579A pdb=" N PHE C 40 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 254 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR C 257 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 273 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 271 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS C 261 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 69 through 70 removed outlier: 4.025A pdb=" N GLY C 88 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 101 through 103 removed outlier: 7.123A pdb=" N VAL C 115 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 294 through 302 removed outlier: 6.823A pdb=" N VAL C 578 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN C 300 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 576 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 595 " --> pdb=" O CYS C 632 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS C 632 " --> pdb=" O TYR C 595 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 631 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.711A pdb=" N ASN C 337 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 378 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AI2, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AI3, first strand: chain 'C' and resid 642 through 643 removed outlier: 3.913A pdb=" N TYR C 643 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 674 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 658 " --> pdb=" O SER C 674 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 694 through 710 removed outlier: 6.635A pdb=" N SER C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C1059 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C1053 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AI6, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.387A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AI8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AI9, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.710A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.755A pdb=" N LYS L 144 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR L 177 " --> pdb=" O ASP L 145 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 165 through 166 Processing sheet with id=AJ3, first strand: chain 'L' and resid 199 through 201 Processing sheet with id=AJ4, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 19 through 22 removed outlier: 3.622A pdb=" N ASP M 71 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 117 through 119 removed outlier: 3.933A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 155 through 156 removed outlier: 4.611A pdb=" N TRP M 149 " --> pdb=" O GLN M 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS M 146 " --> pdb=" O THR M 198 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS M 195 " --> pdb=" O LYS M 208 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS M 208 " --> pdb=" O CYS M 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 197 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL M 206 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS M 199 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER M 204 " --> pdb=" O HIS M 199 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.686A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.798A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.642A pdb=" N THR O 74 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.608A pdb=" N VAL O 11 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'O' and resid 45 through 48 removed outlier: 6.011A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE O 48 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 3690 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: 19.51 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11794 1.33 - 1.46: 10502 1.46 - 1.59: 17373 1.59 - 1.72: 0 1.72 - 1.85: 213 Bond restraints: 39882 Sorted by residual: bond pdb=" CA SER A 332 " pdb=" CB SER A 332 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.47e+01 bond pdb=" N VAL B 416 " pdb=" CA VAL B 416 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N VAL B 598 " pdb=" CA VAL B 598 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.69e+00 ... (remaining 39877 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.96: 971 105.96 - 113.02: 21626 113.02 - 120.08: 13126 120.08 - 127.14: 18129 127.14 - 134.20: 400 Bond angle restraints: 54252 Sorted by residual: angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" N PRO B 604 " ideal model delta sigma weight residual 120.83 124.25 -3.42 6.10e-01 2.69e+00 3.14e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 113.28 107.06 6.22 1.22e+00 6.72e-01 2.60e+01 angle pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" O SER A 332 " ideal model delta sigma weight residual 121.87 116.68 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" CA VAL A 333 " pdb=" C VAL A 333 " pdb=" O VAL A 333 " ideal model delta sigma weight residual 120.95 116.51 4.44 1.04e+00 9.25e-01 1.82e+01 angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" O VAL B 603 " ideal model delta sigma weight residual 118.69 115.89 2.80 6.70e-01 2.23e+00 1.75e+01 ... (remaining 54247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22077 17.97 - 35.94: 1737 35.94 - 53.92: 331 53.92 - 71.89: 69 71.89 - 89.86: 35 Dihedral angle restraints: 24249 sinusoidal: 9801 harmonic: 14448 Sorted by residual: dihedral pdb=" CB CYS C 600 " pdb=" SG CYS C 600 " pdb=" SG CYS C 632 " pdb=" CB CYS C 632 " ideal model delta sinusoidal sigma weight residual -86.00 -165.30 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 463 " pdb=" SG CYS A 463 " pdb=" SG CYS A 471 " pdb=" CB CYS A 471 " ideal model delta sinusoidal sigma weight residual 93.00 163.93 -70.93 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS C 319 " pdb=" SG CYS C 319 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -152.15 66.15 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 24246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 6210 0.154 - 0.308: 14 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.769: 3 Chirality restraints: 6228 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A1081 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1081 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1081 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 6225 not shown) Planarity restraints: 6987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 13 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO D 14 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 7 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO I 8 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 8 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 80 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO G 81 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.024 5.00e-02 4.00e+02 ... (remaining 6984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2953 2.74 - 3.28: 37477 3.28 - 3.82: 62035 3.82 - 4.36: 73561 4.36 - 4.90: 131626 Nonbonded interactions: 307652 Sorted by model distance: nonbonded pdb=" OD1 ASP O 82 " pdb=" OH TYR O 86 " model vdw 2.200 2.440 nonbonded pdb=" OE1 GLN B 476 " pdb=" OG SER J 30 " model vdw 2.202 2.440 nonbonded pdb=" O GLY E 28 " pdb=" ND2 ASN E 92 " model vdw 2.206 2.520 nonbonded pdb=" OD2 ASP B 513 " pdb=" NE2 GLN B 563 " model vdw 2.209 2.520 nonbonded pdb=" OG1 THR F 152 " pdb=" OD1 ASN F 200 " model vdw 2.223 2.440 ... (remaining 307647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.330 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 101.740 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.004 0.062 39882 Z= 0.233 Angle : 0.572 7.763 54252 Z= 0.308 Chirality : 0.047 0.769 6228 Planarity : 0.004 0.048 6963 Dihedral : 13.490 89.861 14808 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4923 helix: 2.09 (0.21), residues: 687 sheet: -0.32 (0.13), residues: 1539 loop : -1.01 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 869 HIS 0.006 0.001 HIS G 199 PHE 0.020 0.001 PHE B 889 TYR 0.019 0.001 TYR A 334 ARG 0.008 0.000 ARG N 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 463 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8992 (t) cc_final: 0.8748 (t) REVERT: B 1033 MET cc_start: 0.8918 (ptp) cc_final: 0.8716 (ptm) REVERT: K 142 LEU cc_start: 0.6407 (tt) cc_final: 0.6162 (tp) REVERT: J 150 LYS cc_start: 0.4670 (pttm) cc_final: 0.3522 (pttt) REVERT: I 90 GLN cc_start: 0.8464 (pp30) cc_final: 0.8240 (pp30) REVERT: C 413 THR cc_start: 0.8135 (t) cc_final: 0.7714 (m) outliers start: 5 outliers final: 2 residues processed: 466 average time/residue: 0.5196 time to fit residues: 390.6024 Evaluate side-chains 383 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 385 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 446 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN K 6 GLN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 589 ASN C 884 GLN C 890 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C1084 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN O 92 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 39882 Z= 0.538 Angle : 0.701 14.438 54252 Z= 0.359 Chirality : 0.051 0.636 6228 Planarity : 0.005 0.051 6963 Dihedral : 5.601 55.196 6105 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.14 % Allowed : 8.47 % Favored : 90.39 % 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: -0.82 (0.12), residues: 4923 helix: 1.64 (0.20), residues: 690 sheet: -0.45 (0.13), residues: 1647 loop : -1.20 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 869 HIS 0.009 0.001 HIS A1031 PHE 0.037 0.002 PHE B 889 TYR 0.028 0.002 TYR M 92 ARG 0.005 0.001 ARG A1074 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 414 time to evaluate : 4.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 106 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7529 (tp40) REVERT: E 2 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7828 (mm) REVERT: J 4 MET cc_start: 0.7960 (mmt) cc_final: 0.7468 (mmt) REVERT: I 35 TRP cc_start: 0.7517 (m100) cc_final: 0.7316 (m-10) REVERT: C 413 THR cc_start: 0.8261 (t) cc_final: 0.7879 (m) REVERT: C 1033 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8454 (ptm) outliers start: 49 outliers final: 36 residues processed: 435 average time/residue: 0.5489 time to fit residues: 382.5613 Evaluate side-chains 423 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 385 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1033 MET Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 371 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 447 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 398 optimal weight: 4.9990 chunk 443 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 359 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 27 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39882 Z= 0.263 Angle : 0.575 10.694 54252 Z= 0.294 Chirality : 0.047 0.612 6228 Planarity : 0.004 0.048 6963 Dihedral : 5.198 52.346 6103 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.65 % Allowed : 11.07 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4923 helix: 2.04 (0.21), residues: 687 sheet: -0.43 (0.13), residues: 1674 loop : -1.15 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 47 HIS 0.004 0.001 HIS F 201 PHE 0.019 0.001 PHE B 889 TYR 0.019 0.001 TYR C1050 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 403 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8327 (tt) REVERT: F 106 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7470 (tp40) REVERT: C 413 THR cc_start: 0.8183 (t) cc_final: 0.7802 (m) outliers start: 71 outliers final: 45 residues processed: 445 average time/residue: 0.5435 time to fit residues: 390.9484 Evaluate side-chains 419 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 373 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 232 optimal weight: 0.0770 chunk 49 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 300 optimal weight: 50.0000 chunk 449 optimal weight: 3.9990 chunk 475 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 425 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN B 624 ASN C 66 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 39882 Z= 0.368 Angle : 0.600 10.819 54252 Z= 0.306 Chirality : 0.047 0.615 6228 Planarity : 0.004 0.049 6963 Dihedral : 5.128 47.323 6102 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.97 % Allowed : 12.91 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4923 helix: 2.01 (0.21), residues: 685 sheet: -0.45 (0.13), residues: 1657 loop : -1.20 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 35 HIS 0.005 0.001 HIS A1031 PHE 0.023 0.002 PHE E 94 TYR 0.019 0.002 TYR C1050 ARG 0.006 0.000 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 388 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8397 (tt) REVERT: F 106 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7515 (tp40) REVERT: C 1033 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8469 (ptm) outliers start: 85 outliers final: 67 residues processed: 443 average time/residue: 0.5167 time to fit residues: 375.0911 Evaluate side-chains 443 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 374 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1033 MET Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 193 GLN Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 2.9990 chunk 269 optimal weight: 0.0470 chunk 6 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 chunk 196 optimal weight: 0.1980 chunk 405 optimal weight: 0.5980 chunk 328 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 426 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN C 66 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39882 Z= 0.219 Angle : 0.550 10.227 54252 Z= 0.279 Chirality : 0.046 0.595 6228 Planarity : 0.004 0.049 6963 Dihedral : 4.821 41.364 6102 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.27 % Allowed : 13.88 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4923 helix: 2.28 (0.21), residues: 681 sheet: -0.38 (0.13), residues: 1644 loop : -1.15 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 35 HIS 0.004 0.001 HIS F 201 PHE 0.024 0.001 PHE E 94 TYR 0.019 0.001 TYR C1050 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 408 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 973 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: F 106 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7407 (tp40) REVERT: D 58 LYS cc_start: 0.8204 (mttp) cc_final: 0.7969 (mttp) REVERT: E 4 MET cc_start: 0.5714 (mmp) cc_final: 0.5388 (mmm) REVERT: B 401 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 600 CYS cc_start: 0.4394 (OUTLIER) cc_final: 0.3852 (m) REVERT: B 742 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7124 (t80) REVERT: J 4 MET cc_start: 0.7975 (mmt) cc_final: 0.7457 (mmt) REVERT: C 401 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8273 (tt) REVERT: C 478 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8036 (m-80) outliers start: 98 outliers final: 71 residues processed: 471 average time/residue: 0.5268 time to fit residues: 404.8305 Evaluate side-chains 449 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 371 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain L residue 209 ASP Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 40.0000 chunk 428 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 476 optimal weight: 10.0000 chunk 395 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN A 937 GLN G 125 GLN G 190 HIS B1066 HIS ** H 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 147 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 39882 Z= 0.486 Angle : 0.663 10.420 54252 Z= 0.338 Chirality : 0.050 0.630 6228 Planarity : 0.005 0.053 6963 Dihedral : 5.167 41.918 6102 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.11 % Allowed : 14.44 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4923 helix: 1.79 (0.21), residues: 689 sheet: -0.49 (0.13), residues: 1671 loop : -1.28 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP I 35 HIS 0.008 0.001 HIS A1031 PHE 0.032 0.002 PHE E 94 TYR 0.020 0.002 TYR B1050 ARG 0.007 0.001 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 394 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8412 (tt) REVERT: A 973 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: F 106 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7484 (tp40) REVERT: B 742 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7220 (t80) REVERT: J 4 MET cc_start: 0.8065 (mmt) cc_final: 0.7675 (mmt) REVERT: C 401 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8385 (tt) REVERT: C 478 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: C 956 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7217 (pt) REVERT: C 1033 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8561 (ptm) outliers start: 134 outliers final: 99 residues processed: 485 average time/residue: 0.5152 time to fit residues: 408.6865 Evaluate side-chains 481 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 375 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1033 MET Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 400 optimal weight: 0.0060 chunk 265 optimal weight: 3.9990 chunk 474 optimal weight: 0.0970 chunk 296 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 147 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39882 Z= 0.206 Angle : 0.561 10.335 54252 Z= 0.286 Chirality : 0.046 0.605 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.834 41.443 6102 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.37 % Allowed : 15.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 4923 helix: 2.24 (0.21), residues: 681 sheet: -0.45 (0.13), residues: 1665 loop : -1.16 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP I 35 HIS 0.006 0.001 HIS F 53 PHE 0.029 0.001 PHE E 94 TYR 0.028 0.001 TYR A1121 ARG 0.007 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 391 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8345 (tt) REVERT: F 106 GLN cc_start: 0.7641 (tp-100) cc_final: 0.7391 (tp40) REVERT: B 401 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 600 CYS cc_start: 0.4628 (OUTLIER) cc_final: 0.3859 (m) REVERT: B 742 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7274 (t80) REVERT: J 4 MET cc_start: 0.8016 (mmt) cc_final: 0.7635 (mmt) REVERT: C 401 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 478 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: C 567 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8432 (mm) REVERT: C 1033 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8462 (ptm) REVERT: O 38 GLN cc_start: 0.7615 (tp40) cc_final: 0.7075 (tp40) REVERT: O 78 LEU cc_start: 0.6305 (mp) cc_final: 0.6064 (tt) outliers start: 102 outliers final: 84 residues processed: 455 average time/residue: 0.5143 time to fit residues: 383.1741 Evaluate side-chains 470 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 378 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1033 MET Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 301 optimal weight: 0.0770 chunk 323 optimal weight: 0.0000 chunk 234 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 372 optimal weight: 0.5980 overall best weight: 0.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN B 596 GLN H 74 ASN I 79 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 39882 Z= 0.139 Angle : 0.526 9.951 54252 Z= 0.268 Chirality : 0.044 0.564 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.415 39.070 6102 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.81 % Allowed : 16.69 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4923 helix: 2.51 (0.21), residues: 680 sheet: -0.31 (0.13), residues: 1641 loop : -0.97 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP I 35 HIS 0.006 0.001 HIS F 53 PHE 0.019 0.001 PHE E 94 TYR 0.024 0.001 TYR A1121 ARG 0.008 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 421 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8674 (t) cc_final: 0.8401 (t) REVERT: F 106 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7407 (tp40) REVERT: E 90 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: B 401 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 600 CYS cc_start: 0.4390 (OUTLIER) cc_final: 0.3439 (m) REVERT: B 742 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7266 (t80) REVERT: J 4 MET cc_start: 0.7944 (mmt) cc_final: 0.7597 (mmt) REVERT: C 478 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: C 1033 MET cc_start: 0.8784 (ptp) cc_final: 0.8507 (ptm) REVERT: O 38 GLN cc_start: 0.7542 (tp40) cc_final: 0.7049 (tp-100) outliers start: 78 outliers final: 62 residues processed: 466 average time/residue: 0.5330 time to fit residues: 403.0405 Evaluate side-chains 452 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 385 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 869 TRP Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 71 ASP Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 6.9990 chunk 454 optimal weight: 8.9990 chunk 414 optimal weight: 5.9990 chunk 441 optimal weight: 0.7980 chunk 265 optimal weight: 0.4980 chunk 192 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 399 optimal weight: 0.6980 chunk 417 optimal weight: 1.9990 chunk 440 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN B 596 GLN K 205 ASN I 79 GLN C 119 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39882 Z= 0.186 Angle : 0.539 9.989 54252 Z= 0.272 Chirality : 0.045 0.571 6228 Planarity : 0.004 0.055 6963 Dihedral : 4.405 42.858 6102 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.93 % Allowed : 16.83 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4923 helix: 2.46 (0.21), residues: 684 sheet: -0.26 (0.13), residues: 1650 loop : -0.95 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP I 35 HIS 0.005 0.001 HIS F 53 PHE 0.055 0.001 PHE J 210 TYR 0.024 0.001 TYR A1121 ARG 0.010 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 393 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8996 (t) cc_final: 0.8730 (t) REVERT: F 106 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7401 (tp40) REVERT: B 401 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 535 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8704 (mt) REVERT: B 600 CYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3461 (m) REVERT: B 742 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7334 (t80) REVERT: J 4 MET cc_start: 0.7950 (mmt) cc_final: 0.7626 (mmt) REVERT: H 38 ARG cc_start: 0.7940 (ptt180) cc_final: 0.7735 (ptt180) REVERT: C 119 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4837 (pp30) REVERT: C 478 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: C 1033 MET cc_start: 0.8782 (ptp) cc_final: 0.8506 (ptm) REVERT: O 38 GLN cc_start: 0.7487 (tp40) cc_final: 0.7079 (tp40) outliers start: 83 outliers final: 65 residues processed: 446 average time/residue: 0.5072 time to fit residues: 367.7664 Evaluate side-chains 455 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 384 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 0.4980 chunk 467 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 324 optimal weight: 20.0000 chunk 490 optimal weight: 0.8980 chunk 451 optimal weight: 7.9990 chunk 390 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 301 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN B 596 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 39882 Z= 0.215 Angle : 0.630 59.200 54252 Z= 0.337 Chirality : 0.046 0.571 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.411 44.200 6102 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.86 % Allowed : 16.97 % Favored : 81.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4923 helix: 2.45 (0.21), residues: 684 sheet: -0.26 (0.13), residues: 1650 loop : -0.95 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP I 35 HIS 0.005 0.001 HIS F 53 PHE 0.056 0.001 PHE J 210 TYR 0.023 0.001 TYR A1121 ARG 0.007 0.000 ARG N 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 383 time to evaluate : 5.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.9005 (t) cc_final: 0.8759 (t) REVERT: F 106 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7402 (tp40) REVERT: B 401 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8273 (tp) REVERT: B 535 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 600 CYS cc_start: 0.4438 (OUTLIER) cc_final: 0.3465 (m) REVERT: B 742 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7337 (t80) REVERT: J 4 MET cc_start: 0.7956 (mmt) cc_final: 0.7626 (mmt) REVERT: H 38 ARG cc_start: 0.7945 (ptt180) cc_final: 0.7745 (ptt180) REVERT: C 478 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: C 1033 MET cc_start: 0.8784 (ptp) cc_final: 0.8493 (ptm) REVERT: O 38 GLN cc_start: 0.7487 (tp40) cc_final: 0.7096 (tp40) outliers start: 80 outliers final: 73 residues processed: 432 average time/residue: 0.5198 time to fit residues: 366.4883 Evaluate side-chains 459 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 381 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 153 ASN Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 3.9990 chunk 415 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 401 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN B 596 GLN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114026 restraints weight = 61554.084| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.48 r_work: 0.3109 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 39882 Z= 0.215 Angle : 0.630 59.200 54252 Z= 0.337 Chirality : 0.046 0.571 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.411 44.200 6102 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.83 % Allowed : 16.90 % Favored : 81.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4923 helix: 2.45 (0.21), residues: 684 sheet: -0.26 (0.13), residues: 1650 loop : -0.95 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP I 35 HIS 0.005 0.001 HIS F 53 PHE 0.056 0.001 PHE J 210 TYR 0.023 0.001 TYR A1121 ARG 0.007 0.000 ARG N 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8517.61 seconds wall clock time: 155 minutes 32.13 seconds (9332.13 seconds total)