Starting phenix.real_space_refine on Mon Sep 14 23:22:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_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/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5w9h_8783/09_2026/5w9h_8783.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 7.53, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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=1, 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.7 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: 1.74 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: 13.32 Time building geometry restraints manager: 4.59 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: 0.00 - 3.87: 45137 3.87 - 7.74: 1784 7.74 - 11.62: 138 11.62 - 15.49: 12 15.49 - 19.36: 2 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 - 17.94: 19384 17.94 - 35.88: 490 35.88 - 53.82: 165 53.82 - 71.75: 77 71.75 - 89.69: 20 Dihedral angle restraints: 20136 sinusoidal: 7746 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 20133 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: 1.34 - 2.05: 16 2.05 - 2.76: 6813 2.76 - 3.47: 46170 3.47 - 4.19: 83460 4.19 - 4.90: 138558 Nonbonded interactions: 275017 Sorted by model distance: 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 3.040 nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.506 3.470 nonbonded pdb=" OH TYR A 905 " pdb=" CB PRO A 936 " model vdw 1.514 3.440 ... (remaining 275012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 40.170 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.330 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.014 0.561 34737 Z= 0.877 Angle : 1.801 38.176 47374 Z= 1.163 Chirality : 0.090 1.478 5406 Planarity : 0.011 0.104 6024 Dihedral : 10.427 89.692 12066 Min Nonbonded Distance : 1.336 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG p 652 TYR 0.057 0.006 TYR q 469 PHE 0.030 0.004 PHE I 32 TRP 0.059 0.007 TRP H 47 HIS 0.007 0.002 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.85 (34617) covalent geometry : angle 1.70362 / 1.14 (47073) SS BOND : bond 0.11026 / 7.82 ( 56) SS BOND : angle 6.80442 / 4.34 ( 112) hydrogen bonds : bond 0.19413 / 12.83 ( 1252) hydrogen bonds : angle 8.22885 / 5.86 ( 3228) Misc. bond : bond 0.14995 / 7.89 ( 1) link_BETA1-4 : bond 0.01317 / 0.87 ( 21) link_BETA1-4 : angle 5.38855 / 3.38 ( 63) link_NAG-ASN : bond 0.01926 / 1.34 ( 42) link_NAG-ASN : angle 8.95277 / 6.29 ( 126) *********************** 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 to be fit. rotamer outliers: 6 poor density : 791 time to evaluate : 1.287 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: 0.7053 (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: 0.8992 (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: 0.6802 (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: 0.2240 time to fit residues: 285.8497 Evaluate side-chains 357 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN B 1 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1208 GLN ** F 6 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 ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 107 GLN ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 377 GLN q 398 ASN r 280 GLN ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.097333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072776 restraints weight = 148806.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076193 restraints weight = 81243.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.076392 restraints weight = 45725.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.076694 restraints weight = 38283.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076826 restraints weight = 37409.859| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34737 Z= 0.204 Angle : 0.862 14.551 47374 Z= 0.438 Chirality : 0.053 0.563 5406 Planarity : 0.007 0.094 6024 Dihedral : 5.750 40.672 4633 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.26 % Rotamer: Outliers : 2.30 % Allowed : 8.10 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 4227 helix: 0.93 (0.19), residues: 697 sheet: 0.62 (0.15), residues: 1049 loop : 0.94 (0.13), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 61 TYR 0.030 0.002 TYR A 905 PHE 0.029 0.002 PHE r 385 TRP 0.022 0.002 TRP F 35 HIS 0.008 0.002 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (34617) covalent geometry : angle 0.81510 / 0.43 (47073) SS BOND : bond 0.00520 / 0.33 ( 56) SS BOND : angle 1.97825 / 1.18 ( 112) hydrogen bonds : bond 0.06422 / 4.32 ( 1252) hydrogen bonds : angle 6.52693 / 4.69 ( 3228) Misc. bond : bond 0.00169 / 0.09 ( 1) link_BETA1-4 : bond 0.00605 / 0.37 ( 21) link_BETA1-4 : angle 3.37999 / 2.11 ( 63) link_NAG-ASN : bond 0.00802 / 0.53 ( 42) link_NAG-ASN : angle 4.69638 / 3.32 ( 126) *********************** 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 530 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 446 time to evaluate : 1.374 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 924 ILE cc_start: 0.6464 (mt) cc_final: 0.6044 (pt) REVERT: A 967 PHE cc_start: 0.8215 (t80) cc_final: 0.7903 (t80) REVERT: B 45 LEU cc_start: 0.8685 (mp) cc_final: 0.8323 (mt) REVERT: B 46 GLU cc_start: 0.8699 (pt0) cc_final: 0.8111 (pm20) REVERT: C 33 MET cc_start: 0.8669 (tpp) cc_final: 0.8310 (tpp) REVERT: C 34 ASN cc_start: 0.8857 (m-40) cc_final: 0.7964 (m110) REVERT: C 92 LYS cc_start: 0.9268 (tptm) cc_final: 0.8772 (ttmt) REVERT: D 816 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8338 (tptt) REVERT: D 843 ASP cc_start: 0.8432 (m-30) cc_final: 0.8042 (t0) REVERT: D 911 ASP cc_start: 0.7547 (m-30) cc_final: 0.7345 (t0) REVERT: D 927 GLN cc_start: 0.8220 (tt0) cc_final: 0.7071 (pt0) REVERT: D 933 LYS cc_start: 0.8152 (mttt) cc_final: 0.7780 (mttt) REVERT: D 1078 LEU cc_start: 0.9278 (mt) cc_final: 0.8814 (tp) REVERT: D 1097 GLN cc_start: 0.8481 (tp40) cc_final: 0.7812 (tm-30) REVERT: D 1101 ASP cc_start: 0.8389 (m-30) cc_final: 0.7963 (m-30) REVERT: D 1222 LEU cc_start: 0.9001 (tp) cc_final: 0.8734 (pt) REVERT: E 51 PHE cc_start: 0.8166 (t80) cc_final: 0.7652 (t80) REVERT: E 56 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7014 (t0) REVERT: E 61 GLN cc_start: 0.7326 (tp40) cc_final: 0.7105 (tp40) REVERT: F 33 MET cc_start: 0.8913 (tpp) cc_final: 0.8682 (tpp) REVERT: F 73 LEU cc_start: 0.8404 (tp) cc_final: 0.7961 (tp) REVERT: F 86 TYR cc_start: 0.7630 (m-80) cc_final: 0.7379 (m-80) REVERT: F 87 PHE cc_start: 0.8408 (m-80) cc_final: 0.8046 (m-80) REVERT: G 909 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.6038 (t80) REVERT: G 1104 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8701 (t0) REVERT: G 1180 ILE cc_start: 0.9160 (mp) cc_final: 0.8743 (tt) REVERT: H 38 LYS cc_start: 0.8131 (tttm) cc_final: 0.7858 (ttmm) REVERT: H 59 TYR cc_start: 0.7839 (m-10) cc_final: 0.7267 (m-10) REVERT: H 60 ASN cc_start: 0.8545 (t0) cc_final: 0.8328 (t0) REVERT: H 85 GLU cc_start: 0.8937 (mm-30) cc_final: 0.7992 (mp0) REVERT: I 38 GLN cc_start: 0.8116 (tt0) cc_final: 0.7255 (tt0) REVERT: p 147 PHE cc_start: 0.8168 (m-80) cc_final: 0.7779 (m-80) REVERT: p 287 TYR cc_start: 0.6718 (p90) cc_final: 0.6219 (p90) REVERT: p 330 ASP cc_start: 0.8228 (p0) cc_final: 0.8004 (p0) REVERT: p 332 TYR cc_start: 0.8479 (m-80) cc_final: 0.8240 (m-80) REVERT: p 563 MET cc_start: 0.3566 (ptp) cc_final: 0.2648 (tpp) REVERT: p 696 MET cc_start: 0.3358 (ptm) cc_final: 0.3112 (ppp) REVERT: q 148 MET cc_start: 0.8370 (ttt) cc_final: 0.8165 (ttt) REVERT: q 149 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (mm) REVERT: q 563 MET cc_start: 0.6745 (ptt) cc_final: 0.6123 (tpt) REVERT: q 637 ASN cc_start: 0.8200 (t0) cc_final: 0.7950 (t0) REVERT: q 728 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7784 (tptt) REVERT: q 729 LEU cc_start: 0.9043 (mt) cc_final: 0.8788 (mp) REVERT: r 388 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6128 (mt) REVERT: r 401 ARG cc_start: 0.7434 (ttm170) cc_final: 0.7061 (mpt-90) REVERT: r 436 ASN cc_start: 0.7797 (m-40) cc_final: 0.7480 (t0) REVERT: r 505 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7529 (ptm160) REVERT: r 553 TRP cc_start: 0.6502 (m100) cc_final: 0.6288 (m100) REVERT: r 663 TYR cc_start: 0.8752 (t80) cc_final: 0.8538 (t80) outliers start: 84 outliers final: 45 residues processed: 505 average time/residue: 0.2109 time to fit residues: 176.6238 Evaluate side-chains 376 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 326 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 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 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 909 TYR Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1104 ASN Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL 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 100 LEU Chi-restraints excluded: chain p residue 104 ASN 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 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 724 VAL Chi-restraints excluded: chain q residue 735 LEU 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 676 SER Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 225 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 300 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 386 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN B 58 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 90 GLN D 857 GLN D 927 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1212 GLN E 58 ASN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 167 HIS p 280 GLN p 421 ASN ** 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 475 ASN ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 98 GLN r 468 ASN r 637 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.094126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070228 restraints weight = 149600.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073410 restraints weight = 82265.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.073561 restraints weight = 47154.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.073778 restraints weight = 39870.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073950 restraints weight = 39741.828| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 34737 Z= 0.265 Angle : 0.867 16.152 47374 Z= 0.435 Chirality : 0.055 0.955 5406 Planarity : 0.006 0.083 6024 Dihedral : 5.514 30.414 4629 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 9.72 % Favored : 87.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4227 helix: 0.89 (0.19), residues: 692 sheet: 0.49 (0.15), residues: 1034 loop : 0.23 (0.13), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1057 TYR 0.033 0.002 TYR A 905 PHE 0.026 0.002 PHE I 98 TRP 0.031 0.002 TRP F 35 HIS 0.010 0.002 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (34617) covalent geometry : angle 0.82370 / 0.43 (47073) SS BOND : bond 0.00528 / 0.37 ( 56) SS BOND : angle 1.72605 / 1.05 ( 112) hydrogen bonds : bond 0.05910 / 3.94 ( 1252) hydrogen bonds : angle 6.32725 / 4.52 ( 3228) Misc. bond : bond 0.02863 / 1.51 ( 1) link_BETA1-4 : bond 0.00650 / 0.42 ( 21) link_BETA1-4 : angle 3.29129 / 2.04 ( 63) link_NAG-ASN : bond 0.01194 / 0.59 ( 42) link_NAG-ASN : angle 4.58030 / 3.27 ( 126) *********************** 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 456 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 354 time to evaluate : 1.304 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 967 PHE cc_start: 0.8384 (t80) cc_final: 0.8058 (t80) REVERT: B 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8197 (p0) REVERT: C 27 GLU cc_start: 0.7973 (pt0) cc_final: 0.7674 (pm20) REVERT: C 32 PHE cc_start: 0.7852 (m-80) cc_final: 0.7622 (m-10) REVERT: C 75 ILE cc_start: 0.8921 (mm) cc_final: 0.8211 (mm) REVERT: C 90 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8155 (pp30) REVERT: C 92 LYS cc_start: 0.9462 (tptm) cc_final: 0.9012 (tppp) REVERT: C 93 GLU cc_start: 0.8953 (pm20) cc_final: 0.8698 (pm20) REVERT: D 816 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7980 (tptm) REVERT: D 1097 GLN cc_start: 0.8575 (tp40) cc_final: 0.8300 (tm-30) REVERT: D 1182 ASP cc_start: 0.7956 (t0) cc_final: 0.7673 (t70) REVERT: D 1222 LEU cc_start: 0.8966 (tp) cc_final: 0.8724 (pt) REVERT: F 33 MET cc_start: 0.8842 (tpp) cc_final: 0.8543 (tpp) REVERT: F 34 ASN cc_start: 0.8961 (m-40) cc_final: 0.8599 (m-40) REVERT: F 73 LEU cc_start: 0.8428 (tp) cc_final: 0.7973 (tp) REVERT: G 757 MET cc_start: 0.8299 (mmp) cc_final: 0.7851 (mmp) REVERT: G 909 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6222 (t80) REVERT: G 1039 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8443 (tp30) REVERT: G 1180 ILE cc_start: 0.9312 (mp) cc_final: 0.8779 (tt) REVERT: H 38 LYS cc_start: 0.7943 (tttm) cc_final: 0.7492 (tppt) REVERT: H 59 TYR cc_start: 0.7991 (m-10) cc_final: 0.7408 (m-10) REVERT: H 81 GLU cc_start: 0.8486 (tt0) cc_final: 0.7761 (tp30) REVERT: H 85 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8165 (mp0) REVERT: I 38 GLN cc_start: 0.8028 (tt0) cc_final: 0.7664 (tt0) REVERT: I 89 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7994 (tm-30) REVERT: p 116 PHE cc_start: 0.8164 (p90) cc_final: 0.7931 (p90) REVERT: p 147 PHE cc_start: 0.8315 (m-80) cc_final: 0.7907 (m-80) REVERT: p 563 MET cc_start: 0.3686 (ptp) cc_final: 0.2723 (tpp) REVERT: q 148 MET cc_start: 0.8507 (ttt) cc_final: 0.7729 (ttt) REVERT: q 149 LEU cc_start: 0.9020 (mm) cc_final: 0.8701 (mt) REVERT: q 324 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8904 (mm) REVERT: q 563 MET cc_start: 0.6877 (ptt) cc_final: 0.6131 (tpt) REVERT: q 637 ASN cc_start: 0.8415 (t0) cc_final: 0.8064 (t0) REVERT: q 728 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7899 (tptt) REVERT: r 346 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: r 436 ASN cc_start: 0.8106 (m-40) cc_final: 0.7582 (t0) REVERT: r 505 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7477 (ptm160) REVERT: r 592 ASN cc_start: 0.7324 (m-40) cc_final: 0.7110 (t0) REVERT: r 663 TYR cc_start: 0.8758 (t80) cc_final: 0.8518 (t80) outliers start: 102 outliers final: 72 residues processed: 434 average time/residue: 0.2036 time to fit residues: 148.5749 Evaluate side-chains 375 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 299 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 A residue 1107 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 766 HIS 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 1076 THR 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 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 63 ILE 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 909 TYR 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 1151 SER Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1214 ILE 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 148 MET Chi-restraints excluded: chain p residue 206 THR 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 183 PHE 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 445 TYR 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 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 459 SER Chi-restraints excluded: chain r residue 468 ASN Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 676 SER Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 413 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 304 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 987 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN A1212 GLN B 1 GLN B 39 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 90 GLN ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 38 GLN G1104 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 167 HIS ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 521 ASN r 60 GLN r 107 GLN ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.095020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070382 restraints weight = 147410.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073464 restraints weight = 82498.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073730 restraints weight = 47888.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074149 restraints weight = 40094.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074287 restraints weight = 37768.322| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34737 Z= 0.151 Angle : 0.734 13.246 47374 Z= 0.361 Chirality : 0.049 0.528 5406 Planarity : 0.005 0.075 6024 Dihedral : 5.178 29.167 4629 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.74 % Rotamer: Outliers : 2.49 % Allowed : 11.33 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4227 helix: 1.11 (0.20), residues: 710 sheet: 0.54 (0.15), residues: 1070 loop : 0.08 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG r 542 TYR 0.027 0.001 TYR A 905 PHE 0.019 0.001 PHE p 116 TRP 0.034 0.002 TRP F 35 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (34617) covalent geometry : angle 0.69650 / 0.35 (47073) SS BOND : bond 0.00381 / 0.22 ( 56) SS BOND : angle 1.31555 / 0.83 ( 112) hydrogen bonds : bond 0.05039 / 3.38 ( 1252) hydrogen bonds : angle 5.86376 / 4.21 ( 3228) Misc. bond : bond 0.00569 / 0.30 ( 1) link_BETA1-4 : bond 0.00631 / 0.40 ( 21) link_BETA1-4 : angle 3.03466 / 1.89 ( 63) link_NAG-ASN : bond 0.00795 / 0.49 ( 42) link_NAG-ASN : angle 3.90323 / 2.78 ( 126) *********************** 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 448 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 357 time to evaluate : 1.496 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: 0.8118 (mtp) cc_final: 0.7800 (ptp) REVERT: C 22 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7509 (p) REVERT: C 27 GLU cc_start: 0.7982 (pt0) cc_final: 0.7707 (pm20) REVERT: C 32 PHE cc_start: 0.8021 (m-80) cc_final: 0.7805 (m-10) REVERT: C 42 GLN cc_start: 0.9035 (pt0) cc_final: 0.8554 (pm20) REVERT: C 90 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: C 92 LYS cc_start: 0.9412 (tptm) cc_final: 0.8972 (tppp) REVERT: C 93 GLU cc_start: 0.8919 (pm20) cc_final: 0.8677 (pm20) REVERT: D 843 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7784 (t70) REVERT: D 1097 GLN cc_start: 0.8521 (tp40) cc_final: 0.8321 (tm-30) REVERT: D 1222 LEU cc_start: 0.8961 (tp) cc_final: 0.8686 (pt) REVERT: E 51 PHE cc_start: 0.8043 (t80) cc_final: 0.7685 (t80) REVERT: E 56 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.7668 (t0) REVERT: E 61 GLN cc_start: 0.7472 (tp40) cc_final: 0.7203 (tp40) REVERT: E 81 GLU cc_start: 0.7905 (pt0) cc_final: 0.7697 (tm-30) REVERT: F 15 LEU cc_start: 0.8038 (tp) cc_final: 0.7514 (mp) REVERT: F 27 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8226 (tm-30) REVERT: F 33 MET cc_start: 0.8928 (tpp) cc_final: 0.8643 (tpp) REVERT: F 34 ASN cc_start: 0.8884 (m-40) cc_final: 0.8606 (m-40) REVERT: F 87 PHE cc_start: 0.8486 (m-80) cc_final: 0.8173 (m-80) REVERT: G 909 TYR cc_start: 0.6537 (t80) cc_final: 0.6170 (t80) REVERT: G 1180 ILE cc_start: 0.9189 (mp) cc_final: 0.8706 (tt) REVERT: H 39 GLN cc_start: 0.7882 (tt0) cc_final: 0.7661 (tt0) REVERT: H 59 TYR cc_start: 0.8043 (m-80) cc_final: 0.7828 (m-10) REVERT: H 81 GLU cc_start: 0.8598 (tt0) cc_final: 0.7830 (tp30) REVERT: H 85 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8282 (mp0) REVERT: I 38 GLN cc_start: 0.7955 (tt0) cc_final: 0.7459 (tt0) REVERT: p 278 MET cc_start: 0.7705 (tpp) cc_final: 0.7382 (tpp) REVERT: p 330 ASP cc_start: 0.8449 (p0) cc_final: 0.8229 (p0) REVERT: p 332 TYR cc_start: 0.8718 (m-80) cc_final: 0.8268 (m-80) REVERT: p 563 MET cc_start: 0.3724 (ptp) cc_final: 0.2480 (tpp) REVERT: q 148 MET cc_start: 0.8570 (ttt) cc_final: 0.8134 (ttt) REVERT: q 468 ASN cc_start: 0.4215 (m-40) cc_final: 0.3102 (m-40) REVERT: q 637 ASN cc_start: 0.8427 (t0) cc_final: 0.8019 (t0) REVERT: q 686 MET cc_start: 0.5144 (mmm) cc_final: 0.4921 (mmm) REVERT: q 728 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7830 (tptt) REVERT: r 436 ASN cc_start: 0.8102 (m-40) cc_final: 0.7562 (t0) outliers start: 91 outliers final: 50 residues processed: 419 average time/residue: 0.1998 time to fit residues: 141.8822 Evaluate side-chains 363 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 1 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 798 THR 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 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN 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 1117 CYS Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 382 GLU Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain p residue 734 SER Chi-restraints excluded: chain q residue 183 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 426 SER Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 333 ILE 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 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 173 optimal weight: 0.9990 chunk 324 optimal weight: 40.0000 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 249 optimal weight: 40.0000 chunk 301 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1016 ASN A1104 ASN B 39 GLN B 61 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 819 GLN ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 GLN D1056 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 833 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN p 98 GLN p 167 HIS p 319 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.092056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068009 restraints weight = 150648.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070096 restraints weight = 85762.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070383 restraints weight = 57235.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070803 restraints weight = 46340.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070933 restraints weight = 44429.927| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34737 Z= 0.273 Angle : 0.815 13.084 47374 Z= 0.406 Chirality : 0.051 0.576 5406 Planarity : 0.006 0.075 6024 Dihedral : 5.380 31.415 4629 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.18 % Favored : 94.61 % Rotamer: Outliers : 3.17 % Allowed : 12.21 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4227 helix: 0.82 (0.19), residues: 709 sheet: 0.25 (0.15), residues: 1050 loop : -0.24 (0.13), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 822 TYR 0.035 0.002 TYR D 777 PHE 0.028 0.002 PHE B 63 TRP 0.040 0.002 TRP F 35 HIS 0.007 0.002 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (34617) covalent geometry : angle 0.78219 / 0.40 (47073) SS BOND : bond 0.00559 / 0.35 ( 56) SS BOND : angle 1.52671 / 0.98 ( 112) hydrogen bonds : bond 0.05381 / 3.57 ( 1252) hydrogen bonds : angle 6.06328 / 4.34 ( 3228) Misc. bond : bond 0.00462 / 0.24 ( 1) link_BETA1-4 : bond 0.00659 / 0.42 ( 21) link_BETA1-4 : angle 3.11935 / 1.93 ( 63) link_NAG-ASN : bond 0.00683 / 0.45 ( 42) link_NAG-ASN : angle 3.79613 / 2.68 ( 126) *********************** 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 430 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 314 time to evaluate : 1.387 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: B 45 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 27 GLU cc_start: 0.8029 (pt0) cc_final: 0.7779 (pm20) REVERT: C 90 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: C 92 LYS cc_start: 0.9509 (tptm) cc_final: 0.9057 (tppp) REVERT: C 93 GLU cc_start: 0.9027 (pm20) cc_final: 0.8759 (pm20) REVERT: D 843 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7975 (t70) REVERT: D 1097 GLN cc_start: 0.8632 (tp40) cc_final: 0.8252 (tm-30) REVERT: D 1222 LEU cc_start: 0.9007 (tp) cc_final: 0.8742 (pt) REVERT: E 80 MET cc_start: 0.8336 (ttm) cc_final: 0.7615 (tmm) REVERT: F 27 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8353 (tm-30) REVERT: F 33 MET cc_start: 0.8938 (tpp) cc_final: 0.8644 (tpp) REVERT: F 34 ASN cc_start: 0.8901 (m-40) cc_final: 0.8596 (m-40) REVERT: F 73 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8126 (tp) REVERT: F 87 PHE cc_start: 0.8563 (m-80) cc_final: 0.8200 (m-80) REVERT: G 1180 ILE cc_start: 0.9160 (mp) cc_final: 0.8640 (tt) REVERT: H 59 TYR cc_start: 0.8054 (m-80) cc_final: 0.7497 (m-10) REVERT: H 81 GLU cc_start: 0.8616 (tt0) cc_final: 0.7835 (tp30) REVERT: H 85 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8264 (mp0) REVERT: I 38 GLN cc_start: 0.8021 (tt0) cc_final: 0.7489 (tt0) REVERT: I 90 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7810 (pp30) REVERT: p 147 PHE cc_start: 0.8615 (m-80) cc_final: 0.7967 (m-80) REVERT: p 278 MET cc_start: 0.7848 (tpp) cc_final: 0.7539 (tpp) REVERT: p 330 ASP cc_start: 0.8549 (p0) cc_final: 0.8296 (p0) REVERT: p 563 MET cc_start: 0.3364 (ptp) cc_final: 0.2124 (tpp) REVERT: q 148 MET cc_start: 0.8511 (ttt) cc_final: 0.8156 (ttt) REVERT: q 468 ASN cc_start: 0.4117 (m-40) cc_final: 0.3066 (m-40) REVERT: q 637 ASN cc_start: 0.8548 (t0) cc_final: 0.8133 (t0) REVERT: q 686 MET cc_start: 0.4858 (mmm) cc_final: 0.4648 (mmm) REVERT: q 728 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7891 (tptt) REVERT: r 346 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8814 (tm-30) REVERT: r 592 ASN cc_start: 0.7646 (m-40) cc_final: 0.7109 (p0) outliers start: 116 outliers final: 90 residues processed: 398 average time/residue: 0.2040 time to fit residues: 137.7260 Evaluate side-chains 380 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 284 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL 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 1005 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 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 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 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 63 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU 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 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 1151 SER 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 I residue 30 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR 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 452 MET Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 621 THR 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 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE 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 575 VAL Chi-restraints excluded: chain q residue 604 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 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 Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 399 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 108 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 857 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN p 516 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 398 ASN ** q 681 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.092724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068613 restraints weight = 148167.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071389 restraints weight = 80007.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071651 restraints weight = 46104.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072091 restraints weight = 40855.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072126 restraints weight = 38135.889| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 34737 Z= 0.172 Angle : 0.746 13.225 47374 Z= 0.367 Chirality : 0.050 0.640 5406 Planarity : 0.005 0.071 6024 Dihedral : 5.212 34.548 4629 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.57 % Favored : 95.22 % Rotamer: Outliers : 2.96 % Allowed : 13.19 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4227 helix: 0.95 (0.19), residues: 722 sheet: 0.28 (0.15), residues: 1068 loop : -0.29 (0.13), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG q 699 TYR 0.029 0.001 TYR A 905 PHE 0.023 0.001 PHE p 116 TRP 0.041 0.002 TRP F 35 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (34617) covalent geometry : angle 0.71296 / 0.36 (47073) SS BOND : bond 0.00369 / 0.25 ( 56) SS BOND : angle 1.37970 / 0.91 ( 112) hydrogen bonds : bond 0.04948 / 3.31 ( 1252) hydrogen bonds : angle 5.75767 / 4.12 ( 3228) Misc. bond : bond 0.00889 / 0.47 ( 1) link_BETA1-4 : bond 0.00647 / 0.40 ( 21) link_BETA1-4 : angle 2.97164 / 1.85 ( 63) link_NAG-ASN : bond 0.00644 / 0.43 ( 42) link_NAG-ASN : angle 3.61622 / 2.58 ( 126) *********************** 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 435 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 327 time to evaluate : 1.305 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: 0.8804 (mm-30) cc_final: 0.8602 (tp30) REVERT: C 27 GLU cc_start: 0.8085 (pt0) cc_final: 0.7803 (pm20) REVERT: C 42 GLN cc_start: 0.9051 (pt0) cc_final: 0.8688 (pm20) REVERT: C 87 PHE cc_start: 0.9126 (m-80) cc_final: 0.8884 (m-80) REVERT: C 90 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: C 92 LYS cc_start: 0.9503 (tptm) cc_final: 0.9201 (tppp) REVERT: C 93 GLU cc_start: 0.9017 (pm20) cc_final: 0.8800 (pm20) REVERT: D 843 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7972 (t70) REVERT: D 857 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: D 1097 GLN cc_start: 0.8584 (tp40) cc_final: 0.8273 (tm-30) REVERT: D 1222 LEU cc_start: 0.8975 (tp) cc_final: 0.8762 (pt) REVERT: E 28 THR cc_start: 0.7698 (p) cc_final: 0.7430 (p) REVERT: E 51 PHE cc_start: 0.8212 (t80) cc_final: 0.7842 (t80) REVERT: F 15 LEU cc_start: 0.8107 (tp) cc_final: 0.7511 (mp) REVERT: F 27 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8342 (tm-30) REVERT: F 33 MET cc_start: 0.8921 (tpp) cc_final: 0.8651 (tpp) REVERT: F 34 ASN cc_start: 0.8969 (m-40) cc_final: 0.8767 (m-40) REVERT: F 87 PHE cc_start: 0.8543 (m-80) cc_final: 0.8218 (m-80) REVERT: G 913 MET cc_start: 0.4410 (mtt) cc_final: 0.3929 (ptp) REVERT: G 1067 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8498 (mm) REVERT: G 1180 ILE cc_start: 0.9135 (mp) cc_final: 0.8614 (tt) REVERT: G 1222 LEU cc_start: 0.8129 (tp) cc_final: 0.7046 (pt) REVERT: H 59 TYR cc_start: 0.8011 (m-80) cc_final: 0.7533 (m-10) REVERT: H 81 GLU cc_start: 0.8618 (tt0) cc_final: 0.7853 (tp30) REVERT: H 85 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8276 (mp0) REVERT: p 147 PHE cc_start: 0.8584 (m-80) cc_final: 0.8159 (m-80) REVERT: p 278 MET cc_start: 0.7844 (tpp) cc_final: 0.7516 (tpp) REVERT: p 330 ASP cc_start: 0.8517 (p0) cc_final: 0.8283 (p0) REVERT: p 563 MET cc_start: 0.3303 (ptp) cc_final: 0.1940 (tpp) REVERT: q 148 MET cc_start: 0.8489 (ttt) cc_final: 0.8149 (ttt) REVERT: q 278 MET cc_start: 0.8353 (mpp) cc_final: 0.8062 (mmm) REVERT: q 468 ASN cc_start: 0.4112 (m-40) cc_final: 0.3324 (m-40) REVERT: q 637 ASN cc_start: 0.8570 (t0) cc_final: 0.8149 (t0) REVERT: q 728 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7978 (tptt) REVERT: r 346 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: r 592 ASN cc_start: 0.7546 (m-40) cc_final: 0.7019 (p0) outliers start: 108 outliers final: 77 residues processed: 404 average time/residue: 0.1987 time to fit residues: 135.6322 Evaluate side-chains 378 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 296 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 A residue 1008 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER 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 857 GLN 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 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 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1067 ILE 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 I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 206 THR 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 p residue 621 THR Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 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 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 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 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 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 119 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN D1145 ASN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 637 ASN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 194 HIS ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 421 ASN r 733 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.098337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078014 restraints weight = 166042.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078664 restraints weight = 109102.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078523 restraints weight = 76895.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078730 restraints weight = 80872.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078879 restraints weight = 71787.915| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 34737 Z= 0.287 Angle : 0.848 15.720 47374 Z= 0.420 Chirality : 0.052 0.556 5406 Planarity : 0.006 0.070 6024 Dihedral : 5.515 32.621 4629 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.57 % Rotamer: Outliers : 3.37 % Allowed : 13.46 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4227 helix: 0.61 (0.19), residues: 720 sheet: 0.07 (0.15), residues: 1048 loop : -0.64 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 181 TYR 0.034 0.002 TYR A 905 PHE 0.019 0.002 PHE p 116 TRP 0.032 0.002 TRP F 35 HIS 0.008 0.002 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 (34617) covalent geometry : angle 0.81235 / 0.41 (47073) SS BOND : bond 0.00482 / 0.33 ( 56) SS BOND : angle 1.46488 / 0.97 ( 112) hydrogen bonds : bond 0.05436 / 3.61 ( 1252) hydrogen bonds : angle 6.05116 / 4.33 ( 3228) Misc. bond : bond 0.00444 / 0.23 ( 1) link_BETA1-4 : bond 0.00688 / 0.44 ( 21) link_BETA1-4 : angle 3.05853 / 1.89 ( 63) link_NAG-ASN : bond 0.00657 / 0.45 ( 42) link_NAG-ASN : angle 4.17509 / 2.96 ( 126) *********************** 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 426 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 303 time to evaluate : 1.340 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: C 90 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: C 92 LYS cc_start: 0.9479 (tptm) cc_final: 0.9206 (tppp) REVERT: C 93 GLU cc_start: 0.8993 (pm20) cc_final: 0.8769 (pm20) REVERT: D 843 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7839 (t0) REVERT: D 1097 GLN cc_start: 0.8754 (tp40) cc_final: 0.8320 (tm-30) REVERT: D 1222 LEU cc_start: 0.9014 (tp) cc_final: 0.8790 (pt) REVERT: F 4 LEU cc_start: 0.8033 (mt) cc_final: 0.7812 (mm) REVERT: F 33 MET cc_start: 0.8886 (tpp) cc_final: 0.8682 (tpp) REVERT: F 87 PHE cc_start: 0.8551 (m-80) cc_final: 0.8142 (m-80) REVERT: F 89 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: F 90 GLN cc_start: 0.7556 (pp30) cc_final: 0.6954 (pp30) REVERT: G 757 MET cc_start: 0.8517 (mmt) cc_final: 0.8285 (mmp) REVERT: G 1105 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: H 81 GLU cc_start: 0.8617 (tt0) cc_final: 0.7824 (tp30) REVERT: H 85 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8388 (mp0) REVERT: p 147 PHE cc_start: 0.8592 (m-80) cc_final: 0.7907 (m-80) REVERT: p 278 MET cc_start: 0.7904 (tpp) cc_final: 0.7603 (tpp) REVERT: p 563 MET cc_start: 0.3412 (ptp) cc_final: 0.2203 (tpp) REVERT: q 148 MET cc_start: 0.8591 (ttt) cc_final: 0.8282 (ttt) REVERT: q 278 MET cc_start: 0.8529 (mpp) cc_final: 0.8116 (mpp) REVERT: q 428 ILE cc_start: 0.8151 (tt) cc_final: 0.7944 (tt) REVERT: q 468 ASN cc_start: 0.4046 (m-40) cc_final: 0.3240 (m-40) REVERT: q 637 ASN cc_start: 0.8657 (t0) cc_final: 0.8225 (t0) REVERT: q 728 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7932 (tptt) REVERT: r 204 PHE cc_start: 0.8179 (t80) cc_final: 0.7972 (t80) REVERT: r 346 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8820 (tm-30) outliers start: 123 outliers final: 93 residues processed: 398 average time/residue: 0.2026 time to fit residues: 136.1188 Evaluate side-chains 389 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 291 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL 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 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 22 SER 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 951 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 E residue 18 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 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 89 GLN 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 1005 LEU Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1105 GLU 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 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE 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 100 LEU Chi-restraints excluded: chain p residue 141 ARG Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR 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 p residue 621 THR Chi-restraints excluded: chain p residue 629 ARG Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 135 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 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 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 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 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 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 Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 255 optimal weight: 40.0000 chunk 392 optimal weight: 0.8980 chunk 296 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 286 optimal weight: 8.9990 chunk 313 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** G1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.093021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068520 restraints weight = 145920.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071001 restraints weight = 81146.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071227 restraints weight = 48648.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071638 restraints weight = 43476.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071699 restraints weight = 40173.497| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34737 Z= 0.153 Angle : 0.757 17.987 47374 Z= 0.369 Chirality : 0.049 0.501 5406 Planarity : 0.005 0.068 6024 Dihedral : 5.211 35.230 4629 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.99 % Favored : 94.80 % Rotamer: Outliers : 2.60 % Allowed : 14.92 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4227 helix: 1.11 (0.20), residues: 690 sheet: 0.16 (0.15), residues: 1054 loop : -0.53 (0.13), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG q 235 TYR 0.029 0.001 TYR A 905 PHE 0.027 0.001 PHE p 116 TRP 0.026 0.001 TRP F 35 HIS 0.007 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (34617) covalent geometry : angle 0.71998 / 0.36 (47073) SS BOND : bond 0.00449 / 0.25 ( 56) SS BOND : angle 1.51822 / 1.09 ( 112) hydrogen bonds : bond 0.04865 / 3.26 ( 1252) hydrogen bonds : angle 5.64652 / 4.04 ( 3228) Misc. bond : bond 0.00754 / 0.40 ( 1) link_BETA1-4 : bond 0.00659 / 0.41 ( 21) link_BETA1-4 : angle 2.89498 / 1.81 ( 63) link_NAG-ASN : bond 0.00717 / 0.44 ( 42) link_NAG-ASN : angle 3.93850 / 2.84 ( 126) *********************** 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 410 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 315 time to evaluate : 1.332 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: B 39 GLN cc_start: 0.9195 (tp40) cc_final: 0.8686 (tp-100) REVERT: C 92 LYS cc_start: 0.9431 (tptm) cc_final: 0.9132 (tppp) REVERT: C 93 GLU cc_start: 0.8966 (pm20) cc_final: 0.8694 (pm20) REVERT: D 843 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7958 (t70) REVERT: E 28 THR cc_start: 0.7653 (p) cc_final: 0.7368 (t) REVERT: F 4 LEU cc_start: 0.8089 (mt) cc_final: 0.7860 (mm) REVERT: F 35 TRP cc_start: 0.7543 (m-10) cc_final: 0.7292 (m-10) REVERT: F 87 PHE cc_start: 0.8397 (m-80) cc_final: 0.8081 (m-80) REVERT: F 89 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: F 90 GLN cc_start: 0.7543 (pp30) cc_final: 0.6880 (pp30) REVERT: G 1119 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: G 1132 ASN cc_start: 0.9014 (p0) cc_final: 0.8697 (p0) REVERT: H 59 TYR cc_start: 0.7807 (m-10) cc_final: 0.7283 (m-10) REVERT: H 81 GLU cc_start: 0.8601 (tt0) cc_final: 0.7746 (tp30) REVERT: H 85 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8276 (mp0) REVERT: p 147 PHE cc_start: 0.8504 (m-80) cc_final: 0.7670 (m-80) REVERT: p 278 MET cc_start: 0.7834 (tpp) cc_final: 0.7460 (tpp) REVERT: p 330 ASP cc_start: 0.8631 (p0) cc_final: 0.8293 (p0) REVERT: p 332 TYR cc_start: 0.8726 (m-80) cc_final: 0.8379 (m-80) REVERT: p 563 MET cc_start: 0.3839 (ptp) cc_final: 0.2483 (tpp) REVERT: q 148 MET cc_start: 0.8511 (ttt) cc_final: 0.8264 (ttt) REVERT: q 278 MET cc_start: 0.8598 (mpp) cc_final: 0.8292 (mmm) REVERT: q 468 ASN cc_start: 0.4117 (m-40) cc_final: 0.3281 (m-40) REVERT: q 637 ASN cc_start: 0.8635 (t0) cc_final: 0.8170 (t0) REVERT: q 686 MET cc_start: 0.4685 (mmm) cc_final: 0.4389 (mmm) REVERT: q 728 LYS cc_start: 0.8475 (mmtt) cc_final: 0.7931 (tptt) REVERT: r 346 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: r 563 MET cc_start: 0.5203 (mmp) cc_final: 0.2262 (tpp) outliers start: 95 outliers final: 76 residues processed: 385 average time/residue: 0.2048 time to fit residues: 133.5100 Evaluate side-chains 367 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL 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 1103 VAL 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 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER 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 1075 LEU 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 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 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 89 GLN 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 1005 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 1119 GLN Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER 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 p residue 621 THR 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 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE 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 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE 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 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 Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 233 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 405 optimal weight: 0.0570 chunk 397 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D1084 GLN ** 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 ** G1132 ASN ** 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.098519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071413 restraints weight = 126791.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.073171 restraints weight = 75712.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074303 restraints weight = 55246.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.075044 restraints weight = 45584.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075409 restraints weight = 40417.024| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34737 Z= 0.179 Angle : 0.768 18.026 47374 Z= 0.375 Chirality : 0.049 0.505 5406 Planarity : 0.005 0.067 6024 Dihedral : 5.156 32.042 4629 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.04 % Rotamer: Outliers : 2.60 % Allowed : 15.35 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4227 helix: 1.13 (0.20), residues: 690 sheet: 0.14 (0.15), residues: 1099 loop : -0.58 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG r 542 TYR 0.045 0.001 TYR D 777 PHE 0.026 0.002 PHE r 313 TRP 0.027 0.002 TRP F 35 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (34617) covalent geometry : angle 0.73249 / 0.37 (47073) SS BOND : bond 0.00483 / 0.27 ( 56) SS BOND : angle 1.73282 / 1.23 ( 112) hydrogen bonds : bond 0.04805 / 3.21 ( 1252) hydrogen bonds : angle 5.60020 / 4.00 ( 3228) Misc. bond : bond 0.00711 / 0.37 ( 1) link_BETA1-4 : bond 0.00661 / 0.42 ( 21) link_BETA1-4 : angle 2.84890 / 1.78 ( 63) link_NAG-ASN : bond 0.00667 / 0.41 ( 42) link_NAG-ASN : angle 3.85476 / 2.77 ( 126) *********************** 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 400 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 305 time to evaluate : 1.292 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: B 39 GLN cc_start: 0.9152 (tp40) cc_final: 0.8748 (tp-100) REVERT: C 90 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: C 92 LYS cc_start: 0.9453 (tptm) cc_final: 0.9232 (tppp) REVERT: C 93 GLU cc_start: 0.8981 (pm20) cc_final: 0.8780 (pm20) REVERT: D 843 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7736 (t0) REVERT: D 913 MET cc_start: 0.6951 (ptt) cc_final: 0.6279 (ptp) REVERT: E 28 THR cc_start: 0.7616 (p) cc_final: 0.7363 (t) REVERT: E 51 PHE cc_start: 0.8246 (t80) cc_final: 0.7877 (t80) REVERT: F 15 LEU cc_start: 0.8061 (tp) cc_final: 0.7549 (mm) REVERT: F 90 GLN cc_start: 0.7894 (pp30) cc_final: 0.7661 (pp30) REVERT: G 1119 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: G 1132 ASN cc_start: 0.9098 (p0) cc_final: 0.8822 (p0) REVERT: H 81 GLU cc_start: 0.8635 (tt0) cc_final: 0.7761 (tp30) REVERT: H 85 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8277 (mp0) REVERT: I 92 LYS cc_start: 0.8580 (tttt) cc_final: 0.8325 (tttt) REVERT: p 100 LEU cc_start: 0.7144 (mm) cc_final: 0.6704 (mm) REVERT: p 147 PHE cc_start: 0.8231 (m-80) cc_final: 0.7451 (m-80) REVERT: p 278 MET cc_start: 0.7855 (tpp) cc_final: 0.7510 (tpp) REVERT: p 330 ASP cc_start: 0.8649 (p0) cc_final: 0.8275 (p0) REVERT: p 332 TYR cc_start: 0.8774 (m-80) cc_final: 0.8381 (m-80) REVERT: p 400 LYS cc_start: 0.3860 (mmtt) cc_final: 0.3629 (mmtm) REVERT: p 563 MET cc_start: 0.3678 (ptp) cc_final: 0.2480 (tpp) REVERT: q 278 MET cc_start: 0.8527 (mpp) cc_final: 0.8245 (mmm) REVERT: q 428 ILE cc_start: 0.7559 (tt) cc_final: 0.7353 (tt) REVERT: q 468 ASN cc_start: 0.4070 (m-40) cc_final: 0.3325 (m-40) REVERT: q 637 ASN cc_start: 0.8638 (t0) cc_final: 0.8174 (t0) REVERT: q 686 MET cc_start: 0.4848 (mmm) cc_final: 0.4635 (mmm) REVERT: q 728 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7938 (tptt) REVERT: r 346 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8855 (tm-30) REVERT: r 563 MET cc_start: 0.4886 (mmp) cc_final: 0.1891 (tpp) REVERT: r 592 ASN cc_start: 0.7545 (m-40) cc_final: 0.7167 (p0) outliers start: 95 outliers final: 80 residues processed: 378 average time/residue: 0.1982 time to fit residues: 127.6267 Evaluate side-chains 369 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL 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 1103 VAL 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 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER 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 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 1181 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 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 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 1005 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 1119 GLN Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 206 THR 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 p residue 621 THR Chi-restraints excluded: chain p residue 727 CYS 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 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE 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 170 VAL Chi-restraints excluded: chain r residue 183 PHE 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 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 Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 409 optimal weight: 7.9990 chunk 377 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 681 HIS ** r 36 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069029 restraints weight = 138591.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071725 restraints weight = 82485.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071884 restraints weight = 51415.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072304 restraints weight = 44068.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072430 restraints weight = 42157.226| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34737 Z= 0.195 Angle : 0.786 18.031 47374 Z= 0.384 Chirality : 0.050 0.602 5406 Planarity : 0.005 0.067 6024 Dihedral : 5.211 39.445 4629 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.87 % Favored : 93.90 % Rotamer: Outliers : 2.57 % Allowed : 15.46 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4227 helix: 1.08 (0.20), residues: 690 sheet: 0.09 (0.15), residues: 1103 loop : -0.61 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 629 TYR 0.051 0.002 TYR D 777 PHE 0.019 0.002 PHE p 116 TRP 0.056 0.002 TRP r 553 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (34617) covalent geometry : angle 0.75117 / 0.38 (47073) SS BOND : bond 0.00491 / 0.27 ( 56) SS BOND : angle 1.71748 / 1.22 ( 112) hydrogen bonds : bond 0.04815 / 3.21 ( 1252) hydrogen bonds : angle 5.61581 / 4.01 ( 3228) Misc. bond : bond 0.00972 / 0.51 ( 1) link_BETA1-4 : bond 0.00662 / 0.42 ( 21) link_BETA1-4 : angle 2.83122 / 1.77 ( 63) link_NAG-ASN : bond 0.00669 / 0.41 ( 42) link_NAG-ASN : angle 3.83227 / 2.75 ( 126) ********************** 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 382 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 1.488 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: A 891 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7230 (mt-10) REVERT: B 39 GLN cc_start: 0.9291 (tp40) cc_final: 0.8761 (tp-100) REVERT: C 92 LYS cc_start: 0.9419 (tptm) cc_final: 0.9215 (tppp) REVERT: C 93 GLU cc_start: 0.8970 (pm20) cc_final: 0.8736 (pm20) REVERT: D 843 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7789 (t0) REVERT: D 913 MET cc_start: 0.6899 (ptt) cc_final: 0.6241 (ptp) REVERT: D 1039 GLU cc_start: 0.8679 (tp30) cc_final: 0.8442 (tp30) REVERT: D 1182 ASP cc_start: 0.7682 (t0) cc_final: 0.7436 (p0) REVERT: E 28 THR cc_start: 0.7474 (p) cc_final: 0.7197 (t) REVERT: E 51 PHE cc_start: 0.8289 (t80) cc_final: 0.7950 (t80) REVERT: F 15 LEU cc_start: 0.8088 (tp) cc_final: 0.7630 (mm) REVERT: F 33 MET cc_start: 0.8504 (tpt) cc_final: 0.6342 (ptt) REVERT: F 87 PHE cc_start: 0.8502 (m-80) cc_final: 0.8196 (m-80) REVERT: G 1119 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: G 1132 ASN cc_start: 0.9102 (p0) cc_final: 0.8842 (p0) REVERT: H 69 MET cc_start: 0.7228 (mtm) cc_final: 0.6899 (mtm) REVERT: H 81 GLU cc_start: 0.8554 (tt0) cc_final: 0.8242 (mp0) REVERT: H 85 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8387 (mp0) REVERT: I 89 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7587 (tm-30) REVERT: p 100 LEU cc_start: 0.7572 (mm) cc_final: 0.7127 (mm) REVERT: p 147 PHE cc_start: 0.8360 (m-80) cc_final: 0.7582 (m-80) REVERT: p 278 MET cc_start: 0.7853 (tpp) cc_final: 0.7518 (tpp) REVERT: p 330 ASP cc_start: 0.8648 (p0) cc_final: 0.8309 (p0) REVERT: p 332 TYR cc_start: 0.8725 (m-80) cc_final: 0.8312 (m-80) REVERT: p 400 LYS cc_start: 0.3816 (mmtt) cc_final: 0.3548 (mmtm) REVERT: p 563 MET cc_start: 0.3769 (ptp) cc_final: 0.2498 (tpp) REVERT: q 148 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7934 (ttt) REVERT: q 149 LEU cc_start: 0.8946 (mm) cc_final: 0.8742 (tp) REVERT: q 278 MET cc_start: 0.8560 (mpp) cc_final: 0.8140 (mpp) REVERT: q 428 ILE cc_start: 0.7530 (tt) cc_final: 0.7329 (tt) REVERT: q 468 ASN cc_start: 0.4114 (m-40) cc_final: 0.3294 (m-40) REVERT: q 637 ASN cc_start: 0.8649 (t0) cc_final: 0.8177 (t0) REVERT: q 686 MET cc_start: 0.4844 (mmm) cc_final: 0.4623 (mmm) REVERT: q 728 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7986 (tptt) REVERT: r 148 MET cc_start: 0.8543 (tpp) cc_final: 0.7946 (tpp) REVERT: r 346 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8818 (tm-30) REVERT: r 563 MET cc_start: 0.5085 (mmp) cc_final: 0.2122 (tpp) REVERT: r 592 ASN cc_start: 0.7608 (m-40) cc_final: 0.7216 (p0) outliers start: 94 outliers final: 83 residues processed: 361 average time/residue: 0.1857 time to fit residues: 115.6157 Evaluate side-chains 372 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL 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 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER 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 1008 MET Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1087 VAL 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 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 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 1005 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 1119 GLN Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 206 THR 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 621 THR Chi-restraints excluded: chain p residue 727 CYS Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 148 MET Chi-restraints excluded: chain q residue 183 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 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 170 VAL Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 240 MET 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 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 352 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 382 optimal weight: 0.0040 chunk 319 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1063 GLN G1132 ASN H 6 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 167 HIS ** r 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 688 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068538 restraints weight = 146518.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.071169 restraints weight = 81594.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071724 restraints weight = 55738.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072341 restraints weight = 39481.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072478 restraints weight = 35784.213| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 34737 Z= 0.146 Angle : 0.749 17.389 47374 Z= 0.363 Chirality : 0.050 0.909 5406 Planarity : 0.005 0.066 6024 Dihedral : 4.992 36.501 4629 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.51 % Favored : 94.25 % Rotamer: Outliers : 2.60 % Allowed : 15.52 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4227 helix: 1.32 (0.20), residues: 687 sheet: 0.17 (0.15), residues: 1088 loop : -0.58 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 629 TYR 0.044 0.001 TYR D 777 PHE 0.022 0.001 PHE p 116 TRP 0.027 0.002 TRP F 35 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (34617) covalent geometry : angle 0.71507 / 0.35 (47073) SS BOND : bond 0.00421 / 0.22 ( 56) SS BOND : angle 1.60236 / 1.15 ( 112) hydrogen bonds : bond 0.04490 / 3.01 ( 1252) hydrogen bonds : angle 5.38537 / 3.85 ( 3228) Misc. bond : bond 0.00780 / 0.41 ( 1) link_BETA1-4 : bond 0.00652 / 0.41 ( 21) link_BETA1-4 : angle 2.72178 / 1.71 ( 63) link_NAG-ASN : bond 0.00691 / 0.42 ( 42) link_NAG-ASN : angle 3.69552 / 2.67 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6263.63 seconds wall clock time: 109 minutes 23.93 seconds (6563.93 seconds total)