Starting phenix.real_space_refine on Sat Mar 23 23:20:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdl_33151/03_2024/7xdl_33151.pdb" } resolution = 3.08 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= 0.002 sd= 0.053 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 162 5.16 5 C 24768 2.51 5 N 6427 2.21 5 O 7630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 372": "OD1" <-> "OD2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 209": "OD1" <-> "OD2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "F GLU 1": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "I ASP 102": "OD1" <-> "OD2" Residue "I TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38987 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7863 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 954} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7858 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7858 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "G" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "I" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "J" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "N" 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: 20.02, per 1000 atoms: 0.51 Number of scatterers: 38987 At special positions: 0 Unit cell: (182.82, 182.16, 242.22, 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 162 16.00 O 7630 8.00 N 6427 7.00 C 24768 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=2.03 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 471 " distance=2.02 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 573 " distance=2.03 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 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=2.05 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=2.04 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 C 116 " - pdb=" SG CYS C 149 " distance=2.05 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=2.04 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 D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 197 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS G 141 " - pdb=" SG CYS G 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 141 " - pdb=" SG CYS I 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " 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 N 1 " - " NAG N 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 N 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: 15.14 Conformation dependent library (CDL) restraints added in 7.4 seconds 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9224 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 85 sheets defined 17.0% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 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 367 through 371 removed outlier: 3.934A pdb=" N ASN A 371 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.891A pdb=" N ARG A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 393 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 599 through 606 removed outlier: 3.709A pdb=" N VAL A 603 " --> pdb=" O CYS A 600 " (cutoff:3.500A) Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.550A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.684A pdb=" N SER A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) 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: 3.896A 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 902 removed outlier: 4.359A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 removed outlier: 3.505A pdb=" N THR A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.625A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.639A pdb=" N ARG A 966 " --> pdb=" O ASP A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.640A pdb=" N TYR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 144 " --> pdb=" O GLY B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 144' Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.620A pdb=" N ASN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.804A pdb=" N ARG B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.611A pdb=" N ASN B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 737 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 744 through 766 Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.541A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.300A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 928 through 949 removed outlier: 3.608A pdb=" N GLN B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 3.767A 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 'C' and resid 277 through 287 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.276A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 387 through 393 removed outlier: 4.021A pdb=" N ARG C 391 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 393 " --> pdb=" O VAL C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 744 through 766 Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.524A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) 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 896 through 901 Processing helix chain 'C' and resid 902 through 924 Processing helix chain 'C' and resid 928 through 950 removed outlier: 3.700A pdb=" N GLN C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 966 removed outlier: 3.911A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1016 Processing helix chain 'D' and resid 29 through 32 removed outlier: 3.536A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.804A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 183 through 190 removed outlier: 4.084A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.524A pdb=" N LYS E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.885A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.785A pdb=" N GLY E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'F' and resid 29 through 32 removed outlier: 3.553A pdb=" N SER F 32 " --> pdb=" O ILE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 29 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.117A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 removed outlier: 3.706A pdb=" N LEU F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.890A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'H' and resid 29 through 32 Processing helix chain 'H' and resid 122 through 129 removed outlier: 4.082A pdb=" N SER H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY H 129 " --> pdb=" O GLN H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.590A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.960A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.810A pdb=" N THR I 132 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.568A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.623A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.778A pdb=" N ALA A 12 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASN A 46 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 252 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE A 184 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 211 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 186 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS A 190 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ALA A 205 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 21 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.654A pdb=" N GLY B 549 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B 557 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.588A pdb=" N VAL A 32 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 257 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 273 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 259 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 271 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.919A 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: 3.726A pdb=" N GLY A 88 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 91 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.786A pdb=" N PHE A 151 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 294 through 302 removed outlier: 6.780A pdb=" N VAL A 578 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN A 300 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 576 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A 577 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.420A pdb=" N GLU A 307 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN A 525 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 309 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP A 557 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 549 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 548 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.657A pdb=" N CYS A 344 " --> pdb=" O CYS A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 436 through 437 Processing sheet with id=AB2, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.532A pdb=" N ILE A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 685 removed outlier: 6.822A pdb=" N ALA A 684 " --> pdb=" O ILE C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.710A pdb=" N SER A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1059 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.521A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 842 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 770 through 772 removed outlier: 5.721A pdb=" N ILE A 771 " --> pdb=" O ASN B 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB8, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 15 removed outlier: 4.084A pdb=" N ALA B 12 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN B 46 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 252 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 184 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP B 211 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 186 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 207 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS B 190 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ALA B 205 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 21 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 28 removed outlier: 5.366A pdb=" N ASP C 557 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 529 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 307 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 523 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 40 removed outlier: 6.806A pdb=" N LYS B 261 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 70 removed outlier: 4.400A pdb=" N GLY B 88 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 115 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 294 through 302 removed outlier: 6.818A pdb=" N VAL B 578 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN B 300 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 576 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 577 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AC6, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AC7, first strand: chain 'B' and resid 637 through 643 removed outlier: 5.979A pdb=" N GLU B 637 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR B 679 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N VAL B 639 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 655 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.847A pdb=" N SER B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B1059 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.704A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 772 removed outlier: 5.774A pdb=" N ILE B 771 " --> pdb=" O ASN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.291A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AD4, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.801A pdb=" N ALA C 12 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASN C 46 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR C 252 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE C 184 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C 211 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 186 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N HIS C 190 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ALA C 205 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C 21 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 40 removed outlier: 7.752A pdb=" N THR C 257 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 273 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA C 271 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS C 261 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.923A pdb=" N GLY C 88 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 294 through 302 removed outlier: 6.815A pdb=" N VAL C 578 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 300 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 576 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 577 " --> pdb=" O GLN C 596 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.811A pdb=" N ASN C 337 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 377 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AE1, first strand: chain 'C' and resid 637 through 643 removed outlier: 5.702A pdb=" N THR C 679 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C 641 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.672A pdb=" N SER C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C1059 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER C1038 " --> pdb=" O GLY C1042 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C1044 " --> pdb=" O PRO C1036 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C1046 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1034 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C1048 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.603A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.405A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.571A pdb=" N LEU D 13 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.571A pdb=" N LEU D 13 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 98 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.536A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 145 through 151 Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.691A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.147A pdb=" N TYR E 177 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.147A pdb=" N TYR E 177 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.644A pdb=" N TYR E 195 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.271A pdb=" N LEU F 11 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.271A pdb=" N LEU F 11 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 132 through 136 removed outlier: 3.654A pdb=" N VAL F 133 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.710A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 206 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 3 through 8 Processing sheet with id=AG4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.186A pdb=" N TRP G 34 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.812A pdb=" N LEU G 142 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR G 177 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.812A pdb=" N LEU G 142 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR G 177 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AG8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG9, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.029A pdb=" N LEU H 11 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 50 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.029A pdb=" N LEU H 11 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR H 98 " --> pdb=" O GLN H 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 118 through 119 removed outlier: 4.184A pdb=" N PHE H 119 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL H 134 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 131 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 179 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN H 161 " --> pdb=" O THR H 179 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.219A pdb=" N TYR H 193 " --> pdb=" O PHE H 210 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE H 210 " --> pdb=" O TYR H 193 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AH5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.620A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 121 through 123 removed outlier: 3.730A pdb=" N LEU I 142 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR I 177 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 151 through 155 Processing sheet with id=AH8, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AH9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.734A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=AI2, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.192A pdb=" N CYS K 22 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA K 80 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.720A pdb=" N GLU K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.000A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE K 35 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP K 34 " --> pdb=" O HIS K 100 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.075A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI8, first strand: chain 'M' and resid 58 through 59 removed outlier: 4.601A pdb=" N TRP M 37 " --> pdb=" O MET M 49 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE M 51 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE M 35 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP M 34 " --> pdb=" O HIS M 100 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU M 110 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 5 through 6 removed outlier: 3.577A pdb=" N THR O 5 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE O 71 " --> pdb=" O CYS O 23 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AJ2, first strand: chain 'O' and resid 44 through 48 removed outlier: 6.540A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AJ4, first strand: chain 'P' and resid 58 through 59 removed outlier: 3.569A pdb=" N ASP P 58 " --> pdb=" O TYR P 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP P 48 " --> pdb=" O ARG P 39 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG P 39 " --> pdb=" O TRP P 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY P 50 " --> pdb=" O TRP P 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP P 37 " --> pdb=" O GLY P 50 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP P 34 " --> pdb=" O HIS P 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR P 96 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU P 110 " --> pdb=" O ARG P 99 " (cutoff:3.500A) 1425 hydrogen bonds defined for protein. 3792 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: 18.89 Time building geometry restraints manager: 16.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7113 1.33 - 1.46: 12894 1.46 - 1.59: 19688 1.59 - 1.72: 0 1.72 - 1.85: 207 Bond restraints: 39902 Sorted by residual: bond pdb=" N VAL B 324 " pdb=" CA VAL B 324 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N VAL F 133 " pdb=" CA VAL F 133 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N ILE F 118 " pdb=" CA ILE F 118 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" CA SER C 574 " pdb=" CB SER C 574 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.69e-02 3.50e+03 1.03e+01 bond pdb=" N SER H 183 " pdb=" CA SER H 183 " ideal model delta sigma weight residual 1.453 1.495 -0.042 1.31e-02 5.83e+03 1.03e+01 ... (remaining 39897 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.55: 878 105.55 - 112.73: 21172 112.73 - 119.91: 13069 119.91 - 127.09: 18739 127.09 - 134.26: 425 Bond angle restraints: 54283 Sorted by residual: angle pdb=" N PRO C 875 " pdb=" CA PRO C 875 " pdb=" CB PRO C 875 " ideal model delta sigma weight residual 103.36 110.30 -6.94 8.30e-01 1.45e+00 6.99e+01 angle pdb=" N PRO C 925 " pdb=" CA PRO C 925 " pdb=" CB PRO C 925 " ideal model delta sigma weight residual 101.88 110.04 -8.16 1.01e+00 9.80e-01 6.53e+01 angle pdb=" N PRO A 875 " pdb=" CA PRO A 875 " pdb=" CB PRO A 875 " ideal model delta sigma weight residual 103.34 110.30 -6.96 9.30e-01 1.16e+00 5.60e+01 angle pdb=" N PRO B 875 " pdb=" CA PRO B 875 " pdb=" CB PRO B 875 " ideal model delta sigma weight residual 103.19 110.24 -7.05 9.50e-01 1.11e+00 5.50e+01 angle pdb=" N PRO A 925 " pdb=" CA PRO A 925 " pdb=" CB PRO A 925 " ideal model delta sigma weight residual 102.76 110.12 -7.36 1.12e+00 7.97e-01 4.32e+01 ... (remaining 54278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22013 17.98 - 35.95: 1749 35.95 - 53.93: 330 53.93 - 71.91: 57 71.91 - 89.88: 43 Dihedral angle restraints: 24192 sinusoidal: 9804 harmonic: 14388 Sorted by residual: dihedral pdb=" CB CYS C 274 " pdb=" SG CYS C 274 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual -86.00 -173.84 87.84 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 170.16 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 89 " pdb=" CB CYS F 89 " ideal model delta sinusoidal sigma weight residual 93.00 166.75 -73.75 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 24189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 6141 0.181 - 0.362: 58 0.362 - 0.543: 0 0.543 - 0.725: 1 0.725 - 0.906: 2 Chirality restraints: 6202 Sorted by residual: 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 -1.49 -0.91 2.00e-01 2.50e+01 2.05e+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 -1.64 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1081 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 6199 not shown) Planarity restraints: 6955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 179 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.73e+00 pdb=" C THR H 179 " 0.054 2.00e-02 2.50e+03 pdb=" O THR H 179 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 180 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 190 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C HIS H 190 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS H 190 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS H 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 316 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C THR C 316 " -0.042 2.00e-02 2.50e+03 pdb=" O THR C 316 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN C 317 " 0.014 2.00e-02 2.50e+03 ... (remaining 6952 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2663 2.74 - 3.28: 36795 3.28 - 3.82: 60363 3.82 - 4.36: 73650 4.36 - 4.90: 130559 Nonbonded interactions: 304030 Sorted by model distance: nonbonded pdb=" NH1 ARG A 440 " pdb=" OD2 ASP A 450 " model vdw 2.195 2.520 nonbonded pdb=" OG SER E 154 " pdb=" OD1 ASN E 198 " model vdw 2.208 2.440 nonbonded pdb=" OH TYR B 22 " pdb=" O LEU B 39 " model vdw 2.208 2.440 nonbonded pdb=" O ASN C 484 " pdb=" NE2 GLN C 489 " model vdw 2.210 2.520 nonbonded pdb=" OG SER H 122 " pdb=" OE1 GLU H 124 " model vdw 2.212 2.440 ... (remaining 304025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 605 or resid 623 through 1126 or resid 1201 thr \ ough 1204)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' 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: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 29.720 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 103.810 Find NCS groups from input model: 2.520 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39902 Z= 0.330 Angle : 0.750 9.264 54283 Z= 0.457 Chirality : 0.056 0.906 6202 Planarity : 0.004 0.059 6931 Dihedral : 13.527 89.885 14797 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 0.56 % Allowed : 1.04 % Favored : 98.40 % 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: -0.28 (0.12), residues: 4894 helix: 1.97 (0.20), residues: 692 sheet: 0.41 (0.13), residues: 1583 loop : -1.21 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 111 HIS 0.008 0.001 HIS I 101 PHE 0.029 0.002 PHE B 889 TYR 0.031 0.001 TYR D 33 ARG 0.014 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 416 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 MET cc_start: 0.4213 (ptt) cc_final: 0.3834 (ttt) REVERT: D 18 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7253 (ttm-80) REVERT: K 20 ILE cc_start: 0.5021 (mt) cc_final: 0.4809 (mt) outliers start: 24 outliers final: 10 residues processed: 435 average time/residue: 0.5039 time to fit residues: 363.2282 Evaluate side-chains 351 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 341 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 185 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A1084 HIS B 171 ASN B 179 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 975 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 139 ASN G 50 GLN H 125 GLN I 53 HIS J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39902 Z= 0.215 Angle : 0.569 8.730 54283 Z= 0.293 Chirality : 0.046 0.647 6202 Planarity : 0.004 0.053 6931 Dihedral : 5.824 57.474 6085 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 0.79 % Allowed : 7.71 % Favored : 91.50 % 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: -0.17 (0.12), residues: 4894 helix: 2.13 (0.20), residues: 704 sheet: 0.52 (0.13), residues: 1582 loop : -1.20 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 155 HIS 0.012 0.001 HIS I 53 PHE 0.026 0.001 PHE C 151 TYR 0.020 0.001 TYR A 334 ARG 0.006 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 365 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 CYS cc_start: 0.4077 (OUTLIER) cc_final: 0.3782 (m) REVERT: C 138 MET cc_start: 0.4107 (ptt) cc_final: 0.3631 (ttt) REVERT: I 155 TRP cc_start: 0.5362 (m100) cc_final: 0.4706 (m100) REVERT: J 4 MET cc_start: 0.4707 (ttt) cc_final: 0.4394 (ttt) REVERT: P 23 LYS cc_start: 0.6539 (tttp) cc_final: 0.6114 (tttp) REVERT: P 94 MET cc_start: 0.6325 (tmm) cc_final: 0.5658 (tmm) REVERT: P 96 TYR cc_start: 0.4686 (m-10) cc_final: 0.4365 (m-80) outliers start: 34 outliers final: 23 residues processed: 390 average time/residue: 0.5179 time to fit residues: 332.9758 Evaluate side-chains 361 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 444 optimal weight: 4.9990 chunk 480 optimal weight: 0.5980 chunk 396 optimal weight: 8.9990 chunk 441 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN D 156 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 39902 Z= 0.320 Angle : 0.604 8.859 54283 Z= 0.310 Chirality : 0.048 0.747 6202 Planarity : 0.004 0.054 6931 Dihedral : 5.718 56.097 6083 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 1.51 % Allowed : 10.75 % Favored : 87.74 % 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: -0.24 (0.12), residues: 4894 helix: 2.11 (0.20), residues: 700 sheet: 0.48 (0.13), residues: 1602 loop : -1.27 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 35 HIS 0.012 0.001 HIS I 101 PHE 0.028 0.002 PHE B 889 TYR 0.023 0.002 TYR L 49 ARG 0.009 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 341 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 PHE cc_start: 0.7852 (p90) cc_final: 0.7621 (p90) REVERT: C 138 MET cc_start: 0.4168 (ptt) cc_final: 0.3735 (ttt) REVERT: D 18 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7075 (ttm-80) REVERT: I 155 TRP cc_start: 0.5675 (m100) cc_final: 0.5237 (m100) REVERT: K 49 MET cc_start: 0.4318 (pmm) cc_final: 0.3678 (ppp) REVERT: P 23 LYS cc_start: 0.6508 (tttp) cc_final: 0.6089 (tttp) outliers start: 65 outliers final: 50 residues processed: 390 average time/residue: 0.5362 time to fit residues: 342.9539 Evaluate side-chains 370 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 320 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 536 THR 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 769 LYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 446 optimal weight: 9.9990 chunk 472 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 423 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN C 747 ASN F 6 GLN I 172 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39902 Z= 0.242 Angle : 0.563 9.582 54283 Z= 0.288 Chirality : 0.046 0.735 6202 Planarity : 0.004 0.054 6931 Dihedral : 5.444 55.909 6080 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.84 % Favored : 95.12 % Rotamer: Outliers : 1.65 % Allowed : 12.95 % Favored : 85.40 % 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: -0.20 (0.12), residues: 4894 helix: 2.19 (0.20), residues: 699 sheet: 0.55 (0.13), residues: 1589 loop : -1.28 (0.11), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 111 HIS 0.009 0.001 HIS I 53 PHE 0.019 0.001 PHE B 77 TYR 0.025 0.001 TYR L 49 ARG 0.010 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 342 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8171 (mm) REVERT: A 334 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7939 (p90) REVERT: C 138 MET cc_start: 0.4148 (ptt) cc_final: 0.3692 (ttt) REVERT: I 155 TRP cc_start: 0.5644 (m100) cc_final: 0.5433 (m100) REVERT: K 49 MET cc_start: 0.4171 (pmm) cc_final: 0.3696 (ppp) REVERT: O 55 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6767 (tm-30) REVERT: P 23 LYS cc_start: 0.6514 (tttp) cc_final: 0.6117 (tttp) REVERT: P 94 MET cc_start: 0.6236 (tmm) cc_final: 0.5574 (tmm) outliers start: 71 outliers final: 51 residues processed: 397 average time/residue: 0.5111 time to fit residues: 332.9016 Evaluate side-chains 376 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 323 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 334 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 351 optimal weight: 0.0070 chunk 195 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 424 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN C 300 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 39902 Z= 0.429 Angle : 0.648 9.025 54283 Z= 0.332 Chirality : 0.049 0.764 6202 Planarity : 0.005 0.055 6931 Dihedral : 5.702 58.622 6078 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 2.83 % Allowed : 13.56 % Favored : 83.61 % 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: -0.35 (0.12), residues: 4894 helix: 1.95 (0.20), residues: 700 sheet: 0.49 (0.13), residues: 1551 loop : -1.34 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 47 HIS 0.013 0.001 HIS I 101 PHE 0.031 0.002 PHE C 321 TYR 0.026 0.002 TYR L 49 ARG 0.010 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 334 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 116 CYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4996 (m) REVERT: A 143 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.2119 (m-80) REVERT: C 138 MET cc_start: 0.4053 (ptt) cc_final: 0.3703 (ttt) REVERT: D 90 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: D 184 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7707 (mmmm) REVERT: K 40 GLN cc_start: 0.6465 (tm130) cc_final: 0.5908 (tm-30) REVERT: K 49 MET cc_start: 0.4337 (OUTLIER) cc_final: 0.3924 (ppp) REVERT: P 94 MET cc_start: 0.6244 (tmm) cc_final: 0.5507 (tmm) REVERT: P 111 TRP cc_start: 0.7108 (OUTLIER) cc_final: 0.5959 (m-10) outliers start: 122 outliers final: 86 residues processed: 435 average time/residue: 0.5112 time to fit residues: 370.0805 Evaluate side-chains 419 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 326 time to evaluate : 4.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 536 THR 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 769 LYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 0.7980 chunk 425 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 473 optimal weight: 0.0970 chunk 392 optimal weight: 0.0670 chunk 219 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN B 171 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN F 6 GLN F 125 GLN J 90 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN P 6 GLN P 66 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 39902 Z= 0.142 Angle : 0.527 8.461 54283 Z= 0.270 Chirality : 0.045 0.672 6202 Planarity : 0.004 0.058 6931 Dihedral : 5.086 55.750 6078 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 1.69 % Allowed : 15.27 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4894 helix: 2.33 (0.20), residues: 698 sheet: 0.64 (0.13), residues: 1549 loop : -1.22 (0.11), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 155 HIS 0.008 0.001 HIS I 53 PHE 0.021 0.001 PHE B 77 TYR 0.038 0.001 TYR A 334 ARG 0.011 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 351 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4796 (m) REVERT: C 138 MET cc_start: 0.4015 (ptt) cc_final: 0.3630 (ttt) REVERT: H 150 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6877 (mtmm) REVERT: H 176 LEU cc_start: 0.6575 (mt) cc_final: 0.6211 (mt) REVERT: K 49 MET cc_start: 0.4263 (OUTLIER) cc_final: 0.3948 (ppp) REVERT: P 94 MET cc_start: 0.6123 (tmm) cc_final: 0.5500 (tmm) REVERT: P 111 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.6057 (m-10) outliers start: 73 outliers final: 52 residues processed: 408 average time/residue: 0.5165 time to fit residues: 348.7403 Evaluate side-chains 390 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 869 TRP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 345 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 471 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39902 Z= 0.279 Angle : 0.580 9.315 54283 Z= 0.296 Chirality : 0.046 0.666 6202 Planarity : 0.004 0.054 6931 Dihedral : 5.189 52.108 6078 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 2.53 % Allowed : 14.95 % Favored : 82.52 % 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: -0.13 (0.12), residues: 4894 helix: 2.27 (0.21), residues: 698 sheet: 0.62 (0.13), residues: 1560 loop : -1.24 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 155 HIS 0.009 0.001 HIS I 101 PHE 0.022 0.002 PHE C 321 TYR 0.029 0.001 TYR A 334 ARG 0.012 0.000 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 329 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 116 CYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4912 (m) REVERT: A 143 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.1917 (m-80) REVERT: A 1094 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: C 138 MET cc_start: 0.3927 (ptt) cc_final: 0.3646 (ttt) REVERT: D 184 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7620 (mmmm) REVERT: H 150 LYS cc_start: 0.7192 (mtpp) cc_final: 0.6890 (mtmm) REVERT: H 176 LEU cc_start: 0.6647 (mt) cc_final: 0.6426 (mt) REVERT: I 69 MET cc_start: 0.8567 (mtt) cc_final: 0.8285 (mtt) REVERT: K 49 MET cc_start: 0.4303 (pmm) cc_final: 0.3932 (ppp) REVERT: P 94 MET cc_start: 0.6189 (tmm) cc_final: 0.5581 (tmm) REVERT: P 111 TRP cc_start: 0.7094 (OUTLIER) cc_final: 0.6043 (m-10) outliers start: 109 outliers final: 82 residues processed: 418 average time/residue: 0.5014 time to fit residues: 345.9571 Evaluate side-chains 409 residues out of total 4317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 321 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 869 TRP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2221 > 50: distance: 88 - 92: 27.104 distance: 92 - 93: 21.294 distance: 93 - 94: 17.001 distance: 94 - 95: 34.463 distance: 94 - 96: 19.015 distance: 96 - 97: 17.549 distance: 97 - 98: 22.797 distance: 97 - 100: 11.658 distance: 98 - 99: 5.025 distance: 98 - 105: 25.247 distance: 100 - 101: 9.715 distance: 101 - 102: 20.433 distance: 102 - 103: 5.598 distance: 103 - 104: 49.539 distance: 105 - 106: 30.805 distance: 106 - 107: 20.459 distance: 107 - 108: 22.847 distance: 107 - 109: 52.499 distance: 109 - 110: 37.358 distance: 110 - 111: 37.327 distance: 110 - 113: 34.610 distance: 111 - 112: 6.802 distance: 111 - 121: 48.964 distance: 113 - 114: 38.860 distance: 114 - 115: 42.156 distance: 115 - 117: 5.481 distance: 116 - 118: 24.909 distance: 117 - 119: 23.496 distance: 118 - 119: 33.699 distance: 119 - 120: 26.611 distance: 121 - 122: 3.446 distance: 122 - 123: 21.286 distance: 122 - 125: 21.756 distance: 123 - 124: 26.067 distance: 123 - 131: 33.572 distance: 125 - 126: 19.430 distance: 126 - 127: 27.257 distance: 126 - 128: 37.569 distance: 127 - 129: 17.444 distance: 128 - 130: 27.731 distance: 129 - 130: 21.696 distance: 131 - 132: 46.089 distance: 132 - 133: 5.412 distance: 132 - 135: 6.395 distance: 133 - 134: 4.291 distance: 133 - 139: 41.489 distance: 135 - 136: 50.259 distance: 136 - 137: 27.266 distance: 136 - 138: 56.715 distance: 139 - 212: 29.096 distance: 140 - 141: 37.291 distance: 140 - 143: 20.946 distance: 141 - 142: 14.958 distance: 141 - 147: 9.288 distance: 142 - 209: 27.418 distance: 143 - 144: 38.297 distance: 144 - 145: 12.411 distance: 145 - 146: 5.231 distance: 147 - 148: 5.103 distance: 148 - 149: 42.456 distance: 148 - 151: 19.430 distance: 149 - 150: 12.445 distance: 149 - 153: 13.891 distance: 151 - 152: 41.896 distance: 153 - 154: 39.902 distance: 153 - 194: 36.461 distance: 154 - 155: 41.154 distance: 154 - 157: 50.369 distance: 155 - 156: 27.911 distance: 155 - 164: 54.494 distance: 156 - 191: 26.520 distance: 157 - 158: 32.828 distance: 158 - 159: 24.629 distance: 158 - 160: 13.548 distance: 159 - 161: 5.126 distance: 160 - 162: 12.994 distance: 161 - 163: 45.893 distance: 162 - 163: 25.488 distance: 164 - 165: 31.236 distance: 164 - 170: 7.555 distance: 165 - 166: 41.468 distance: 165 - 168: 20.610 distance: 166 - 167: 11.891 distance: 166 - 171: 28.920 distance: 168 - 169: 37.156