Starting phenix.real_space_refine on Sat Jul 4 00:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.map" model { file = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uds_26458/07_2026/7uds_26458.cif" } resolution = 3.1 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= 0.001 sd= 0.017 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 105 5.16 5 C 10672 2.51 5 N 2837 2.21 5 O 3418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17032 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "C" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "a" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "c" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "b" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "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: "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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "c" 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: "b" 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 Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 17032 At special positions: 0 Unit cell: (209.336, 198.376, 89.872, 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 105 16.00 O 3418 8.00 N 2837 7.00 C 10672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.05 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 301 " - " ASN A 166 " " NAG A 302 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 118 " " NAG C 301 " - " ASN C 166 " " NAG C 302 " - " ASN C 118 " " NAG I 1 " - " ASN A 78 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 98 " " NAG M 1 " - " ASN A 108 " " NAG N 1 " - " ASN A 223 " " NAG O 1 " - " ASN C 78 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 98 " " NAG R 1 " - " ASN C 108 " " NAG S 1 " - " ASN C 223 " " NAG T 1 " - " ASN B 78 " " NAG U 1 " - " ASN B 88 " " NAG V 1 " - " ASN B 98 " " NAG W 1 " - " ASN B 223 " " NAG a 501 " - " ASN a 372 " " NAG b 501 " - " ASN b 372 " " NAG c 501 " - " ASN c 372 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 708.8 milliseconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 40 sheets defined 23.2% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N LYS D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.145A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.516A pdb=" N LYS F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N PHE L 82 " --> pdb=" O PRO L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 125 Processing helix chain 'L' and resid 179 through 185 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.510A pdb=" N LYS H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 194 through 200 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.953A pdb=" N PHE G 82 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 179 through 185 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.955A pdb=" N PHE E 82 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.766A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.019A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.553A pdb=" N MET A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'C' and resid 73 through 78 removed outlier: 4.026A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.057A pdb=" N ASN C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.559A pdb=" N MET C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.044A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.850A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.028A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.683A pdb=" N MET B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS B 160 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 308 through 324 Processing helix chain 'a' and resid 332 through 344 removed outlier: 3.529A pdb=" N ILE a 336 " --> pdb=" O SER a 332 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE a 344 " --> pdb=" O VAL a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 Processing helix chain 'a' and resid 395 through 397 No H-bonds generated for 'chain 'a' and resid 395 through 397' Processing helix chain 'a' and resid 398 through 414 removed outlier: 3.620A pdb=" N ILE a 402 " --> pdb=" O PHE a 398 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU a 414 " --> pdb=" O ILE a 410 " (cutoff:3.500A) Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 removed outlier: 3.588A pdb=" N GLU c 302 " --> pdb=" O LYS c 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 299 through 302' Processing helix chain 'c' and resid 308 through 325 Processing helix chain 'c' and resid 333 through 344 removed outlier: 4.047A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE c 344 " --> pdb=" O VAL c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 394 through 397 Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.520A pdb=" N ILE c 402 " --> pdb=" O PHE c 398 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 removed outlier: 3.650A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 302' Processing helix chain 'b' and resid 308 through 324 Processing helix chain 'b' and resid 332 through 344 removed outlier: 3.573A pdb=" N ILE b 336 " --> pdb=" O SER b 332 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE b 344 " --> pdb=" O VAL b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.595A pdb=" N ILE b 402 " --> pdb=" O PHE b 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.786A pdb=" N ASN D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.952A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'F' and resid 128 through 132 removed outlier: 5.878A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AB3, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.644A pdb=" N ASP L 102 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR L 48 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 111 through 115 Processing sheet with id=AB6, first strand: chain 'L' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.896A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.970A pdb=" N LEU H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 100 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA H 108 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.753A pdb=" N ASP G 102 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU G 32 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR G 48 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP G 34 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 111 through 115 Processing sheet with id=AC7, first strand: chain 'G' and resid 141 through 147 Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.548A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 111 through 115 Processing sheet with id=AD2, first strand: chain 'E' and resid 141 through 147 Processing sheet with id=AD3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AD4, first strand: chain 'A' and resid 83 through 88 removed outlier: 3.548A pdb=" N LYS A 87 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 67 through 71 Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.686A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.613A pdb=" N TYR B 93 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 87 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'c' and resid 278 through 279 removed outlier: 3.704A pdb=" N LEU c 279 " --> pdb=" O LYS c 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS c 290 " --> pdb=" O LEU c 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'b' and resid 278 through 279 removed outlier: 3.748A pdb=" N LEU b 279 " --> pdb=" O LYS b 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS b 290 " --> pdb=" O LEU b 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'b' and resid 387 through 388 741 hydrogen bonds defined for protein. 1941 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: 1.95 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5361 1.35 - 1.47: 4536 1.47 - 1.60: 7317 1.60 - 1.73: 1 1.73 - 1.85: 153 Bond restraints: 17368 Sorted by residual: bond pdb=" C1 MAN V 4 " pdb=" C2 MAN V 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG C 301 " pdb=" O5 NAG C 301 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 MAN V 4 " pdb=" O5 MAN V 4 " ideal model delta sigma weight residual 1.399 1.474 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23059 2.35 - 4.70: 416 4.70 - 7.05: 50 7.05 - 9.39: 7 9.39 - 11.74: 2 Bond angle restraints: 23534 Sorted by residual: angle pdb=" C SER G 29 " pdb=" CA SER G 29 " pdb=" CB SER G 29 " ideal model delta sigma weight residual 117.23 110.83 6.40 1.36e+00 5.41e-01 2.21e+01 angle pdb=" CA CYS c 291 " pdb=" CB CYS c 291 " pdb=" SG CYS c 291 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA SER G 29 " pdb=" C SER G 29 " pdb=" N SER G 30 " ideal model delta sigma weight residual 119.98 117.11 2.87 8.50e-01 1.38e+00 1.14e+01 angle pdb=" N TRP a 385 " pdb=" CA TRP a 385 " pdb=" C TRP a 385 " ideal model delta sigma weight residual 110.55 106.31 4.24 1.35e+00 5.49e-01 9.85e+00 angle pdb=" CA CYS a 291 " pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " ideal model delta sigma weight residual 114.40 121.28 -6.88 2.30e+00 1.89e-01 8.94e+00 ... (remaining 23529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 9053 17.53 - 35.06: 820 35.06 - 52.59: 175 52.59 - 70.12: 11 70.12 - 87.65: 9 Dihedral angle restraints: 10068 sinusoidal: 3969 harmonic: 6099 Sorted by residual: dihedral pdb=" CB CYS c 363 " pdb=" SG CYS c 363 " pdb=" SG CYS c 384 " pdb=" CB CYS c 384 " ideal model delta sinusoidal sigma weight residual -86.00 -170.32 84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.32 82.32 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.12 82.12 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 10065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2273 0.057 - 0.113: 453 0.113 - 0.170: 66 0.170 - 0.227: 10 0.227 - 0.283: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B 78 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2809 not shown) Planarity restraints: 2936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " -0.030 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP a 385 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 192 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO H 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 192 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO D 193 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " -0.027 5.00e-02 4.00e+02 ... (remaining 2933 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 172 2.59 - 3.17: 13658 3.17 - 3.75: 24480 3.75 - 4.32: 34315 4.32 - 4.90: 56703 Nonbonded interactions: 129328 Sorted by model distance: nonbonded pdb=" OE1 GLU L 192 " pdb=" OG1 THR L 203 " model vdw 2.015 3.040 nonbonded pdb=" OE1 GLU G 192 " pdb=" OG1 THR G 203 " model vdw 2.097 3.040 nonbonded pdb=" O TRP F 106 " pdb=" OG SER G 90 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLU E 192 " pdb=" OG1 THR E 203 " model vdw 2.164 3.040 nonbonded pdb=" OG SER B 90 " pdb=" O7 NAG U 1 " model vdw 2.213 3.040 ... (remaining 129323 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 66 through 302) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.760 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17448 Z= 0.226 Angle : 0.776 13.345 23747 Z= 0.363 Chirality : 0.049 0.283 2812 Planarity : 0.004 0.050 2912 Dihedral : 13.457 87.653 6045 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.23 (0.19), residues: 2046 helix: 0.69 (0.29), residues: 345 sheet: 0.67 (0.19), residues: 783 loop : -1.22 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.019 0.002 TYR E 48 PHE 0.017 0.002 PHE G 70 TRP 0.073 0.002 TRP a 385 HIS 0.006 0.001 HIS a 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (17368) covalent geometry : angle 0.74309 / 0.35 (23534) SS BOND : bond 0.00708 / 0.47 ( 27) SS BOND : angle 1.73256 / 1.04 ( 54) hydrogen bonds : bond 0.13650 / 8.63 ( 691) hydrogen bonds : angle 6.36723 / 4.43 ( 1941) link_ALPHA1-3 : bond 0.01221 / 0.53 ( 6) link_ALPHA1-3 : angle 2.22594 / 1.15 ( 18) link_ALPHA1-6 : bond 0.00739 / 0.36 ( 3) link_ALPHA1-6 : angle 1.60110 / 0.96 ( 9) link_BETA1-4 : bond 0.00775 / 0.57 ( 20) link_BETA1-4 : angle 2.28829 / 1.61 ( 60) link_NAG-ASN : bond 0.00443 / 0.25 ( 24) link_NAG-ASN : angle 3.19058 / 1.79 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.384 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: F 143 THR cc_start: 0.6360 (t) cc_final: 0.6067 (m) REVERT: H 153 TYR cc_start: 0.6062 (p90) cc_final: 0.5472 (p90) REVERT: G 3 MET cc_start: 0.7598 (mmm) cc_final: 0.7239 (mmm) REVERT: a 394 ASN cc_start: 0.7658 (p0) cc_final: 0.7441 (p0) REVERT: a 413 MET cc_start: 0.6709 (tmm) cc_final: 0.6452 (tmm) REVERT: c 286 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5820 (tm-30) REVERT: b 350 MET cc_start: 0.7231 (mmm) cc_final: 0.6932 (mmm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1088 time to fit residues: 46.0554 Evaluate side-chains 254 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN D 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS a 318 ASN ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 318 ASN c 405 GLN b 318 ASN b 353 HIS b 364 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.173201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147824 restraints weight = 27777.623| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.51 r_work: 0.3778 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17448 Z= 0.195 Angle : 0.721 11.813 23747 Z= 0.350 Chirality : 0.046 0.271 2812 Planarity : 0.005 0.051 2912 Dihedral : 4.834 19.452 2238 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.92 % Allowed : 8.29 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.33 (0.19), residues: 2046 helix: 0.49 (0.27), residues: 357 sheet: 0.59 (0.19), residues: 789 loop : -1.23 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 105 TYR 0.024 0.002 TYR F 94 PHE 0.018 0.002 PHE D 80 TRP 0.020 0.002 TRP a 385 HIS 0.005 0.001 HIS c 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (17368) covalent geometry : angle 0.68660 / 0.34 (23534) SS BOND : bond 0.00777 / 0.51 ( 27) SS BOND : angle 1.94457 / 1.19 ( 54) hydrogen bonds : bond 0.04221 / 2.67 ( 691) hydrogen bonds : angle 5.42778 / 3.74 ( 1941) link_ALPHA1-3 : bond 0.01530 / 0.71 ( 6) link_ALPHA1-3 : angle 2.38334 / 1.23 ( 18) link_ALPHA1-6 : bond 0.00858 / 0.42 ( 3) link_ALPHA1-6 : angle 1.64681 / 0.95 ( 9) link_BETA1-4 : bond 0.00669 / 0.49 ( 20) link_BETA1-4 : angle 1.89615 / 1.35 ( 60) link_NAG-ASN : bond 0.00508 / 0.28 ( 24) link_NAG-ASN : angle 3.08976 / 1.75 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 258 time to evaluate : 0.609 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: F 143 THR cc_start: 0.6426 (t) cc_final: 0.6144 (m) REVERT: H 153 TYR cc_start: 0.6253 (p90) cc_final: 0.5629 (p90) REVERT: G 81 ASP cc_start: 0.7055 (m-30) cc_final: 0.6827 (m-30) REVERT: B 81 MET cc_start: 0.7004 (mtp) cc_final: 0.6787 (mtp) REVERT: a 392 TYR cc_start: 0.8605 (m-80) cc_final: 0.8395 (m-80) REVERT: a 409 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5814 (mpp) REVERT: a 413 MET cc_start: 0.7010 (tmm) cc_final: 0.6561 (tmm) REVERT: c 286 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6371 (tm-30) REVERT: c 335 LEU cc_start: 0.7731 (tt) cc_final: 0.7502 (tp) REVERT: c 338 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7875 (ptmt) REVERT: b 350 MET cc_start: 0.7642 (mmm) cc_final: 0.7383 (mpp) outliers start: 17 outliers final: 13 residues processed: 264 average time/residue: 0.1185 time to fit residues: 48.9209 Evaluate side-chains 266 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 42 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148395 restraints weight = 28133.157| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.53 r_work: 0.3781 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17448 Z= 0.160 Angle : 0.669 11.633 23747 Z= 0.324 Chirality : 0.045 0.277 2812 Planarity : 0.005 0.050 2912 Dihedral : 4.694 17.627 2238 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.41 % Allowed : 12.09 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.29 (0.19), residues: 2046 helix: 0.52 (0.27), residues: 357 sheet: 0.58 (0.19), residues: 786 loop : -1.17 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 105 TYR 0.018 0.002 TYR F 94 PHE 0.019 0.002 PHE D 80 TRP 0.011 0.002 TRP a 385 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (17368) covalent geometry : angle 0.63636 / 0.32 (23534) SS BOND : bond 0.00706 / 0.47 ( 27) SS BOND : angle 1.75854 / 1.07 ( 54) hydrogen bonds : bond 0.03922 / 2.48 ( 691) hydrogen bonds : angle 5.21100 / 3.59 ( 1941) link_ALPHA1-3 : bond 0.01340 / 0.64 ( 6) link_ALPHA1-3 : angle 2.18903 / 1.11 ( 18) link_ALPHA1-6 : bond 0.00881 / 0.43 ( 3) link_ALPHA1-6 : angle 1.56524 / 0.93 ( 9) link_BETA1-4 : bond 0.00665 / 0.48 ( 20) link_BETA1-4 : angle 1.83084 / 1.30 ( 60) link_NAG-ASN : bond 0.00424 / 0.24 ( 24) link_NAG-ASN : angle 2.90870 / 1.66 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 143 THR cc_start: 0.6334 (t) cc_final: 0.6056 (m) REVERT: H 153 TYR cc_start: 0.6199 (p90) cc_final: 0.5561 (p90) REVERT: G 81 ASP cc_start: 0.7094 (m-30) cc_final: 0.6817 (m-30) REVERT: a 286 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6582 (tm-30) REVERT: a 392 TYR cc_start: 0.8609 (m-80) cc_final: 0.8312 (m-80) REVERT: a 409 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5870 (mpp) REVERT: a 413 MET cc_start: 0.7040 (tmm) cc_final: 0.6638 (tmm) REVERT: c 286 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6347 (tm-30) REVERT: c 338 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7878 (ptmt) REVERT: b 350 MET cc_start: 0.7661 (mmm) cc_final: 0.7078 (mmm) outliers start: 26 outliers final: 17 residues processed: 269 average time/residue: 0.1264 time to fit residues: 52.7354 Evaluate side-chains 269 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 129 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 141 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.173259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147932 restraints weight = 27975.866| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.48 r_work: 0.3805 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17448 Z= 0.129 Angle : 0.634 11.372 23747 Z= 0.306 Chirality : 0.044 0.274 2812 Planarity : 0.004 0.051 2912 Dihedral : 4.536 17.083 2238 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.63 % Allowed : 14.85 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.21 (0.19), residues: 2046 helix: 0.67 (0.27), residues: 357 sheet: 0.63 (0.19), residues: 786 loop : -1.17 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.015 0.001 TYR G 48 PHE 0.013 0.001 PHE b 398 TRP 0.007 0.001 TRP a 385 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17368) covalent geometry : angle 0.60473 / 0.30 (23534) SS BOND : bond 0.00678 / 0.45 ( 27) SS BOND : angle 1.48828 / 0.93 ( 54) hydrogen bonds : bond 0.03518 / 2.23 ( 691) hydrogen bonds : angle 5.00885 / 3.45 ( 1941) link_ALPHA1-3 : bond 0.01154 / 0.57 ( 6) link_ALPHA1-3 : angle 1.98325 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00815 / 0.40 ( 3) link_ALPHA1-6 : angle 1.51658 / 0.92 ( 9) link_BETA1-4 : bond 0.00646 / 0.47 ( 20) link_BETA1-4 : angle 1.72005 / 1.23 ( 60) link_NAG-ASN : bond 0.00406 / 0.24 ( 24) link_NAG-ASN : angle 2.79843 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7132 (t) REVERT: D 64 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6674 (pp) REVERT: F 143 THR cc_start: 0.6293 (t) cc_final: 0.6041 (m) REVERT: H 153 TYR cc_start: 0.6186 (p90) cc_final: 0.4471 (p90) REVERT: G 81 ASP cc_start: 0.6962 (m-30) cc_final: 0.6679 (m-30) REVERT: A 138 THR cc_start: 0.7776 (t) cc_final: 0.7523 (p) REVERT: a 286 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6549 (tm-30) REVERT: a 392 TYR cc_start: 0.8610 (m-80) cc_final: 0.8251 (m-80) REVERT: a 409 MET cc_start: 0.6430 (mpp) cc_final: 0.5934 (mpp) REVERT: a 413 MET cc_start: 0.6948 (tmm) cc_final: 0.6569 (tmm) REVERT: c 286 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6433 (tm-30) REVERT: c 338 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7864 (ptmt) REVERT: b 409 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6524 (mpp) outliers start: 30 outliers final: 18 residues processed: 266 average time/residue: 0.1254 time to fit residues: 51.9229 Evaluate side-chains 265 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 10 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 196 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147430 restraints weight = 27784.802| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.43 r_work: 0.3795 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17448 Z= 0.168 Angle : 0.668 11.652 23747 Z= 0.321 Chirality : 0.045 0.279 2812 Planarity : 0.005 0.051 2912 Dihedral : 4.651 17.247 2238 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.11 % Allowed : 16.37 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.24 (0.19), residues: 2046 helix: 0.62 (0.27), residues: 357 sheet: 0.63 (0.19), residues: 780 loop : -1.19 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.020 0.002 TYR G 48 PHE 0.012 0.002 PHE D 27 TRP 0.008 0.002 TRP H 111 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (17368) covalent geometry : angle 0.63708 / 0.31 (23534) SS BOND : bond 0.00746 / 0.48 ( 27) SS BOND : angle 1.72978 / 1.09 ( 54) hydrogen bonds : bond 0.03803 / 2.42 ( 691) hydrogen bonds : angle 5.05509 / 3.48 ( 1941) link_ALPHA1-3 : bond 0.01179 / 0.60 ( 6) link_ALPHA1-3 : angle 2.01469 / 1.08 ( 18) link_ALPHA1-6 : bond 0.00839 / 0.41 ( 3) link_ALPHA1-6 : angle 1.51981 / 0.90 ( 9) link_BETA1-4 : bond 0.00642 / 0.47 ( 20) link_BETA1-4 : angle 1.80724 / 1.29 ( 60) link_NAG-ASN : bond 0.00427 / 0.24 ( 24) link_NAG-ASN : angle 2.88282 / 1.63 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.596 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: D 64 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6762 (pp) REVERT: F 105 THR cc_start: 0.6604 (OUTLIER) cc_final: 0.6350 (m) REVERT: F 143 THR cc_start: 0.6392 (t) cc_final: 0.6142 (m) REVERT: H 110 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8336 (tp) REVERT: H 153 TYR cc_start: 0.6384 (p90) cc_final: 0.4589 (p90) REVERT: G 81 ASP cc_start: 0.7244 (m-30) cc_final: 0.6960 (m-30) REVERT: A 138 THR cc_start: 0.7866 (t) cc_final: 0.7559 (p) REVERT: C 95 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7299 (mtt-85) REVERT: C 193 MET cc_start: 0.5627 (mmt) cc_final: 0.5340 (mmt) REVERT: a 286 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6938 (tm-30) REVERT: a 307 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: a 392 TYR cc_start: 0.8640 (m-80) cc_final: 0.8246 (m-80) REVERT: a 409 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6096 (mpp) REVERT: a 413 MET cc_start: 0.7376 (tmm) cc_final: 0.6951 (tmm) REVERT: c 286 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6861 (tm-30) REVERT: c 338 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7940 (ptmt) REVERT: b 338 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7887 (ttpp) REVERT: b 350 MET cc_start: 0.7751 (mmm) cc_final: 0.7253 (mmm) REVERT: b 409 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6752 (mpp) outliers start: 39 outliers final: 24 residues processed: 272 average time/residue: 0.1247 time to fit residues: 53.0040 Evaluate side-chains 273 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 140 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 188 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146899 restraints weight = 27684.728| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.42 r_work: 0.3784 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17448 Z= 0.197 Angle : 0.707 12.171 23747 Z= 0.341 Chirality : 0.046 0.282 2812 Planarity : 0.005 0.052 2912 Dihedral : 4.819 27.200 2238 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.55 % Allowed : 16.96 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.33 (0.19), residues: 2046 helix: 0.56 (0.27), residues: 357 sheet: 0.56 (0.19), residues: 801 loop : -1.28 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.021 0.002 TYR L 48 PHE 0.014 0.002 PHE D 27 TRP 0.011 0.002 TRP a 385 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (17368) covalent geometry : angle 0.67292 / 0.33 (23534) SS BOND : bond 0.00812 / 0.52 ( 27) SS BOND : angle 2.29065 / 1.35 ( 54) hydrogen bonds : bond 0.03991 / 2.54 ( 691) hydrogen bonds : angle 5.13295 / 3.53 ( 1941) link_ALPHA1-3 : bond 0.01193 / 0.61 ( 6) link_ALPHA1-3 : angle 2.03968 / 1.12 ( 18) link_ALPHA1-6 : bond 0.00842 / 0.41 ( 3) link_ALPHA1-6 : angle 1.55885 / 0.92 ( 9) link_BETA1-4 : bond 0.00652 / 0.47 ( 20) link_BETA1-4 : angle 1.87618 / 1.33 ( 60) link_NAG-ASN : bond 0.00447 / 0.25 ( 24) link_NAG-ASN : angle 2.97133 / 1.69 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7224 (t) REVERT: D 64 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6837 (pp) REVERT: D 132 LEU cc_start: 0.3639 (OUTLIER) cc_final: 0.2945 (tt) REVERT: F 105 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6298 (m) REVERT: H 110 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8339 (tp) REVERT: H 153 TYR cc_start: 0.6405 (p90) cc_final: 0.4637 (p90) REVERT: G 3 MET cc_start: 0.7977 (mmm) cc_final: 0.7441 (mmm) REVERT: G 81 ASP cc_start: 0.7300 (m-30) cc_final: 0.7026 (m-30) REVERT: A 138 THR cc_start: 0.7895 (t) cc_final: 0.7592 (p) REVERT: C 95 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7316 (mtt-85) REVERT: a 277 TYR cc_start: 0.8145 (t80) cc_final: 0.7760 (t80) REVERT: a 286 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6900 (tm-30) REVERT: a 307 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: a 392 TYR cc_start: 0.8614 (m-80) cc_final: 0.8197 (m-80) REVERT: a 409 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6140 (mpp) REVERT: a 413 MET cc_start: 0.7450 (tmm) cc_final: 0.7038 (tmm) REVERT: c 286 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6867 (tm-30) REVERT: c 338 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7949 (ptmt) REVERT: b 350 MET cc_start: 0.7780 (mmm) cc_final: 0.7336 (mmm) REVERT: b 409 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6850 (mpp) outliers start: 47 outliers final: 33 residues processed: 284 average time/residue: 0.1217 time to fit residues: 54.4680 Evaluate side-chains 290 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 198 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 192 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.0970 chunk 196 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.172794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147631 restraints weight = 27779.379| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.43 r_work: 0.3799 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17448 Z= 0.137 Angle : 0.645 11.506 23747 Z= 0.311 Chirality : 0.044 0.279 2812 Planarity : 0.004 0.052 2912 Dihedral : 4.589 19.502 2238 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.38 % Allowed : 17.40 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.28 (0.19), residues: 2046 helix: 0.69 (0.27), residues: 357 sheet: 0.50 (0.18), residues: 828 loop : -1.23 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.016 0.001 TYR G 48 PHE 0.017 0.001 PHE H 68 TRP 0.007 0.001 TRP D 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (17368) covalent geometry : angle 0.61428 / 0.30 (23534) SS BOND : bond 0.00706 / 0.47 ( 27) SS BOND : angle 1.84276 / 1.09 ( 54) hydrogen bonds : bond 0.03543 / 2.24 ( 691) hydrogen bonds : angle 4.96554 / 3.42 ( 1941) link_ALPHA1-3 : bond 0.01049 / 0.55 ( 6) link_ALPHA1-3 : angle 1.78737 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00810 / 0.39 ( 3) link_ALPHA1-6 : angle 1.50739 / 0.92 ( 9) link_BETA1-4 : bond 0.00622 / 0.45 ( 20) link_BETA1-4 : angle 1.69176 / 1.21 ( 60) link_NAG-ASN : bond 0.00417 / 0.24 ( 24) link_NAG-ASN : angle 2.78778 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.586 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: D 64 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6841 (pp) REVERT: D 132 LEU cc_start: 0.3607 (OUTLIER) cc_final: 0.2968 (tt) REVERT: F 38 ARG cc_start: 0.7980 (ttm170) cc_final: 0.5927 (ttt180) REVERT: F 105 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6173 (m) REVERT: H 110 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8323 (tp) REVERT: H 153 TYR cc_start: 0.6410 (p90) cc_final: 0.4584 (p90) REVERT: G 3 MET cc_start: 0.7875 (mmm) cc_final: 0.7453 (mmm) REVERT: G 81 ASP cc_start: 0.7213 (m-30) cc_final: 0.6956 (m-30) REVERT: A 138 THR cc_start: 0.7843 (t) cc_final: 0.7552 (p) REVERT: C 95 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7281 (mtt-85) REVERT: a 286 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6885 (tm-30) REVERT: a 307 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: a 409 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6108 (mpp) REVERT: c 286 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6873 (tm-30) REVERT: c 338 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7952 (ptmt) REVERT: b 338 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7930 (ptmt) REVERT: b 350 MET cc_start: 0.7740 (mmm) cc_final: 0.7258 (mmm) REVERT: b 409 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6700 (mpp) outliers start: 44 outliers final: 31 residues processed: 273 average time/residue: 0.1171 time to fit residues: 49.7048 Evaluate side-chains 286 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 56 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146566 restraints weight = 27837.766| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.42 r_work: 0.3780 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17448 Z= 0.202 Angle : 0.712 12.463 23747 Z= 0.342 Chirality : 0.047 0.285 2812 Planarity : 0.005 0.053 2912 Dihedral : 4.798 20.467 2238 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.82 % Allowed : 17.72 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.37 (0.19), residues: 2046 helix: 0.53 (0.27), residues: 357 sheet: 0.60 (0.19), residues: 792 loop : -1.36 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 105 TYR 0.021 0.002 TYR L 48 PHE 0.019 0.002 PHE H 68 TRP 0.010 0.002 TRP H 111 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (17368) covalent geometry : angle 0.67936 / 0.33 (23534) SS BOND : bond 0.00846 / 0.56 ( 27) SS BOND : angle 2.04654 / 1.26 ( 54) hydrogen bonds : bond 0.04047 / 2.57 ( 691) hydrogen bonds : angle 5.15185 / 3.54 ( 1941) link_ALPHA1-3 : bond 0.01162 / 0.60 ( 6) link_ALPHA1-3 : angle 2.04150 / 1.14 ( 18) link_ALPHA1-6 : bond 0.00835 / 0.41 ( 3) link_ALPHA1-6 : angle 1.54082 / 0.91 ( 9) link_BETA1-4 : bond 0.00654 / 0.47 ( 20) link_BETA1-4 : angle 1.89729 / 1.34 ( 60) link_NAG-ASN : bond 0.00431 / 0.24 ( 24) link_NAG-ASN : angle 2.97464 / 1.69 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.539 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: D 64 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6805 (pp) REVERT: D 132 LEU cc_start: 0.3718 (OUTLIER) cc_final: 0.3071 (tt) REVERT: F 105 THR cc_start: 0.6682 (OUTLIER) cc_final: 0.6310 (m) REVERT: H 87 ARG cc_start: 0.6516 (ttp-170) cc_final: 0.6311 (ttm170) REVERT: H 110 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8344 (tp) REVERT: H 153 TYR cc_start: 0.6403 (p90) cc_final: 0.4634 (p90) REVERT: G 3 MET cc_start: 0.7865 (mmm) cc_final: 0.7455 (mmm) REVERT: G 81 ASP cc_start: 0.7288 (m-30) cc_final: 0.7071 (m-30) REVERT: A 138 THR cc_start: 0.7831 (t) cc_final: 0.7527 (p) REVERT: C 95 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7342 (mtt-85) REVERT: a 286 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6845 (tm-30) REVERT: a 307 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: a 409 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6151 (mpp) REVERT: c 286 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6896 (tm-30) REVERT: c 338 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7949 (ptmt) REVERT: b 338 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7991 (ptmt) REVERT: b 350 MET cc_start: 0.7780 (mmm) cc_final: 0.7348 (mmm) REVERT: b 409 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6722 (mpp) outliers start: 52 outliers final: 37 residues processed: 288 average time/residue: 0.1162 time to fit residues: 52.3742 Evaluate side-chains 303 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 193 optimal weight: 0.0570 chunk 54 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS b 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.171931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146847 restraints weight = 27827.494| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.42 r_work: 0.3789 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17448 Z= 0.170 Angle : 0.681 12.093 23747 Z= 0.329 Chirality : 0.046 0.281 2812 Planarity : 0.005 0.052 2912 Dihedral : 4.740 19.667 2238 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.44 % Allowed : 18.64 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.38 (0.19), residues: 2046 helix: 0.52 (0.27), residues: 357 sheet: 0.52 (0.19), residues: 801 loop : -1.30 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.019 0.002 TYR G 48 PHE 0.017 0.002 PHE H 68 TRP 0.009 0.002 TRP D 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17368) covalent geometry : angle 0.65025 / 0.32 (23534) SS BOND : bond 0.00792 / 0.51 ( 27) SS BOND : angle 1.82164 / 1.11 ( 54) hydrogen bonds : bond 0.03828 / 2.43 ( 691) hydrogen bonds : angle 5.09191 / 3.51 ( 1941) link_ALPHA1-3 : bond 0.01130 / 0.59 ( 6) link_ALPHA1-3 : angle 1.93574 / 1.08 ( 18) link_ALPHA1-6 : bond 0.00814 / 0.40 ( 3) link_ALPHA1-6 : angle 1.53553 / 0.92 ( 9) link_BETA1-4 : bond 0.00640 / 0.46 ( 20) link_BETA1-4 : angle 1.78517 / 1.27 ( 60) link_NAG-ASN : bond 0.00404 / 0.23 ( 24) link_NAG-ASN : angle 2.87922 / 1.65 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.715 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: D 64 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6812 (pp) REVERT: D 132 LEU cc_start: 0.3756 (OUTLIER) cc_final: 0.3118 (tt) REVERT: F 105 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6277 (m) REVERT: H 110 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8338 (tp) REVERT: H 153 TYR cc_start: 0.6375 (p90) cc_final: 0.4594 (p90) REVERT: G 3 MET cc_start: 0.7793 (mmm) cc_final: 0.7423 (mmm) REVERT: G 81 ASP cc_start: 0.7267 (m-30) cc_final: 0.7044 (m-30) REVERT: A 138 THR cc_start: 0.7861 (t) cc_final: 0.7549 (p) REVERT: C 95 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7311 (mtt-85) REVERT: a 277 TYR cc_start: 0.8131 (t80) cc_final: 0.7903 (t80) REVERT: a 286 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6851 (tm-30) REVERT: a 307 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: a 409 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6157 (mpp) REVERT: c 286 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6905 (tm-30) REVERT: c 338 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7930 (ptmt) REVERT: b 338 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7966 (ptmt) REVERT: b 350 MET cc_start: 0.7729 (mmm) cc_final: 0.7292 (mmm) REVERT: b 409 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6817 (mpp) outliers start: 45 outliers final: 37 residues processed: 281 average time/residue: 0.1162 time to fit residues: 51.3333 Evaluate side-chains 297 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 130 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.171790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146813 restraints weight = 27531.520| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.40 r_work: 0.3788 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17448 Z= 0.171 Angle : 0.684 12.251 23747 Z= 0.331 Chirality : 0.046 0.280 2812 Planarity : 0.005 0.052 2912 Dihedral : 4.747 19.036 2238 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.71 % Allowed : 18.48 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.40 (0.19), residues: 2046 helix: 0.49 (0.27), residues: 357 sheet: 0.52 (0.19), residues: 801 loop : -1.30 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.019 0.002 TYR G 48 PHE 0.016 0.002 PHE H 68 TRP 0.009 0.002 TRP D 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (17368) covalent geometry : angle 0.65419 / 0.32 (23534) SS BOND : bond 0.00810 / 0.53 ( 27) SS BOND : angle 1.80202 / 1.10 ( 54) hydrogen bonds : bond 0.03833 / 2.43 ( 691) hydrogen bonds : angle 5.10454 / 3.51 ( 1941) link_ALPHA1-3 : bond 0.01139 / 0.60 ( 6) link_ALPHA1-3 : angle 1.95741 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00801 / 0.39 ( 3) link_ALPHA1-6 : angle 1.52447 / 0.91 ( 9) link_BETA1-4 : bond 0.00632 / 0.45 ( 20) link_BETA1-4 : angle 1.79111 / 1.27 ( 60) link_NAG-ASN : bond 0.00401 / 0.23 ( 24) link_NAG-ASN : angle 2.87909 / 1.65 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.592 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: D 64 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6860 (pp) REVERT: D 132 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3122 (tt) REVERT: F 105 THR cc_start: 0.6678 (OUTLIER) cc_final: 0.6287 (m) REVERT: H 110 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8331 (tp) REVERT: H 153 TYR cc_start: 0.6380 (p90) cc_final: 0.4624 (p90) REVERT: G 3 MET cc_start: 0.7743 (mmm) cc_final: 0.7345 (mmm) REVERT: G 81 ASP cc_start: 0.7275 (m-30) cc_final: 0.7035 (m-30) REVERT: A 138 THR cc_start: 0.7886 (t) cc_final: 0.7585 (p) REVERT: C 95 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7333 (mtt-85) REVERT: a 286 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6818 (tm-30) REVERT: a 307 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: a 409 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6152 (mpp) REVERT: c 286 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6898 (tm-30) REVERT: c 338 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7931 (ptmt) REVERT: b 409 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6727 (mpp) outliers start: 50 outliers final: 40 residues processed: 284 average time/residue: 0.1143 time to fit residues: 51.0230 Evaluate side-chains 300 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 183 optimal weight: 0.0050 chunk 61 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.172695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147627 restraints weight = 27796.681| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.42 r_work: 0.3801 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17448 Z= 0.132 Angle : 0.646 12.598 23747 Z= 0.313 Chirality : 0.044 0.274 2812 Planarity : 0.004 0.052 2912 Dihedral : 4.574 17.424 2238 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.38 % Allowed : 18.92 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % 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: -0.28 (0.19), residues: 2046 helix: 0.63 (0.27), residues: 357 sheet: 0.56 (0.19), residues: 810 loop : -1.24 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.016 0.001 TYR a 277 PHE 0.013 0.001 PHE H 68 TRP 0.007 0.001 TRP D 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17368) covalent geometry : angle 0.61844 / 0.31 (23534) SS BOND : bond 0.00673 / 0.44 ( 27) SS BOND : angle 1.55077 / 0.93 ( 54) hydrogen bonds : bond 0.03489 / 2.21 ( 691) hydrogen bonds : angle 4.95037 / 3.41 ( 1941) link_ALPHA1-3 : bond 0.01061 / 0.55 ( 6) link_ALPHA1-3 : angle 1.78010 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00764 / 0.37 ( 3) link_ALPHA1-6 : angle 1.50262 / 0.92 ( 9) link_BETA1-4 : bond 0.00624 / 0.45 ( 20) link_BETA1-4 : angle 1.65593 / 1.19 ( 60) link_NAG-ASN : bond 0.00395 / 0.23 ( 24) link_NAG-ASN : angle 2.71308 / 1.56 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4905.82 seconds wall clock time: 84 minutes 48.83 seconds (5088.83 seconds total)