Starting phenix.real_space_refine on Fri Mar 22 15:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9h_8783/03_2024/5w9h_8783.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 180 5.16 5 C 21408 2.51 5 N 5538 2.21 5 O 6714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "r GLU 549": "OE1" <-> "OE2" Residue "r PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33840 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "p" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "q" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "r" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "J" 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: "K" 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: "L" 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: "M" 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: "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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: "c" 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: "d" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 16.70, per 1000 atoms: 0.49 Number of scatterers: 33840 At special positions: 0 Unit cell: (155.04, 153, 223.38, 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 180 16.00 O 6714 8.00 N 5538 7.00 C 21408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.13 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.05 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.04 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.04 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.21 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.02 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS p 30 " - pdb=" SG CYS p 195 " distance=2.04 Simple disulfide: pdb=" SG CYS p 176 " - pdb=" SG CYS p 214 " distance=2.06 Simple disulfide: pdb=" SG CYS p 185 " - pdb=" SG CYS p 237 " distance=2.09 Simple disulfide: pdb=" SG CYS p 339 " - pdb=" SG CYS p 349 " distance=2.04 Simple disulfide: pdb=" SG CYS p 383 " - pdb=" SG CYS p 407 " distance=2.35 Simple disulfide: pdb=" SG CYS p 425 " - pdb=" SG CYS p 478 " distance=2.02 Simple disulfide: pdb=" SG CYS p 437 " - pdb=" SG CYS p 585 " distance=2.19 Simple disulfide: pdb=" SG CYS p 503 " - pdb=" SG CYS p 526 " distance=2.02 Simple disulfide: pdb=" SG CYS p 603 " - pdb=" SG CYS p 654 " distance=1.85 Simple disulfide: pdb=" SG CYS p 620 " - pdb=" SG CYS p 650 " distance=2.32 Simple disulfide: pdb=" SG CYS p 679 " - pdb=" SG CYS p 713 " distance=2.03 Simple disulfide: pdb=" SG CYS p 727 " - pdb=" SG CYS p 736 " distance=2.08 Simple disulfide: pdb=" SG CYS q 30 " - pdb=" SG CYS q 195 " distance=2.04 Simple disulfide: pdb=" SG CYS q 176 " - pdb=" SG CYS q 214 " distance=2.04 Simple disulfide: pdb=" SG CYS q 185 " - pdb=" SG CYS q 237 " distance=2.03 Simple disulfide: pdb=" SG CYS q 339 " - pdb=" SG CYS q 349 " distance=2.03 Simple disulfide: pdb=" SG CYS q 383 " - pdb=" SG CYS q 407 " distance=2.59 Simple disulfide: pdb=" SG CYS q 425 " - pdb=" SG CYS q 478 " distance=2.14 Simple disulfide: pdb=" SG CYS q 437 " - pdb=" SG CYS q 585 " distance=2.14 Simple disulfide: pdb=" SG CYS q 503 " - pdb=" SG CYS q 526 " distance=2.02 Simple disulfide: pdb=" SG CYS q 603 " - pdb=" SG CYS q 654 " distance=2.05 Simple disulfide: pdb=" SG CYS q 679 " - pdb=" SG CYS q 713 " distance=2.03 Simple disulfide: pdb=" SG CYS q 727 " - pdb=" SG CYS q 736 " distance=2.02 Simple disulfide: pdb=" SG CYS r 30 " - pdb=" SG CYS r 195 " distance=2.05 Simple disulfide: pdb=" SG CYS r 176 " - pdb=" SG CYS r 214 " distance=2.10 Simple disulfide: pdb=" SG CYS r 185 " - pdb=" SG CYS r 237 " distance=2.08 Simple disulfide: pdb=" SG CYS r 339 " - pdb=" SG CYS r 349 " distance=2.04 Simple disulfide: pdb=" SG CYS r 383 " - pdb=" SG CYS r 407 " distance=1.94 Simple disulfide: pdb=" SG CYS r 425 " - pdb=" SG CYS r 478 " distance=2.01 Simple disulfide: pdb=" SG CYS r 437 " - pdb=" SG CYS r 585 " distance=2.06 Simple disulfide: pdb=" SG CYS r 503 " - pdb=" SG CYS r 526 " distance=2.02 Simple disulfide: pdb=" SG CYS r 603 " - pdb=" SG CYS r 654 " distance=2.20 Simple disulfide: pdb=" SG CYS r 620 " - pdb=" SG CYS r 650 " distance=2.13 Simple disulfide: pdb=" SG CYS r 679 " - pdb=" SG CYS r 713 " distance=2.03 Simple disulfide: pdb=" SG CYS r 727 " - pdb=" SG CYS r 736 " distance=2.02 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG D1401 " - " ASN D 774 " " NAG G1401 " - " ASN G 774 " " NAG J 1 " - " ASN A1176 " " NAG K 1 " - " ASN A1213 " " NAG L 1 " - " ASN A 785 " " NAG M 1 " - " ASN A 870 " " NAG N 1 " - " ASN D 785 " " NAG O 1 " - " ASN D1213 " " NAG P 1 " - " ASN D 870 " " NAG Q 1 " - " ASN D1176 " " NAG R 1 " - " ASN G 785 " " NAG S 1 " - " ASN G1176 " " NAG T 1 " - " ASN G 870 " " NAG U 1 " - " ASN G1213 " " NAG V 1 " - " ASN p 244 " " NAG W 1 " - " ASN p 66 " " NAG X 1 " - " ASN p 125 " " NAG Y 1 " - " ASN q 66 " " NAG Z 1 " - " ASN q 125 " " NAG a 1 " - " ASN q 244 " " NAG b 1 " - " ASN r 125 " " NAG c 1 " - " ASN r 66 " " NAG d 1 " - " ASN r 244 " " NAG p1401 " - " ASN p 236 " " NAG p1402 " - " ASN p 104 " " NAG p1403 " - " ASN p 166 " " NAG p1404 " - " ASN p 155 " " NAG p1405 " - " ASN p 719 " " NAG p1406 " - " ASN p 619 " " NAG q1401 " - " ASN q 166 " " NAG q1402 " - " ASN q 236 " " NAG q1403 " - " ASN q 619 " " NAG q1404 " - " ASN q 719 " " NAG q1405 " - " ASN q 104 " " NAG q1406 " - " ASN q 155 " " NAG r1401 " - " ASN r 719 " " NAG r1402 " - " ASN r 104 " " NAG r1403 " - " ASN r 166 " " NAG r1404 " - " ASN r 155 " " NAG r1405 " - " ASN r 619 " " NAG r1406 " - " ASN r 236 " Time building additional restraints: 13.72 Conformation dependent library (CDL) restraints added in 5.9 seconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 75 sheets defined 23.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.158A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.883A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.724A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.545A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.852A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 822 removed outlier: 3.740A pdb=" N ARG D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.791A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 4.670A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1039 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 4.075A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.652A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.883A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 912 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.600A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.553A pdb=" N LEU G1033 " --> pdb=" O ASN G1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.257A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'p' and resid 37 through 41 Processing helix chain 'p' and resid 49 through 53 Processing helix chain 'p' and resid 104 through 108 Processing helix chain 'p' and resid 133 through 137 Processing helix chain 'p' and resid 222 through 230 Processing helix chain 'p' and resid 303 through 307 removed outlier: 3.789A pdb=" N ARG p 307 " --> pdb=" O GLN p 304 " (cutoff:3.500A) Processing helix chain 'p' and resid 342 through 351 Processing helix chain 'p' and resid 385 through 390 removed outlier: 3.510A pdb=" N SER p 390 " --> pdb=" O PRO p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 395 through 399 removed outlier: 3.656A pdb=" N PHE p 399 " --> pdb=" O VAL p 396 " (cutoff:3.500A) Processing helix chain 'p' and resid 410 through 415 Processing helix chain 'p' and resid 416 through 418 No H-bonds generated for 'chain 'p' and resid 416 through 418' Processing helix chain 'p' and resid 429 through 436 removed outlier: 3.898A pdb=" N ALA p 434 " --> pdb=" O PRO p 430 " (cutoff:3.500A) Processing helix chain 'p' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER p 454 " --> pdb=" O SER p 451 " (cutoff:3.500A) Processing helix chain 'p' and resid 462 through 468 Processing helix chain 'p' and resid 524 through 529 Processing helix chain 'p' and resid 546 through 550 Processing helix chain 'p' and resid 675 through 678 removed outlier: 3.597A pdb=" N ALA p 678 " --> pdb=" O GLY p 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 675 through 678' Processing helix chain 'p' and resid 694 through 702 removed outlier: 3.569A pdb=" N LYS p 698 " --> pdb=" O ARG p 694 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG p 700 " --> pdb=" O MET p 696 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 41 removed outlier: 4.150A pdb=" N ASP q 41 " --> pdb=" O THR q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 53 Processing helix chain 'q' and resid 104 through 108 Processing helix chain 'q' and resid 133 through 137 Processing helix chain 'q' and resid 222 through 230 Processing helix chain 'q' and resid 303 through 307 removed outlier: 3.945A pdb=" N ARG q 307 " --> pdb=" O GLN q 304 " (cutoff:3.500A) Processing helix chain 'q' and resid 342 through 351 Processing helix chain 'q' and resid 385 through 390 removed outlier: 3.630A pdb=" N SER q 390 " --> pdb=" O PRO q 387 " (cutoff:3.500A) Processing helix chain 'q' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU q 414 " --> pdb=" O ASN q 410 " (cutoff:3.500A) Processing helix chain 'q' and resid 431 through 436 Processing helix chain 'q' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER q 454 " --> pdb=" O SER q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 462 through 468 Processing helix chain 'q' and resid 524 through 529 Processing helix chain 'q' and resid 676 through 678 No H-bonds generated for 'chain 'q' and resid 676 through 678' Processing helix chain 'q' and resid 694 through 702 removed outlier: 3.630A pdb=" N LYS q 698 " --> pdb=" O ARG q 694 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG q 700 " --> pdb=" O MET q 696 " (cutoff:3.500A) Processing helix chain 'r' and resid 37 through 41 Processing helix chain 'r' and resid 49 through 53 Processing helix chain 'r' and resid 104 through 108 Processing helix chain 'r' and resid 133 through 137 Processing helix chain 'r' and resid 222 through 230 Processing helix chain 'r' and resid 268 through 273 removed outlier: 4.130A pdb=" N LEU r 273 " --> pdb=" O ARG r 269 " (cutoff:3.500A) Processing helix chain 'r' and resid 303 through 307 removed outlier: 3.852A pdb=" N ARG r 307 " --> pdb=" O GLN r 304 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 351 Processing helix chain 'r' and resid 385 through 389 Processing helix chain 'r' and resid 410 through 416 removed outlier: 4.007A pdb=" N LEU r 414 " --> pdb=" O ASN r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 429 through 436 Processing helix chain 'r' and resid 449 through 456 removed outlier: 4.518A pdb=" N SER r 454 " --> pdb=" O SER r 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 462 through 468 Processing helix chain 'r' and resid 524 through 529 Processing helix chain 'r' and resid 546 through 550 Processing helix chain 'r' and resid 675 through 678 removed outlier: 3.542A pdb=" N ALA r 678 " --> pdb=" O GLY r 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 675 through 678' Processing helix chain 'r' and resid 694 through 702 removed outlier: 3.602A pdb=" N LYS r 698 " --> pdb=" O ARG r 694 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG r 700 " --> pdb=" O MET r 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'p' and resid 719 through 724 removed outlier: 7.313A pdb=" N LEU A 759 " --> pdb=" O SER p 720 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU p 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.693A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 6.030A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.498A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.498A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.495A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.913A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'q' and resid 719 through 724 removed outlier: 7.307A pdb=" N LEU D 759 " --> pdb=" O SER q 720 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU q 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.632A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.942A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.329A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.270A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.270A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.173A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'r' and resid 719 through 724 removed outlier: 7.265A pdb=" N LEU G 759 " --> pdb=" O SER r 720 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU r 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY r 732 " --> pdb=" O LEU r 735 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA r 737 " --> pdb=" O PRO r 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.962A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 3.605A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.319A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 96 through 99 removed outlier: 5.350A pdb=" N TYR H 97 " --> pdb=" O ALA H 100D" (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA H 100D" --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL H 99 " --> pdb=" O VAL H 100B" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.718A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'p' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'p' and resid 68 through 75 removed outlier: 3.690A pdb=" N ARG p 335 " --> pdb=" O ASP p 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'p' and resid 83 through 85 removed outlier: 6.415A pdb=" N SER p 267 " --> pdb=" O GLN p 280 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN p 280 " --> pdb=" O SER p 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'p' and resid 88 through 89 removed outlier: 7.534A pdb=" N SER p 88 " --> pdb=" O ILE p 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'p' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'p' and resid 110 through 111 removed outlier: 4.432A pdb=" N ALA p 146 " --> pdb=" O ILE p 296 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU p 180 " --> pdb=" O THR p 242 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR p 242 " --> pdb=" O LEU p 180 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA p 182 " --> pdb=" O MET p 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET p 240 " --> pdb=" O ALA p 182 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR p 184 " --> pdb=" O THR p 238 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE p 186 " --> pdb=" O ASN p 236 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN p 236 " --> pdb=" O ILE p 186 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU p 188 " --> pdb=" O LEU p 234 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU p 234 " --> pdb=" O GLU p 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'p' and resid 126 through 127 removed outlier: 4.612A pdb=" N SER p 126 " --> pdb=" O ILE p 140 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA p 309 " --> pdb=" O THR p 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'p' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'p' and resid 359 through 366 removed outlier: 4.314A pdb=" N VAL p 659 " --> pdb=" O VAL p 363 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER p 365 " --> pdb=" O VAL p 657 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL p 657 " --> pdb=" O SER p 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'p' and resid 371 through 376 removed outlier: 4.656A pdb=" N GLU p 605 " --> pdb=" O GLY p 372 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL p 604 " --> pdb=" O GLY p 615 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY p 615 " --> pdb=" O VAL p 604 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'p' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR p 483 " --> pdb=" O VAL p 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL p 420 " --> pdb=" O THR p 483 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'p' and resid 513 through 515 removed outlier: 5.400A pdb=" N SER p 498 " --> pdb=" O VAL p 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL p 561 " --> pdb=" O SER p 498 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE p 500 " --> pdb=" O SER p 559 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER p 559 " --> pdb=" O ILE p 500 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'p' and resid 617 through 619 removed outlier: 4.907A pdb=" N VAL p 639 " --> pdb=" O LEU p 651 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL p 631 " --> pdb=" O VAL p 639 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'q' and resid 33 through 35 Processing sheet with id=AF3, first strand: chain 'q' and resid 68 through 72 removed outlier: 3.670A pdb=" N ARG q 335 " --> pdb=" O ASP q 326 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'q' and resid 75 through 76 Processing sheet with id=AF5, first strand: chain 'q' and resid 75 through 76 removed outlier: 6.509A pdb=" N SER q 267 " --> pdb=" O GLN q 280 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN q 280 " --> pdb=" O SER q 267 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'q' and resid 88 through 89 removed outlier: 7.572A pdb=" N SER q 88 " --> pdb=" O ILE q 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'q' and resid 92 through 93 Processing sheet with id=AF8, first strand: chain 'q' and resid 110 through 111 removed outlier: 4.462A pdb=" N ALA q 146 " --> pdb=" O ILE q 296 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS q 185 " --> pdb=" O THR q 168 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU q 180 " --> pdb=" O THR q 242 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR q 242 " --> pdb=" O LEU q 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA q 182 " --> pdb=" O MET q 240 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET q 240 " --> pdb=" O ALA q 182 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR q 184 " --> pdb=" O THR q 238 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE q 186 " --> pdb=" O ASN q 236 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN q 236 " --> pdb=" O ILE q 186 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU q 188 " --> pdb=" O LEU q 234 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU q 234 " --> pdb=" O GLU q 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 126 through 127 removed outlier: 4.435A pdb=" N SER q 126 " --> pdb=" O ILE q 140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA q 309 " --> pdb=" O THR q 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'q' and resid 153 through 154 Processing sheet with id=AG2, first strand: chain 'q' and resid 359 through 366 removed outlier: 4.164A pdb=" N VAL q 659 " --> pdb=" O VAL q 363 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER q 365 " --> pdb=" O VAL q 657 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL q 657 " --> pdb=" O SER q 365 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY q 675 " --> pdb=" O PRO q 658 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N CYS q 713 " --> pdb=" O PHE q 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 374 through 375 Processing sheet with id=AG4, first strand: chain 'q' and resid 381 through 382 removed outlier: 6.120A pdb=" N VAL q 381 " --> pdb=" O ASN q 408 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N CYS q 407 " --> pdb=" O CYS q 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'q' and resid 400 through 404 removed outlier: 3.565A pdb=" N LYS q 400 " --> pdb=" O TYR q 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR q 483 " --> pdb=" O VAL q 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL q 420 " --> pdb=" O THR q 483 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER q 498 " --> pdb=" O VAL q 561 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL q 561 " --> pdb=" O SER q 498 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE q 500 " --> pdb=" O SER q 559 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER q 559 " --> pdb=" O ILE q 500 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'q' and resid 617 through 619 removed outlier: 5.244A pdb=" N VAL q 639 " --> pdb=" O LEU q 651 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL q 631 " --> pdb=" O VAL q 639 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'r' and resid 33 through 35 Processing sheet with id=AG9, first strand: chain 'r' and resid 68 through 72 removed outlier: 3.709A pdb=" N ARG r 335 " --> pdb=" O ASP r 326 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'r' and resid 83 through 85 removed outlier: 6.434A pdb=" N SER r 267 " --> pdb=" O GLN r 280 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN r 280 " --> pdb=" O SER r 267 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'r' and resid 88 through 89 removed outlier: 7.505A pdb=" N SER r 88 " --> pdb=" O ILE r 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 92 through 93 Processing sheet with id=AH4, first strand: chain 'r' and resid 110 through 111 removed outlier: 4.502A pdb=" N ALA r 146 " --> pdb=" O ILE r 296 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU r 180 " --> pdb=" O THR r 242 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR r 242 " --> pdb=" O LEU r 180 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA r 182 " --> pdb=" O MET r 240 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET r 240 " --> pdb=" O ALA r 182 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR r 184 " --> pdb=" O THR r 238 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE r 186 " --> pdb=" O ASN r 236 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN r 236 " --> pdb=" O ILE r 186 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'r' and resid 126 through 127 removed outlier: 4.356A pdb=" N SER r 126 " --> pdb=" O ILE r 140 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA r 309 " --> pdb=" O THR r 139 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'r' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'r' and resid 359 through 366 removed outlier: 4.397A pdb=" N VAL r 659 " --> pdb=" O VAL r 363 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER r 365 " --> pdb=" O VAL r 657 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL r 657 " --> pdb=" O SER r 365 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'r' and resid 371 through 375 removed outlier: 7.404A pdb=" N SER r 371 " --> pdb=" O GLU r 605 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER r 607 " --> pdb=" O SER r 371 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N SER r 373 " --> pdb=" O SER r 607 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'r' and resid 381 through 382 removed outlier: 6.416A pdb=" N VAL r 381 " --> pdb=" O ASN r 408 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS r 407 " --> pdb=" O CYS r 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'r' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS r 400 " --> pdb=" O TYR r 445 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR r 483 " --> pdb=" O VAL r 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL r 420 " --> pdb=" O THR r 483 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'r' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER r 498 " --> pdb=" O VAL r 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL r 561 " --> pdb=" O SER r 498 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE r 500 " --> pdb=" O SER r 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER r 559 " --> pdb=" O ILE r 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'r' and resid 617 through 620 removed outlier: 4.428A pdb=" N TYR r 648 " --> pdb=" O CYS r 620 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL r 639 " --> pdb=" O LEU r 651 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL r 631 " --> pdb=" O VAL r 639 " (cutoff:3.500A) 1266 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.56 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6079 1.32 - 1.46: 12659 1.46 - 1.60: 15632 1.60 - 1.74: 1 1.74 - 1.88: 246 Bond restraints: 34617 Sorted by residual: bond pdb=" CA VAL r 584 " pdb=" C VAL r 584 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.23e-02 6.61e+03 5.22e+01 bond pdb=" CA CYS p 437 " pdb=" C CYS p 437 " ideal model delta sigma weight residual 1.523 1.608 -0.085 1.30e-02 5.92e+03 4.26e+01 bond pdb=" N CYS p 185 " pdb=" CA CYS p 185 " ideal model delta sigma weight residual 1.455 1.530 -0.075 1.25e-02 6.40e+03 3.60e+01 bond pdb=" C CYS r 437 " pdb=" O CYS r 437 " ideal model delta sigma weight residual 1.235 1.301 -0.067 1.18e-02 7.18e+03 3.19e+01 bond pdb=" C1 NAG D1401 " pdb=" O5 NAG D1401 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 34612 not shown) Histogram of bond angle deviations from ideal: 94.17 - 103.51: 312 103.51 - 112.86: 18083 112.86 - 122.21: 22739 122.21 - 131.56: 5875 131.56 - 140.90: 64 Bond angle restraints: 47073 Sorted by residual: angle pdb=" N GLN r 688 " pdb=" CA GLN r 688 " pdb=" C GLN r 688 " ideal model delta sigma weight residual 111.28 123.29 -12.01 1.09e+00 8.42e-01 1.22e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.00 -7.34 7.20e-01 1.93e+00 1.04e+02 angle pdb=" C THR G 961 " pdb=" N ALA G 962 " pdb=" CA ALA G 962 " ideal model delta sigma weight residual 121.54 140.90 -19.36 1.91e+00 2.74e-01 1.03e+02 angle pdb=" C LEU q 284 " pdb=" N PRO q 285 " pdb=" CA PRO q 285 " ideal model delta sigma weight residual 119.56 129.26 -9.70 1.01e+00 9.80e-01 9.21e+01 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.55 -6.89 7.20e-01 1.93e+00 9.15e+01 ... (remaining 47068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 20723 23.68 - 47.36: 489 47.36 - 71.04: 195 71.04 - 94.72: 28 94.72 - 118.40: 24 Dihedral angle restraints: 21459 sinusoidal: 9069 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 170.28 -77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.03 -75.03 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.41 -74.41 1 1.00e+01 1.00e-02 7.02e+01 ... (remaining 21456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 5377 0.296 - 0.591: 20 0.591 - 0.887: 5 0.887 - 1.182: 3 1.182 - 1.478: 1 Chirality restraints: 5406 Sorted by residual: chirality pdb=" C1 NAG p1402 " pdb=" ND2 ASN p 104 " pdb=" C2 NAG p1402 " pdb=" O5 NAG p1402 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN r 66 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN G 870 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 5403 not shown) Planarity restraints: 6066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN q 166 " -0.172 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" CG ASN q 166 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN q 166 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN q 166 " 0.264 2.00e-02 2.50e+03 pdb=" C1 NAG q1401 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D1213 " 0.045 2.00e-02 2.50e+03 5.22e-02 3.41e+01 pdb=" CG ASN D1213 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN D1213 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D1213 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 806 " 0.026 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" C CYS D 806 " -0.089 2.00e-02 2.50e+03 pdb=" O CYS D 806 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 807 " 0.030 2.00e-02 2.50e+03 ... (remaining 6063 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 17 2.00 - 2.73: 3837 2.73 - 3.45: 47460 3.45 - 4.18: 83548 4.18 - 4.90: 140158 Nonbonded interactions: 275020 Sorted by model distance: nonbonded pdb=" CG2 VAL p 381 " pdb=" ND2 ASN p 408 " model vdw 1.280 3.540 nonbonded pdb=" OH TYR D 905 " pdb=" CA PRO D 936 " model vdw 1.336 3.470 nonbonded pdb=" CD1 LEU D 773 " pdb=" O TYR D 777 " model vdw 1.441 3.460 nonbonded pdb=" OH TYR G 905 " pdb=" O VAL G 934 " model vdw 1.486 2.440 nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.506 3.470 ... (remaining 275015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.980 Check model and map are aligned: 0.460 Set scattering table: 0.310 Process input model: 89.100 Find NCS groups from input model: 2.160 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.013 0.111 34617 Z= 0.874 Angle : 1.704 19.362 47073 Z= 1.144 Chirality : 0.090 1.478 5406 Planarity : 0.011 0.104 6024 Dihedral : 12.297 118.402 13389 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.62 % Favored : 95.77 % Rotamer: Outliers : 0.16 % Allowed : 0.74 % Favored : 99.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.13), residues: 4227 helix: -0.42 (0.16), residues: 688 sheet: 0.94 (0.15), residues: 948 loop : 1.86 (0.13), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.007 TRP H 47 HIS 0.007 0.002 HIS A1138 PHE 0.030 0.004 PHE I 32 TYR 0.057 0.006 TYR q 469 ARG 0.005 0.001 ARG p 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 791 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 877 VAL cc_start: 0.6917 (t) cc_final: 0.5742 (p) REVERT: A 924 ILE cc_start: 0.6273 (mt) cc_final: 0.5933 (pt) REVERT: A 1105 GLU cc_start: 0.7898 (tt0) cc_final: 0.7363 (tt0) REVERT: B 28 THR cc_start: 0.9338 (m) cc_final: 0.9032 (p) REVERT: B 45 LEU cc_start: 0.8562 (mp) cc_final: 0.8329 (mp) REVERT: D 816 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8199 (tptm) REVERT: D 911 ASP cc_start: 0.7791 (m-30) cc_final: 0.7366 (t0) REVERT: D 927 GLN cc_start: 0.8410 (tt0) cc_final: 0.7898 (tt0) REVERT: D 1097 GLN cc_start: 0.8253 (tp40) cc_final: 0.7688 (tm-30) REVERT: D 1101 ASP cc_start: 0.8313 (m-30) cc_final: 0.7988 (m-30) REVERT: D 1222 LEU cc_start: 0.9080 (tp) cc_final: 0.8760 (pt) REVERT: E 51 PHE cc_start: 0.8261 (t80) cc_final: 0.7793 (t80) REVERT: E 82 LEU cc_start: 0.7052 (tt) cc_final: 0.6652 (tt) REVERT: F 33 MET cc_start: 0.8734 (tpp) cc_final: 0.8359 (tpp) REVERT: F 73 LEU cc_start: 0.8178 (tp) cc_final: 0.7242 (tp) REVERT: G 913 MET cc_start: 0.6240 (ttt) cc_final: 0.6025 (ttt) REVERT: G 938 LEU cc_start: 0.9344 (tp) cc_final: 0.8717 (tp) REVERT: G 939 MET cc_start: 0.7259 (mtp) cc_final: 0.6369 (mtp) REVERT: G 1079 ASN cc_start: 0.8834 (m-40) cc_final: 0.8299 (t0) REVERT: p 147 PHE cc_start: 0.8250 (m-80) cc_final: 0.7323 (m-80) REVERT: p 347 LEU cc_start: 0.9271 (tp) cc_final: 0.8991 (tt) REVERT: p 523 TYR cc_start: 0.6091 (m-80) cc_final: 0.5843 (m-80) REVERT: q 563 MET cc_start: 0.6688 (ptt) cc_final: 0.6211 (tpt) REVERT: q 728 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7620 (tptt) REVERT: r 54 ASP cc_start: 0.8379 (m-30) cc_final: 0.7984 (m-30) REVERT: r 218 ASN cc_start: 0.8822 (t0) cc_final: 0.8508 (p0) REVERT: r 278 MET cc_start: 0.8992 (mmm) cc_final: 0.8485 (mmp) REVERT: r 356 VAL cc_start: 0.9062 (t) cc_final: 0.8798 (t) REVERT: r 401 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6857 (mmt90) REVERT: r 402 LEU cc_start: 0.7926 (mt) cc_final: 0.7639 (mp) REVERT: r 436 ASN cc_start: 0.7818 (m-40) cc_final: 0.7573 (t0) REVERT: r 445 TYR cc_start: 0.5082 (p90) cc_final: 0.4823 (p90) REVERT: r 505 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7451 (ptm160) REVERT: r 587 LYS cc_start: 0.6801 (tttt) cc_final: 0.6455 (pttt) REVERT: r 592 ASN cc_start: 0.7337 (m-40) cc_final: 0.6962 (p0) REVERT: r 663 TYR cc_start: 0.8754 (t80) cc_final: 0.8319 (t80) REVERT: r 664 ASP cc_start: 0.7490 (t0) cc_final: 0.7120 (t0) outliers start: 6 outliers final: 1 residues processed: 795 average time/residue: 0.4686 time to fit residues: 589.6526 Evaluate side-chains 357 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 629 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 381 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN D 808 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1208 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN G 836 HIS G1104 ASN G1132 ASN G1217 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN H 61 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 261 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 GLN q 107 GLN ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 377 GLN q 398 ASN r 98 GLN r 280 GLN ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 637 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34617 Z= 0.333 Angle : 0.826 10.977 47073 Z= 0.434 Chirality : 0.053 0.484 5406 Planarity : 0.007 0.096 6024 Dihedral : 10.469 108.874 5956 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.60 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 8.29 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.13), residues: 4227 helix: 1.02 (0.19), residues: 701 sheet: 0.47 (0.15), residues: 981 loop : 0.94 (0.13), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 35 HIS 0.009 0.002 HIS p 670 PHE 0.030 0.002 PHE r 385 TYR 0.028 0.002 TYR A 905 ARG 0.007 0.001 ARG r 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 410 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 THR cc_start: 0.9212 (m) cc_final: 0.8890 (p) REVERT: B 45 LEU cc_start: 0.8403 (mp) cc_final: 0.8107 (mt) REVERT: D 843 ASP cc_start: 0.8341 (m-30) cc_final: 0.7543 (t0) REVERT: D 911 ASP cc_start: 0.7594 (m-30) cc_final: 0.7381 (t0) REVERT: D 927 GLN cc_start: 0.8233 (tt0) cc_final: 0.7053 (pt0) REVERT: D 938 LEU cc_start: 0.9061 (tp) cc_final: 0.8453 (tp) REVERT: D 1078 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8822 (tp) REVERT: D 1097 GLN cc_start: 0.8486 (tp40) cc_final: 0.7904 (tm-30) REVERT: D 1101 ASP cc_start: 0.8339 (m-30) cc_final: 0.7935 (m-30) REVERT: D 1222 LEU cc_start: 0.9068 (tp) cc_final: 0.8812 (pt) REVERT: E 61 GLN cc_start: 0.7305 (tp40) cc_final: 0.7070 (tp40) REVERT: F 73 LEU cc_start: 0.7987 (tp) cc_final: 0.7479 (tp) REVERT: G 933 LYS cc_start: 0.8021 (tppt) cc_final: 0.7700 (tptp) REVERT: G 1079 ASN cc_start: 0.8699 (m-40) cc_final: 0.8482 (t0) REVERT: G 1104 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (t0) REVERT: p 147 PHE cc_start: 0.8116 (m-80) cc_final: 0.7776 (m-80) REVERT: p 330 ASP cc_start: 0.8238 (p0) cc_final: 0.8030 (p0) REVERT: p 696 MET cc_start: 0.3459 (ptm) cc_final: 0.3178 (ppp) REVERT: q 149 LEU cc_start: 0.8825 (mm) cc_final: 0.8533 (mm) REVERT: q 563 MET cc_start: 0.6628 (ptt) cc_final: 0.6097 (tpt) REVERT: q 728 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7817 (tptt) REVERT: r 436 ASN cc_start: 0.7635 (m-40) cc_final: 0.7331 (t0) REVERT: r 629 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (mmp80) REVERT: r 663 TYR cc_start: 0.8875 (t80) cc_final: 0.8574 (t80) outliers start: 91 outliers final: 54 residues processed: 474 average time/residue: 0.4535 time to fit residues: 353.5341 Evaluate side-chains 362 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 305 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1104 ASN Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 240 MET Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 445 TYR Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 108 ASP Chi-restraints excluded: chain r residue 136 THR Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 629 ARG Chi-restraints excluded: chain r residue 676 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 chunk 412 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN B 1 GLN B 58 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D 927 GLN D1056 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 772 GLN G1104 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 421 ASN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 GLN ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34617 Z= 0.289 Angle : 0.739 10.824 47073 Z= 0.382 Chirality : 0.050 0.430 5406 Planarity : 0.006 0.090 6024 Dihedral : 9.590 106.030 5956 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 2.55 % Allowed : 9.96 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4227 helix: 1.06 (0.19), residues: 710 sheet: 0.40 (0.15), residues: 1042 loop : 0.42 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 35 HIS 0.007 0.001 HIS A1122 PHE 0.025 0.002 PHE I 98 TYR 0.029 0.002 TYR A 905 ARG 0.007 0.001 ARG r 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 347 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.8443 (mtp) cc_final: 0.8098 (ptp) REVERT: A 967 PHE cc_start: 0.8354 (t80) cc_final: 0.8041 (t80) REVERT: B 45 LEU cc_start: 0.8338 (mp) cc_final: 0.8107 (mp) REVERT: C 32 PHE cc_start: 0.7886 (m-80) cc_final: 0.7588 (m-10) REVERT: D 816 LYS cc_start: 0.8468 (tptt) cc_final: 0.7815 (tptm) REVERT: D 927 GLN cc_start: 0.8310 (tt0) cc_final: 0.6880 (pt0) REVERT: D 1097 GLN cc_start: 0.8516 (tp40) cc_final: 0.8310 (tm-30) REVERT: D 1222 LEU cc_start: 0.9038 (tp) cc_final: 0.8778 (pt) REVERT: E 80 MET cc_start: 0.7946 (tmm) cc_final: 0.7459 (tmm) REVERT: F 15 LEU cc_start: 0.7459 (tp) cc_final: 0.6713 (mp) REVERT: F 38 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: F 73 LEU cc_start: 0.8096 (tp) cc_final: 0.7578 (tp) REVERT: F 86 TYR cc_start: 0.7967 (m-80) cc_final: 0.7748 (m-80) REVERT: G 1039 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8380 (tp30) REVERT: G 1079 ASN cc_start: 0.8775 (m-40) cc_final: 0.8459 (t0) REVERT: G 1180 ILE cc_start: 0.9422 (mp) cc_final: 0.8848 (tt) REVERT: H 39 GLN cc_start: 0.8214 (tt0) cc_final: 0.7545 (tt0) REVERT: H 81 GLU cc_start: 0.8395 (tt0) cc_final: 0.7776 (tp30) REVERT: H 85 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8199 (mp0) REVERT: p 147 PHE cc_start: 0.8327 (m-80) cc_final: 0.7995 (m-80) REVERT: p 332 TYR cc_start: 0.8465 (m-80) cc_final: 0.8081 (m-80) REVERT: p 563 MET cc_start: 0.3375 (ptp) cc_final: 0.2871 (tpp) REVERT: q 148 MET cc_start: 0.8550 (ttt) cc_final: 0.7933 (tmm) REVERT: q 149 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8524 (mt) REVERT: q 324 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9003 (mm) REVERT: q 728 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7879 (tptt) REVERT: r 288 ASP cc_start: 0.7092 (t0) cc_final: 0.6640 (t0) REVERT: r 663 TYR cc_start: 0.8955 (t80) cc_final: 0.8594 (t80) outliers start: 93 outliers final: 62 residues processed: 416 average time/residue: 0.4148 time to fit residues: 288.4733 Evaluate side-chains 366 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 240 MET Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 324 LEU Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 136 THR Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 676 SER Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 256 optimal weight: 6.9990 chunk 383 optimal weight: 0.0980 chunk 405 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 987 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 819 GLN ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN D1119 GLN D1212 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 89 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 521 ASN r 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34617 Z= 0.220 Angle : 0.694 13.159 47073 Z= 0.349 Chirality : 0.050 0.614 5406 Planarity : 0.005 0.074 6024 Dihedral : 8.762 105.730 5952 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 2.63 % Allowed : 10.67 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4227 helix: 1.21 (0.20), residues: 719 sheet: 0.40 (0.15), residues: 1062 loop : 0.18 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 35 HIS 0.006 0.001 HIS G1122 PHE 0.026 0.001 PHE B 63 TYR 0.028 0.001 TYR A 905 ARG 0.007 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 341 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.8374 (mtp) cc_final: 0.8055 (ptp) REVERT: A 782 ILE cc_start: 0.9151 (mt) cc_final: 0.8856 (mt) REVERT: A 842 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7816 (tp40) REVERT: A 967 PHE cc_start: 0.8356 (t80) cc_final: 0.8019 (t80) REVERT: C 22 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7705 (p) REVERT: C 32 PHE cc_start: 0.7957 (m-80) cc_final: 0.7692 (m-10) REVERT: D 816 LYS cc_start: 0.8510 (tptt) cc_final: 0.8269 (tptm) REVERT: D 843 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7807 (t70) REVERT: D 891 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7948 (tt0) REVERT: D 927 GLN cc_start: 0.8306 (tt0) cc_final: 0.8050 (tt0) REVERT: D 1222 LEU cc_start: 0.9021 (tp) cc_final: 0.8771 (pt) REVERT: E 61 GLN cc_start: 0.7436 (tp40) cc_final: 0.7139 (tp40) REVERT: E 62 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7767 (mmtm) REVERT: F 15 LEU cc_start: 0.7558 (tp) cc_final: 0.6902 (mp) REVERT: F 27 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8282 (tm-30) REVERT: F 73 LEU cc_start: 0.8118 (tp) cc_final: 0.7897 (tp) REVERT: F 86 TYR cc_start: 0.8071 (m-80) cc_final: 0.7862 (m-80) REVERT: F 87 PHE cc_start: 0.7970 (m-80) cc_final: 0.7658 (m-80) REVERT: G 757 MET cc_start: 0.8384 (mmt) cc_final: 0.8164 (mmp) REVERT: G 933 LYS cc_start: 0.7607 (tptp) cc_final: 0.7384 (tptp) REVERT: G 1039 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8349 (tp30) REVERT: G 1079 ASN cc_start: 0.8788 (m-40) cc_final: 0.8470 (t0) REVERT: G 1180 ILE cc_start: 0.9373 (mp) cc_final: 0.8792 (tt) REVERT: H 39 GLN cc_start: 0.8187 (tt0) cc_final: 0.7823 (tt0) REVERT: H 81 GLU cc_start: 0.8522 (tt0) cc_final: 0.7844 (tp30) REVERT: H 85 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8277 (mp0) REVERT: p 330 ASP cc_start: 0.8138 (p0) cc_final: 0.7866 (p0) REVERT: p 332 TYR cc_start: 0.8222 (m-80) cc_final: 0.7946 (m-80) REVERT: p 563 MET cc_start: 0.3448 (ptp) cc_final: 0.2945 (tpp) REVERT: q 148 MET cc_start: 0.8531 (ttt) cc_final: 0.7982 (tmm) REVERT: q 149 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8744 (mm) REVERT: q 333 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (mm) REVERT: q 728 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7880 (tptt) REVERT: r 288 ASP cc_start: 0.7207 (t0) cc_final: 0.6732 (t0) REVERT: r 346 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: r 663 TYR cc_start: 0.8923 (t80) cc_final: 0.8597 (t80) outliers start: 96 outliers final: 70 residues processed: 412 average time/residue: 0.4410 time to fit residues: 307.8532 Evaluate side-chains 379 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 304 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1181 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 149 LEU Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 240 MET Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 472 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain r residue 136 THR Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 364 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 GLN E 1 GLN E 6 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 833 GLN G1208 GLN G1212 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 GLN p 167 HIS ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 637 ASN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 421 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34617 Z= 0.338 Angle : 0.752 14.876 47073 Z= 0.381 Chirality : 0.049 0.438 5406 Planarity : 0.005 0.073 6024 Dihedral : 8.464 103.076 5952 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.97 % Favored : 94.82 % Rotamer: Outliers : 3.37 % Allowed : 11.66 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4227 helix: 0.99 (0.19), residues: 716 sheet: 0.15 (0.15), residues: 1085 loop : -0.16 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 35 HIS 0.007 0.002 HIS A1122 PHE 0.022 0.002 PHE p 116 TYR 0.034 0.002 TYR D 777 ARG 0.006 0.001 ARG r 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 334 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 842 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8137 (tp40) REVERT: C 32 PHE cc_start: 0.8049 (m-80) cc_final: 0.7755 (m-10) REVERT: C 90 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8337 (pp30) REVERT: D 777 TYR cc_start: 0.8896 (p90) cc_final: 0.8674 (p90) REVERT: D 816 LYS cc_start: 0.8543 (tptt) cc_final: 0.8272 (tptp) REVERT: D 843 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7877 (t70) REVERT: D 891 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7992 (mp0) REVERT: D 927 GLN cc_start: 0.8385 (tt0) cc_final: 0.8136 (tt0) REVERT: F 4 LEU cc_start: 0.7765 (mt) cc_final: 0.7480 (mm) REVERT: F 15 LEU cc_start: 0.7680 (tp) cc_final: 0.6969 (mp) REVERT: F 28 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: F 38 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: F 86 TYR cc_start: 0.8119 (m-80) cc_final: 0.7877 (m-80) REVERT: F 87 PHE cc_start: 0.8019 (m-80) cc_final: 0.7720 (m-80) REVERT: G 757 MET cc_start: 0.8522 (mmt) cc_final: 0.8306 (mmt) REVERT: G 1039 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8458 (tp30) REVERT: G 1079 ASN cc_start: 0.8890 (m-40) cc_final: 0.8495 (t0) REVERT: G 1180 ILE cc_start: 0.9331 (mp) cc_final: 0.8769 (tt) REVERT: H 39 GLN cc_start: 0.8389 (tt0) cc_final: 0.8166 (tt0) REVERT: H 81 GLU cc_start: 0.8596 (tt0) cc_final: 0.7889 (tp30) REVERT: H 85 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8241 (mp0) REVERT: p 147 PHE cc_start: 0.8414 (m-80) cc_final: 0.8038 (m-80) REVERT: p 278 MET cc_start: 0.8024 (tpp) cc_final: 0.7742 (tpp) REVERT: p 330 ASP cc_start: 0.8384 (p0) cc_final: 0.8135 (p0) REVERT: p 332 TYR cc_start: 0.8318 (m-80) cc_final: 0.7920 (m-80) REVERT: p 563 MET cc_start: 0.3540 (ptp) cc_final: 0.3019 (tpp) REVERT: q 148 MET cc_start: 0.8576 (ttt) cc_final: 0.8125 (ttt) REVERT: q 728 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7872 (tptt) REVERT: r 204 PHE cc_start: 0.8194 (t80) cc_final: 0.7987 (t80) REVERT: r 288 ASP cc_start: 0.7442 (t0) cc_final: 0.7041 (t0) REVERT: r 346 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: r 563 MET cc_start: 0.6419 (mmm) cc_final: 0.4624 (tpp) REVERT: r 592 ASN cc_start: 0.7612 (m-40) cc_final: 0.7092 (p0) REVERT: r 663 TYR cc_start: 0.8954 (t80) cc_final: 0.8576 (t80) outliers start: 123 outliers final: 94 residues processed: 421 average time/residue: 0.4120 time to fit residues: 292.0655 Evaluate side-chains 393 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 294 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 28 TYR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 136 THR Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 406 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 842 GLN ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 516 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 398 ASN q 475 ASN r 647 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34617 Z= 0.355 Angle : 0.753 11.512 47073 Z= 0.382 Chirality : 0.049 0.444 5406 Planarity : 0.005 0.073 6024 Dihedral : 8.444 103.911 5952 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.28 % Favored : 94.51 % Rotamer: Outliers : 3.45 % Allowed : 12.86 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.19 (0.13), residues: 4227 helix: 0.81 (0.19), residues: 722 sheet: 0.02 (0.14), residues: 1086 loop : -0.42 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 103 HIS 0.008 0.002 HIS q 167 PHE 0.021 0.002 PHE p 116 TYR 0.033 0.002 TYR A 905 ARG 0.007 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 313 time to evaluate : 4.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 842 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8177 (tp40) REVERT: A 1039 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8655 (tp30) REVERT: C 90 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8430 (pp30) REVERT: D 816 LYS cc_start: 0.8517 (tptt) cc_final: 0.8208 (tptp) REVERT: D 843 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7904 (t70) REVERT: D 891 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7975 (mp0) REVERT: D 927 GLN cc_start: 0.8540 (tt0) cc_final: 0.8286 (tt0) REVERT: F 4 LEU cc_start: 0.7761 (mt) cc_final: 0.7464 (mm) REVERT: F 15 LEU cc_start: 0.7735 (tp) cc_final: 0.6986 (mp) REVERT: F 86 TYR cc_start: 0.7985 (m-80) cc_final: 0.7719 (m-80) REVERT: F 87 PHE cc_start: 0.7950 (m-80) cc_final: 0.7668 (m-80) REVERT: G 757 MET cc_start: 0.8501 (mmt) cc_final: 0.8188 (mmt) REVERT: G 1039 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8488 (tp30) REVERT: G 1079 ASN cc_start: 0.8883 (m-40) cc_final: 0.8509 (t0) REVERT: G 1222 LEU cc_start: 0.8243 (tp) cc_final: 0.7187 (pt) REVERT: H 39 GLN cc_start: 0.8527 (tt0) cc_final: 0.8181 (tt0) REVERT: H 81 GLU cc_start: 0.8612 (tt0) cc_final: 0.7866 (tp30) REVERT: H 85 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8259 (mp0) REVERT: p 147 PHE cc_start: 0.8412 (m-80) cc_final: 0.8092 (m-80) REVERT: p 278 MET cc_start: 0.8045 (tpp) cc_final: 0.7736 (tpp) REVERT: p 330 ASP cc_start: 0.8422 (p0) cc_final: 0.8177 (p0) REVERT: p 332 TYR cc_start: 0.8307 (m-80) cc_final: 0.7954 (m-80) REVERT: p 563 MET cc_start: 0.3417 (ptp) cc_final: 0.2962 (tpp) REVERT: q 148 MET cc_start: 0.8518 (ttt) cc_final: 0.8251 (ttt) REVERT: q 278 MET cc_start: 0.7403 (mmm) cc_final: 0.6777 (mmm) REVERT: q 728 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7882 (tptt) REVERT: r 288 ASP cc_start: 0.7559 (t0) cc_final: 0.7147 (t0) REVERT: r 346 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: r 522 GLN cc_start: 0.6718 (tp40) cc_final: 0.6111 (mm-40) REVERT: r 563 MET cc_start: 0.6537 (mmm) cc_final: 0.4761 (tpp) REVERT: r 592 ASN cc_start: 0.7746 (m-40) cc_final: 0.7140 (p0) REVERT: r 663 TYR cc_start: 0.8966 (t80) cc_final: 0.8603 (t80) outliers start: 126 outliers final: 102 residues processed: 408 average time/residue: 0.4204 time to fit residues: 289.5905 Evaluate side-chains 394 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 289 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 575 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 136 THR Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 342 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 chunk 404 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 246 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34617 Z= 0.254 Angle : 0.700 13.567 47073 Z= 0.352 Chirality : 0.048 0.431 5406 Planarity : 0.005 0.068 6024 Dihedral : 8.145 100.603 5952 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.39 % Rotamer: Outliers : 3.23 % Allowed : 13.46 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.18 (0.13), residues: 4227 helix: 0.95 (0.20), residues: 719 sheet: 0.07 (0.15), residues: 1083 loop : -0.49 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 103 HIS 0.006 0.001 HIS A1122 PHE 0.022 0.001 PHE p 116 TYR 0.029 0.001 TYR A 905 ARG 0.006 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 320 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1039 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8627 (tp30) REVERT: D 816 LYS cc_start: 0.8485 (tptt) cc_final: 0.8213 (tptp) REVERT: D 843 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7890 (t70) REVERT: D 891 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7911 (mp0) REVERT: D 927 GLN cc_start: 0.8513 (tt0) cc_final: 0.8279 (tt0) REVERT: E 19 LYS cc_start: 0.7755 (tppt) cc_final: 0.7548 (tppt) REVERT: E 28 THR cc_start: 0.7911 (p) cc_final: 0.7693 (p) REVERT: E 80 MET cc_start: 0.7609 (tpp) cc_final: 0.7034 (tpp) REVERT: F 4 LEU cc_start: 0.7848 (mt) cc_final: 0.7549 (mm) REVERT: F 15 LEU cc_start: 0.7680 (tp) cc_final: 0.7177 (mm) REVERT: F 86 TYR cc_start: 0.7974 (m-80) cc_final: 0.7726 (m-80) REVERT: G 757 MET cc_start: 0.8492 (mmt) cc_final: 0.8201 (mmt) REVERT: G 1039 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8418 (tp30) REVERT: G 1079 ASN cc_start: 0.8914 (m-40) cc_final: 0.8527 (t0) REVERT: H 39 GLN cc_start: 0.8488 (tt0) cc_final: 0.8144 (tt0) REVERT: H 81 GLU cc_start: 0.8709 (tt0) cc_final: 0.7975 (tp30) REVERT: H 85 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8284 (mp0) REVERT: p 147 PHE cc_start: 0.8353 (m-80) cc_final: 0.8086 (m-80) REVERT: p 278 MET cc_start: 0.7964 (tpp) cc_final: 0.7611 (tpp) REVERT: p 330 ASP cc_start: 0.8426 (p0) cc_final: 0.8186 (p0) REVERT: p 332 TYR cc_start: 0.8294 (m-80) cc_final: 0.7959 (m-80) REVERT: p 563 MET cc_start: 0.3415 (ptp) cc_final: 0.2601 (mmm) REVERT: q 278 MET cc_start: 0.7386 (mmm) cc_final: 0.6703 (mmm) REVERT: q 468 ASN cc_start: 0.4203 (m110) cc_final: 0.3269 (m-40) REVERT: q 728 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7882 (tptt) REVERT: r 288 ASP cc_start: 0.7636 (t0) cc_final: 0.7184 (t0) REVERT: r 346 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8737 (tm-30) REVERT: r 522 GLN cc_start: 0.6661 (tp40) cc_final: 0.6037 (mm110) REVERT: r 592 ASN cc_start: 0.7739 (m-40) cc_final: 0.7116 (p0) REVERT: r 663 TYR cc_start: 0.8958 (t80) cc_final: 0.8576 (t80) outliers start: 118 outliers final: 89 residues processed: 407 average time/residue: 0.4265 time to fit residues: 291.4837 Evaluate side-chains 395 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 304 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1082 VAL Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 114 ASN Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 50.0000 chunk 161 optimal weight: 9.9990 chunk 241 optimal weight: 0.0000 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 257 optimal weight: 40.0000 chunk 275 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 318 optimal weight: 30.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 167 HIS ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34617 Z= 0.242 Angle : 0.690 12.371 47073 Z= 0.346 Chirality : 0.047 0.435 5406 Planarity : 0.005 0.067 6024 Dihedral : 7.952 99.040 5952 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.58 % Favored : 94.20 % Rotamer: Outliers : 3.07 % Allowed : 13.68 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.13), residues: 4227 helix: 1.04 (0.20), residues: 719 sheet: 0.05 (0.14), residues: 1117 loop : -0.49 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 103 HIS 0.005 0.001 HIS A1122 PHE 0.018 0.001 PHE C 98 TYR 0.036 0.001 TYR D 777 ARG 0.009 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 319 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1063 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: B 35 HIS cc_start: 0.7679 (m170) cc_final: 0.7322 (m170) REVERT: D 757 MET cc_start: 0.8210 (mmp) cc_final: 0.7889 (mmm) REVERT: D 777 TYR cc_start: 0.8635 (p90) cc_final: 0.8332 (p90) REVERT: D 816 LYS cc_start: 0.8489 (tptt) cc_final: 0.8226 (tptp) REVERT: D 843 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7962 (t70) REVERT: D 857 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: D 891 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7906 (mp0) REVERT: D 927 GLN cc_start: 0.8483 (tt0) cc_final: 0.8252 (tt0) REVERT: E 19 LYS cc_start: 0.7773 (tppt) cc_final: 0.7557 (tppt) REVERT: E 28 THR cc_start: 0.8023 (p) cc_final: 0.7777 (t) REVERT: E 51 PHE cc_start: 0.7712 (t80) cc_final: 0.7277 (t80) REVERT: E 80 MET cc_start: 0.7624 (tpp) cc_final: 0.7264 (tpp) REVERT: F 4 LEU cc_start: 0.7864 (mt) cc_final: 0.7575 (mm) REVERT: F 15 LEU cc_start: 0.7709 (tp) cc_final: 0.7233 (mm) REVERT: F 87 PHE cc_start: 0.7817 (m-80) cc_final: 0.7492 (m-80) REVERT: G 1039 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8424 (tp30) REVERT: H 39 GLN cc_start: 0.8533 (tt0) cc_final: 0.8296 (tt0) REVERT: H 81 GLU cc_start: 0.8703 (tt0) cc_final: 0.8031 (tp30) REVERT: H 85 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8366 (mp0) REVERT: p 147 PHE cc_start: 0.8400 (m-80) cc_final: 0.8069 (m-80) REVERT: p 278 MET cc_start: 0.7952 (tpp) cc_final: 0.7586 (tpp) REVERT: p 330 ASP cc_start: 0.8381 (p0) cc_final: 0.8130 (p0) REVERT: p 332 TYR cc_start: 0.8297 (m-80) cc_final: 0.7945 (m-80) REVERT: p 563 MET cc_start: 0.3491 (ptp) cc_final: 0.2813 (tpp) REVERT: q 148 MET cc_start: 0.8403 (ttt) cc_final: 0.8039 (tmm) REVERT: q 278 MET cc_start: 0.7465 (mmm) cc_final: 0.6828 (mmm) REVERT: q 428 ILE cc_start: 0.6933 (tt) cc_final: 0.6707 (tt) REVERT: q 468 ASN cc_start: 0.4309 (m110) cc_final: 0.3309 (m-40) REVERT: q 686 MET cc_start: 0.4670 (mmm) cc_final: 0.4456 (mmm) REVERT: q 728 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7894 (tptt) REVERT: r 240 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8478 (mmp) REVERT: r 288 ASP cc_start: 0.7748 (t0) cc_final: 0.7471 (t0) REVERT: r 346 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8727 (tm-30) REVERT: r 522 GLN cc_start: 0.6662 (tp40) cc_final: 0.5976 (mm110) REVERT: r 563 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.2563 (tpp) REVERT: r 663 TYR cc_start: 0.8928 (t80) cc_final: 0.8652 (t80) outliers start: 112 outliers final: 94 residues processed: 397 average time/residue: 0.4234 time to fit residues: 284.1544 Evaluate side-chains 401 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 301 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1063 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1008 MET Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1082 VAL Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 288 ASP Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 114 ASN Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 158 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 575 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 240 MET Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 563 MET Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 662 ILE Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 30.0000 chunk 387 optimal weight: 20.0000 chunk 353 optimal weight: 0.9990 chunk 377 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 chunk 340 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 375 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 233 ASN ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 566 GLN ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 566 GLN r 647 ASN r 733 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34617 Z= 0.307 Angle : 0.731 12.343 47073 Z= 0.367 Chirality : 0.048 0.423 5406 Planarity : 0.005 0.068 6024 Dihedral : 8.024 97.679 5952 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.25 % Favored : 93.54 % Rotamer: Outliers : 3.23 % Allowed : 14.23 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4227 helix: 0.92 (0.19), residues: 716 sheet: -0.06 (0.14), residues: 1141 loop : -0.58 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 35 HIS 0.006 0.001 HIS F 76 PHE 0.022 0.002 PHE q 239 TYR 0.029 0.002 TYR A 905 ARG 0.004 0.000 ARG p 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 289 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 777 TYR cc_start: 0.8728 (p90) cc_final: 0.8442 (p90) REVERT: D 816 LYS cc_start: 0.8473 (tptt) cc_final: 0.8226 (tptp) REVERT: D 843 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7973 (t70) REVERT: D 927 GLN cc_start: 0.8520 (tt0) cc_final: 0.8275 (tt0) REVERT: E 19 LYS cc_start: 0.7785 (tppt) cc_final: 0.7545 (tppt) REVERT: E 28 THR cc_start: 0.8047 (p) cc_final: 0.7784 (t) REVERT: E 80 MET cc_start: 0.7667 (tpp) cc_final: 0.7351 (tpp) REVERT: F 4 LEU cc_start: 0.7912 (mt) cc_final: 0.7606 (mm) REVERT: F 15 LEU cc_start: 0.7801 (tp) cc_final: 0.7313 (mm) REVERT: F 87 PHE cc_start: 0.7832 (m-80) cc_final: 0.7550 (m-80) REVERT: F 90 GLN cc_start: 0.7838 (pp30) cc_final: 0.7489 (pp30) REVERT: G 757 MET cc_start: 0.8601 (mmt) cc_final: 0.8292 (mmt) REVERT: G 909 TYR cc_start: 0.6707 (t80) cc_final: 0.6368 (t80) REVERT: G 933 LYS cc_start: 0.7733 (tptp) cc_final: 0.7414 (tmtt) REVERT: G 1039 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8462 (tp30) REVERT: G 1119 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: H 81 GLU cc_start: 0.8734 (tt0) cc_final: 0.8060 (tp30) REVERT: H 85 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8361 (mp0) REVERT: p 100 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6894 (mm) REVERT: p 147 PHE cc_start: 0.8428 (m-80) cc_final: 0.8116 (m-80) REVERT: p 278 MET cc_start: 0.8015 (tpp) cc_final: 0.7666 (tpp) REVERT: p 330 ASP cc_start: 0.8460 (p0) cc_final: 0.8219 (p0) REVERT: p 332 TYR cc_start: 0.8384 (m-80) cc_final: 0.8048 (m-80) REVERT: p 563 MET cc_start: 0.3511 (ptp) cc_final: 0.2830 (tpp) REVERT: q 148 MET cc_start: 0.8230 (ttt) cc_final: 0.7733 (ttt) REVERT: q 149 LEU cc_start: 0.8849 (mm) cc_final: 0.8577 (tp) REVERT: q 428 ILE cc_start: 0.6792 (tt) cc_final: 0.6578 (tt) REVERT: q 468 ASN cc_start: 0.4300 (m110) cc_final: 0.3362 (m-40) REVERT: q 728 LYS cc_start: 0.8508 (mmtt) cc_final: 0.7961 (tptt) REVERT: r 240 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8489 (mmp) REVERT: r 288 ASP cc_start: 0.7873 (t0) cc_final: 0.7559 (t0) REVERT: r 346 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: r 522 GLN cc_start: 0.6702 (tp40) cc_final: 0.6025 (mm110) REVERT: r 563 MET cc_start: 0.5467 (mmp) cc_final: 0.2681 (tpp) REVERT: r 663 TYR cc_start: 0.8934 (t80) cc_final: 0.8620 (t80) outliers start: 118 outliers final: 99 residues processed: 374 average time/residue: 0.4112 time to fit residues: 261.0687 Evaluate side-chains 385 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 281 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1008 MET Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1082 VAL Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1119 GLN Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 273 LEU Chi-restraints excluded: chain p residue 288 ASP Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 114 ASN Chi-restraints excluded: chain q residue 135 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 158 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 575 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 240 MET Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 662 ILE Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 8.9990 chunk 398 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 418 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34617 Z= 0.334 Angle : 0.754 11.731 47073 Z= 0.379 Chirality : 0.049 0.433 5406 Planarity : 0.005 0.068 6024 Dihedral : 8.150 97.578 5952 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % Rotamer: Outliers : 3.09 % Allowed : 14.53 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4227 helix: 0.66 (0.19), residues: 734 sheet: -0.10 (0.15), residues: 1107 loop : -0.73 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 103 HIS 0.006 0.001 HIS A 836 PHE 0.020 0.002 PHE r 313 TYR 0.031 0.002 TYR A 905 ARG 0.008 0.001 ARG r 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 292 time to evaluate : 5.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 VAL cc_start: 0.9279 (t) cc_final: 0.9022 (p) REVERT: A 891 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7011 (mt-10) REVERT: D 757 MET cc_start: 0.8279 (mmp) cc_final: 0.8005 (mmm) REVERT: D 777 TYR cc_start: 0.8774 (p90) cc_final: 0.8502 (p90) REVERT: D 843 ASP cc_start: 0.8370 (t0) cc_final: 0.7943 (t70) REVERT: D 913 MET cc_start: 0.6830 (ptt) cc_final: 0.6504 (ptp) REVERT: E 19 LYS cc_start: 0.7898 (tppt) cc_final: 0.7576 (tppt) REVERT: E 28 THR cc_start: 0.8053 (p) cc_final: 0.7778 (t) REVERT: E 80 MET cc_start: 0.7723 (tpp) cc_final: 0.7223 (tpp) REVERT: F 4 LEU cc_start: 0.7959 (mt) cc_final: 0.7645 (mm) REVERT: F 15 LEU cc_start: 0.7807 (tp) cc_final: 0.7314 (mm) REVERT: F 33 MET cc_start: 0.8845 (tpp) cc_final: 0.7126 (ptp) REVERT: F 87 PHE cc_start: 0.7834 (m-80) cc_final: 0.7558 (m-80) REVERT: G 757 MET cc_start: 0.8572 (mmt) cc_final: 0.8253 (mmt) REVERT: G 909 TYR cc_start: 0.6827 (t80) cc_final: 0.6506 (t80) REVERT: G 1039 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8496 (tp30) REVERT: G 1119 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: H 81 GLU cc_start: 0.8730 (tt0) cc_final: 0.8035 (tp30) REVERT: H 85 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8346 (mp0) REVERT: I 63 ILE cc_start: 0.8550 (mm) cc_final: 0.8264 (mm) REVERT: p 100 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6858 (mm) REVERT: p 147 PHE cc_start: 0.8405 (m-80) cc_final: 0.8109 (m-80) REVERT: p 278 MET cc_start: 0.8071 (tpp) cc_final: 0.7708 (tpp) REVERT: p 330 ASP cc_start: 0.8469 (p0) cc_final: 0.8249 (p0) REVERT: p 332 TYR cc_start: 0.8379 (m-80) cc_final: 0.7994 (m-80) REVERT: p 563 MET cc_start: 0.3672 (ptp) cc_final: 0.3003 (tpp) REVERT: q 148 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7794 (ttt) REVERT: q 149 LEU cc_start: 0.8807 (mm) cc_final: 0.8557 (tp) REVERT: q 267 SER cc_start: 0.8702 (t) cc_final: 0.8213 (m) REVERT: q 428 ILE cc_start: 0.6844 (tt) cc_final: 0.6639 (tt) REVERT: q 468 ASN cc_start: 0.4356 (m110) cc_final: 0.3479 (m-40) REVERT: q 728 LYS cc_start: 0.8520 (mmtt) cc_final: 0.7998 (tptt) REVERT: r 240 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8510 (mmp) REVERT: r 288 ASP cc_start: 0.8008 (t0) cc_final: 0.7702 (t0) REVERT: r 346 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: r 522 GLN cc_start: 0.6710 (tp40) cc_final: 0.6079 (mm110) REVERT: r 563 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.2556 (tpp) REVERT: r 614 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7932 (ptm160) REVERT: r 663 TYR cc_start: 0.8942 (t80) cc_final: 0.8612 (t80) outliers start: 113 outliers final: 101 residues processed: 374 average time/residue: 0.4160 time to fit residues: 263.1505 Evaluate side-chains 384 residues out of total 3654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 276 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 1008 MET Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1180 ILE Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1201 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 944 GLU Chi-restraints excluded: chain G residue 1082 VAL Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1119 GLN Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 288 ASP Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 727 CYS Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 114 ASN Chi-restraints excluded: chain q residue 135 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 148 MET Chi-restraints excluded: chain q residue 158 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 333 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 575 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 240 MET Chi-restraints excluded: chain r residue 277 ASN Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 563 MET Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 0.0470 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067897 restraints weight = 151859.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.070086 restraints weight = 87275.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070598 restraints weight = 52877.171| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34617 Z= 0.286 Angle : 0.733 11.531 47073 Z= 0.367 Chirality : 0.048 0.433 5406 Planarity : 0.005 0.067 6024 Dihedral : 8.066 98.513 5952 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.55 % Favored : 93.23 % Rotamer: Outliers : 3.07 % Allowed : 14.78 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4227 helix: 0.74 (0.19), residues: 724 sheet: -0.11 (0.15), residues: 1119 loop : -0.71 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP r 553 HIS 0.006 0.001 HIS A1122 PHE 0.021 0.002 PHE r 313 TYR 0.029 0.002 TYR A 905 ARG 0.009 0.000 ARG r 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6633.95 seconds wall clock time: 121 minutes 36.65 seconds (7296.65 seconds total)