Starting phenix.real_space_refine on Sun Jun 15 09:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_26458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_26458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_26458.map" model { file = "/net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_26458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uds_26458/06_2025/7uds_26458.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.57, per 1000 atoms: 0.62 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: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.29 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: 5.57 Time building geometry restraints manager: 5.32 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 - 23.17: 10280 23.17 - 46.33: 692 46.33 - 69.50: 89 69.50 - 92.67: 48 92.67 - 115.84: 42 Dihedral angle restraints: 11151 sinusoidal: 5052 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 11148 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 244 or resid 301 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: 4.200 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: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.170 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 17.286 115.837 7128 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.073 0.002 TRP a 385 HIS 0.006 0.001 HIS a 353 PHE 0.017 0.002 PHE G 70 TYR 0.019 0.002 TYR E 48 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 24) link_NAG-ASN : angle 3.19058 ( 72) link_ALPHA1-6 : bond 0.00739 ( 3) link_ALPHA1-6 : angle 1.60110 ( 9) link_BETA1-4 : bond 0.00775 ( 20) link_BETA1-4 : angle 2.28829 ( 60) link_ALPHA1-3 : bond 0.01221 ( 6) link_ALPHA1-3 : angle 2.22594 ( 18) hydrogen bonds : bond 0.13650 ( 691) hydrogen bonds : angle 6.36723 ( 1941) SS BOND : bond 0.00708 ( 27) SS BOND : angle 1.73256 ( 54) covalent geometry : bond 0.00486 (17368) covalent geometry : angle 0.74309 (23534) *********************** 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 : 1.822 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: 0.2632 time to fit residues: 110.0856 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 : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4212 r_free = 0.4212 target = 0.172719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147305 restraints weight = 27758.682| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.51 r_work: 0.3781 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17448 Z= 0.206 Angle : 0.755 12.280 23747 Z= 0.360 Chirality : 0.047 0.276 2812 Planarity : 0.005 0.051 2912 Dihedral : 14.543 101.707 3321 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.92 % Allowed : 8.46 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2046 helix: 0.46 (0.27), residues: 357 sheet: 0.58 (0.19), residues: 789 loop : -1.25 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 385 HIS 0.005 0.001 HIS B 229 PHE 0.017 0.002 PHE D 80 TYR 0.024 0.002 TYR F 94 ARG 0.008 0.001 ARG L 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 24) link_NAG-ASN : angle 3.16296 ( 72) link_ALPHA1-6 : bond 0.00913 ( 3) link_ALPHA1-6 : angle 2.15067 ( 9) link_BETA1-4 : bond 0.00743 ( 20) link_BETA1-4 : angle 2.12700 ( 60) link_ALPHA1-3 : bond 0.02345 ( 6) link_ALPHA1-3 : angle 3.49231 ( 18) hydrogen bonds : bond 0.04307 ( 691) hydrogen bonds : angle 5.45171 ( 1941) SS BOND : bond 0.00823 ( 27) SS BOND : angle 1.99885 ( 54) covalent geometry : bond 0.00477 (17368) covalent geometry : angle 0.71660 (23534) *********************** 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 : 1.833 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: 0.6413 (t) cc_final: 0.6130 (m) REVERT: H 153 TYR cc_start: 0.6248 (p90) cc_final: 0.5604 (p90) REVERT: B 81 MET cc_start: 0.7037 (mtp) cc_final: 0.6832 (mtp) REVERT: a 409 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5887 (mpp) REVERT: a 413 MET cc_start: 0.6983 (tmm) cc_final: 0.6530 (tmm) REVERT: c 286 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6385 (tm-30) REVERT: c 335 LEU cc_start: 0.7725 (tt) cc_final: 0.7495 (tp) REVERT: c 338 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7874 (ptmt) REVERT: b 350 MET cc_start: 0.7649 (mmm) cc_final: 0.7382 (mpp) outliers start: 17 outliers final: 13 residues processed: 264 average time/residue: 0.2692 time to fit residues: 110.0449 Evaluate side-chains 263 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 249 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4222 r_free = 0.4222 target = 0.173785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148264 restraints weight = 27770.855| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.51 r_work: 0.3781 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1010 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 : 0.710 11.998 23747 Z= 0.335 Chirality : 0.045 0.264 2812 Planarity : 0.005 0.051 2912 Dihedral : 12.328 112.552 3321 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.57 % Allowed : 12.14 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2046 helix: 0.49 (0.27), residues: 357 sheet: 0.56 (0.19), residues: 777 loop : -1.17 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 385 HIS 0.006 0.001 HIS A 92 PHE 0.025 0.002 PHE G 70 TYR 0.020 0.002 TYR F 94 ARG 0.005 0.001 ARG L 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 24) link_NAG-ASN : angle 3.27177 ( 72) link_ALPHA1-6 : bond 0.01295 ( 3) link_ALPHA1-6 : angle 2.16699 ( 9) link_BETA1-4 : bond 0.00713 ( 20) link_BETA1-4 : angle 1.96826 ( 60) link_ALPHA1-3 : bond 0.02463 ( 6) link_ALPHA1-3 : angle 3.25231 ( 18) hydrogen bonds : bond 0.03958 ( 691) hydrogen bonds : angle 5.22962 ( 1941) SS BOND : bond 0.00723 ( 27) SS BOND : angle 1.80715 ( 54) covalent geometry : bond 0.00390 (17368) covalent geometry : angle 0.66960 (23534) *********************** 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: 29 poor density : 253 time to evaluate : 1.638 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: 0.6336 (t) cc_final: 0.6060 (m) REVERT: H 153 TYR cc_start: 0.6172 (p90) cc_final: 0.5520 (p90) REVERT: a 286 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6606 (tm-30) REVERT: a 392 TYR cc_start: 0.8579 (m-80) cc_final: 0.8325 (m-80) REVERT: a 409 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5870 (mpp) REVERT: a 413 MET cc_start: 0.7067 (tmm) cc_final: 0.6666 (tmm) REVERT: c 286 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6377 (tm-30) REVERT: c 338 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7878 (ptmt) REVERT: c 409 MET cc_start: 0.7114 (mpp) cc_final: 0.6909 (mpp) REVERT: b 350 MET cc_start: 0.7654 (mmm) cc_final: 0.7111 (mmm) outliers start: 29 outliers final: 19 residues processed: 266 average time/residue: 0.2717 time to fit residues: 111.2502 Evaluate side-chains 268 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain C residue 94 ILE 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 186 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 231 GLN ** 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 = 0.4190 r_free = 0.4190 target = 0.170538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145597 restraints weight = 27612.213| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.40 r_work: 0.3774 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17448 Z= 0.249 Angle : 0.779 12.782 23747 Z= 0.372 Chirality : 0.048 0.296 2812 Planarity : 0.005 0.054 2912 Dihedral : 11.425 111.454 3321 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.44 % Allowed : 15.61 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2046 helix: 0.35 (0.27), residues: 357 sheet: 0.58 (0.19), residues: 765 loop : -1.40 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP b 282 HIS 0.006 0.001 HIS A 92 PHE 0.022 0.002 PHE G 70 TYR 0.024 0.002 TYR G 48 ARG 0.007 0.001 ARG E 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 24) link_NAG-ASN : angle 3.29244 ( 72) link_ALPHA1-6 : bond 0.01478 ( 3) link_ALPHA1-6 : angle 2.24571 ( 9) link_BETA1-4 : bond 0.00706 ( 20) link_BETA1-4 : angle 2.19667 ( 60) link_ALPHA1-3 : bond 0.02423 ( 6) link_ALPHA1-3 : angle 3.55987 ( 18) hydrogen bonds : bond 0.04489 ( 691) hydrogen bonds : angle 5.41304 ( 1941) SS BOND : bond 0.00932 ( 27) SS BOND : angle 2.12668 ( 54) covalent geometry : bond 0.00584 (17368) covalent geometry : angle 0.73843 (23534) *********************** 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 305 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6825 (pp) REVERT: F 4 LEU cc_start: 0.7955 (mt) cc_final: 0.7639 (mp) REVERT: F 105 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6481 (m) REVERT: H 153 TYR cc_start: 0.6443 (p90) cc_final: 0.4698 (p90) REVERT: a 286 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6966 (tm-30) REVERT: a 307 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: a 409 MET cc_start: 0.6750 (mpp) cc_final: 0.6203 (mpp) REVERT: a 413 MET cc_start: 0.7274 (tmm) cc_final: 0.6858 (tmm) REVERT: c 286 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6869 (tm-30) REVERT: c 338 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7974 (ptmt) REVERT: c 409 MET cc_start: 0.7207 (mpp) cc_final: 0.6967 (mpp) REVERT: b 350 MET cc_start: 0.7800 (mmm) cc_final: 0.7348 (mmm) REVERT: b 409 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6550 (mpp) outliers start: 45 outliers final: 29 residues processed: 283 average time/residue: 0.2663 time to fit residues: 117.6950 Evaluate side-chains 283 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 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 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 103 VAL 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 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 c residue 283 MET Chi-restraints excluded: chain c residue 307 GLU 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 140 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 196 optimal weight: 0.0980 chunk 51 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 181 optimal weight: 0.0060 chunk 148 optimal weight: 0.7980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.172666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147515 restraints weight = 28071.296| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.46 r_work: 0.3800 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17448 Z= 0.136 Angle : 0.687 11.835 23747 Z= 0.327 Chirality : 0.044 0.277 2812 Planarity : 0.004 0.052 2912 Dihedral : 10.605 111.569 3321 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.06 % Allowed : 17.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 2046 helix: 0.59 (0.27), residues: 357 sheet: 0.50 (0.19), residues: 786 loop : -1.27 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 226 HIS 0.005 0.001 HIS A 92 PHE 0.021 0.001 PHE G 70 TYR 0.014 0.001 TYR G 48 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 24) link_NAG-ASN : angle 2.96359 ( 72) link_ALPHA1-6 : bond 0.01557 ( 3) link_ALPHA1-6 : angle 2.18197 ( 9) link_BETA1-4 : bond 0.00707 ( 20) link_BETA1-4 : angle 1.86082 ( 60) link_ALPHA1-3 : bond 0.02444 ( 6) link_ALPHA1-3 : angle 3.45126 ( 18) hydrogen bonds : bond 0.03637 ( 691) hydrogen bonds : angle 5.08308 ( 1941) SS BOND : bond 0.00691 ( 27) SS BOND : angle 2.31269 ( 54) covalent geometry : bond 0.00298 (17368) covalent geometry : angle 0.64607 (23534) *********************** 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 296 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 1.825 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: 0.7127 (OUTLIER) cc_final: 0.6800 (pp) REVERT: F 115 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6719 (p) REVERT: H 110 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8334 (tp) REVERT: H 153 TYR cc_start: 0.6404 (p90) cc_final: 0.4573 (p90) REVERT: A 138 THR cc_start: 0.7851 (t) cc_final: 0.7564 (p) REVERT: C 95 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7321 (mtt-85) REVERT: a 286 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6933 (tm-30) REVERT: a 307 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: a 409 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6111 (mpp) REVERT: a 413 MET cc_start: 0.7383 (tmm) cc_final: 0.6956 (tmm) REVERT: c 286 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6837 (tm-30) REVERT: c 338 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7962 (ptmt) REVERT: c 409 MET cc_start: 0.7135 (mpp) cc_final: 0.6910 (mpp) REVERT: b 350 MET cc_start: 0.7738 (mmm) cc_final: 0.7312 (mmm) REVERT: b 409 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6570 (mpp) outliers start: 38 outliers final: 24 residues processed: 276 average time/residue: 0.2647 time to fit residues: 112.8763 Evaluate side-chains 281 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU 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 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 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 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 90 SER 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 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE 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 c residue 384 CYS 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 176 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 231 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.170271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145115 restraints weight = 27797.918| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.42 r_work: 0.3762 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.006 0.072 17448 Z= 0.275 Angle : 0.816 13.207 23747 Z= 0.389 Chirality : 0.050 0.287 2812 Planarity : 0.005 0.054 2912 Dihedral : 10.650 111.151 3321 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.98 % Allowed : 17.67 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2046 helix: 0.35 (0.27), residues: 357 sheet: 0.50 (0.19), residues: 765 loop : -1.49 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP b 282 HIS 0.006 0.001 HIS A 92 PHE 0.024 0.002 PHE G 70 TYR 0.025 0.002 TYR G 48 ARG 0.008 0.001 ARG E 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 24) link_NAG-ASN : angle 3.37330 ( 72) link_ALPHA1-6 : bond 0.01474 ( 3) link_ALPHA1-6 : angle 2.38099 ( 9) link_BETA1-4 : bond 0.00709 ( 20) link_BETA1-4 : angle 2.25001 ( 60) link_ALPHA1-3 : bond 0.02535 ( 6) link_ALPHA1-3 : angle 3.71543 ( 18) hydrogen bonds : bond 0.04604 ( 691) hydrogen bonds : angle 5.40887 ( 1941) SS BOND : bond 0.00969 ( 27) SS BOND : angle 2.77697 ( 54) covalent geometry : bond 0.00644 (17368) covalent geometry : angle 0.77076 (23534) *********************** 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 312 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 1.660 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: 0.7278 (OUTLIER) cc_final: 0.6882 (pp) REVERT: D 132 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3094 (tt) REVERT: F 105 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6514 (m) REVERT: H 87 ARG cc_start: 0.6562 (ttp-170) cc_final: 0.6360 (ttm170) REVERT: H 110 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8324 (tp) REVERT: H 153 TYR cc_start: 0.6458 (p90) cc_final: 0.4784 (p90) REVERT: C 95 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7464 (mtt-85) REVERT: C 193 MET cc_start: 0.5633 (mmt) cc_final: 0.5419 (mmt) REVERT: a 286 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6963 (tm-30) REVERT: a 307 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: a 409 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6165 (mpp) REVERT: a 413 MET cc_start: 0.7412 (tmm) cc_final: 0.6999 (tmm) REVERT: c 286 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6901 (tm-30) REVERT: c 338 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7973 (ptmt) REVERT: c 409 MET cc_start: 0.7198 (mpp) cc_final: 0.6980 (mpp) REVERT: b 338 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7991 (ptmt) REVERT: b 350 MET cc_start: 0.7823 (mmm) cc_final: 0.7394 (mmm) REVERT: b 409 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6554 (mpp) outliers start: 55 outliers final: 42 residues processed: 287 average time/residue: 0.2630 time to fit residues: 117.1598 Evaluate side-chains 305 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR 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 172 LEU Chi-restraints excluded: chain H residue 89 ASP 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 54 GLU 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 A residue 187 LEU Chi-restraints excluded: chain C residue 81 MET 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 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 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 278 CYS Chi-restraints excluded: chain a residue 291 CYS 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 335 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 133 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 231 GLN a 341 ASN a 364 ASN b 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.171292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146287 restraints weight = 27608.097| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.40 r_work: 0.3777 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17448 Z= 0.199 Angle : 0.736 12.449 23747 Z= 0.352 Chirality : 0.047 0.285 2812 Planarity : 0.005 0.054 2912 Dihedral : 10.303 110.726 3321 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.87 % Allowed : 18.92 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 2046 helix: 0.40 (0.27), residues: 357 sheet: 0.37 (0.19), residues: 801 loop : -1.45 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 226 HIS 0.005 0.001 HIS A 92 PHE 0.024 0.002 PHE G 70 TYR 0.020 0.002 TYR G 48 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 24) link_NAG-ASN : angle 3.13557 ( 72) link_ALPHA1-6 : bond 0.01532 ( 3) link_ALPHA1-6 : angle 2.25044 ( 9) link_BETA1-4 : bond 0.00676 ( 20) link_BETA1-4 : angle 1.98443 ( 60) link_ALPHA1-3 : bond 0.02521 ( 6) link_ALPHA1-3 : angle 3.68882 ( 18) hydrogen bonds : bond 0.04091 ( 691) hydrogen bonds : angle 5.23035 ( 1941) SS BOND : bond 0.00847 ( 27) SS BOND : angle 2.36898 ( 54) covalent geometry : bond 0.00458 (17368) covalent geometry : angle 0.69398 (23534) *********************** 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 312 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 2.060 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: 0.7259 (OUTLIER) cc_final: 0.6897 (pp) REVERT: D 132 LEU cc_start: 0.3781 (OUTLIER) cc_final: 0.3135 (tt) REVERT: F 38 ARG cc_start: 0.8044 (ttm170) cc_final: 0.5988 (ttt180) REVERT: F 105 THR cc_start: 0.6765 (OUTLIER) cc_final: 0.6394 (m) REVERT: H 87 ARG cc_start: 0.6547 (ttp-170) cc_final: 0.6323 (ttm170) REVERT: H 110 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8293 (tp) REVERT: H 153 TYR cc_start: 0.6466 (p90) cc_final: 0.4648 (p90) REVERT: A 138 THR cc_start: 0.7921 (t) cc_final: 0.7633 (p) REVERT: C 95 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7398 (mtt-85) REVERT: a 286 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6932 (tm-30) REVERT: a 307 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: a 409 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6164 (mpp) REVERT: c 286 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6878 (tm-30) REVERT: c 338 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7963 (ptmt) REVERT: c 409 MET cc_start: 0.7182 (mpp) cc_final: 0.6978 (mpp) REVERT: b 338 LYS cc_start: 0.8254 (ptmt) cc_final: 0.8017 (ptmt) REVERT: b 350 MET cc_start: 0.7774 (mmm) cc_final: 0.7377 (mmm) REVERT: b 409 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6453 (mpp) outliers start: 53 outliers final: 39 residues processed: 291 average time/residue: 0.2724 time to fit residues: 124.2560 Evaluate side-chains 306 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 11 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 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 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 54 GLU 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 81 MET 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 291 CYS 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 335 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 176 optimal weight: 0.1980 chunk 147 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 364 ASN b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147081 restraints weight = 27627.296| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.41 r_work: 0.3793 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17448 Z= 0.153 Angle : 0.692 11.922 23747 Z= 0.329 Chirality : 0.045 0.268 2812 Planarity : 0.005 0.053 2912 Dihedral : 9.749 109.631 3321 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.04 % Allowed : 19.24 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 2046 helix: 0.55 (0.27), residues: 357 sheet: 0.44 (0.19), residues: 810 loop : -1.40 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 226 HIS 0.004 0.001 HIS A 92 PHE 0.023 0.002 PHE G 70 TYR 0.015 0.001 TYR G 48 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.95201 ( 72) link_ALPHA1-6 : bond 0.01586 ( 3) link_ALPHA1-6 : angle 2.24032 ( 9) link_BETA1-4 : bond 0.00663 ( 20) link_BETA1-4 : angle 1.85655 ( 60) link_ALPHA1-3 : bond 0.02593 ( 6) link_ALPHA1-3 : angle 3.65246 ( 18) hydrogen bonds : bond 0.03683 ( 691) hydrogen bonds : angle 5.04615 ( 1941) SS BOND : bond 0.00702 ( 27) SS BOND : angle 2.08167 ( 54) covalent geometry : bond 0.00343 (17368) covalent geometry : angle 0.65292 (23534) *********************** 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 314 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 1.892 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: 0.7207 (OUTLIER) cc_final: 0.6900 (pp) REVERT: D 132 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3097 (tt) REVERT: F 105 THR cc_start: 0.6619 (OUTLIER) cc_final: 0.6267 (m) REVERT: H 110 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8286 (tp) REVERT: H 153 TYR cc_start: 0.6338 (p90) cc_final: 0.4542 (p90) REVERT: A 138 THR cc_start: 0.7864 (t) cc_final: 0.7572 (p) REVERT: C 95 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7349 (mtt-85) REVERT: C 193 MET cc_start: 0.5453 (mmt) cc_final: 0.5225 (mmt) REVERT: a 286 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6902 (tm-30) REVERT: a 307 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: a 409 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6154 (mpp) REVERT: c 286 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6892 (tm-30) REVERT: c 338 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7927 (ptmt) REVERT: b 338 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7960 (ptmt) REVERT: b 350 MET cc_start: 0.7753 (mmm) cc_final: 0.7288 (mmm) REVERT: b 409 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6467 (mpp) outliers start: 56 outliers final: 36 residues processed: 292 average time/residue: 0.2749 time to fit residues: 123.5638 Evaluate side-chains 296 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 LEU 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 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 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 81 MET 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 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 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 291 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4211 r_free = 0.4211 target = 0.172073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147510 restraints weight = 27870.685| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.60 r_work: 0.3776 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1586 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= 0.169 Angle : 0.710 12.088 23747 Z= 0.336 Chirality : 0.045 0.263 2812 Planarity : 0.005 0.053 2912 Dihedral : 9.528 108.459 3321 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 19.40 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 2046 helix: 0.55 (0.27), residues: 357 sheet: 0.46 (0.19), residues: 810 loop : -1.38 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 226 HIS 0.005 0.001 HIS A 92 PHE 0.024 0.002 PHE G 70 TYR 0.019 0.002 TYR a 277 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 24) link_NAG-ASN : angle 2.96346 ( 72) link_ALPHA1-6 : bond 0.01597 ( 3) link_ALPHA1-6 : angle 2.25723 ( 9) link_BETA1-4 : bond 0.00664 ( 20) link_BETA1-4 : angle 1.90583 ( 60) link_ALPHA1-3 : bond 0.02636 ( 6) link_ALPHA1-3 : angle 3.67416 ( 18) hydrogen bonds : bond 0.03773 ( 691) hydrogen bonds : angle 5.06700 ( 1941) SS BOND : bond 0.00754 ( 27) SS BOND : angle 2.10865 ( 54) covalent geometry : bond 0.00384 (17368) covalent geometry : angle 0.67045 (23534) *********************** 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 308 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 1.641 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: 0.7089 (OUTLIER) cc_final: 0.6814 (pp) REVERT: D 132 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3078 (tt) REVERT: F 105 THR cc_start: 0.6432 (OUTLIER) cc_final: 0.6225 (m) REVERT: H 110 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (tp) REVERT: H 153 TYR cc_start: 0.6148 (p90) cc_final: 0.4492 (p90) REVERT: G 3 MET cc_start: 0.7816 (mmt) cc_final: 0.7311 (mmm) REVERT: A 138 THR cc_start: 0.7757 (t) cc_final: 0.7475 (p) REVERT: C 95 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7202 (mtt-85) REVERT: a 286 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6548 (tm-30) REVERT: a 307 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: a 409 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5950 (mpp) REVERT: c 286 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6553 (tm-30) REVERT: c 338 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7805 (ptmt) REVERT: b 338 LYS cc_start: 0.8085 (ptmt) cc_final: 0.7831 (ptmt) REVERT: b 350 MET cc_start: 0.7550 (mmm) cc_final: 0.7051 (mmm) REVERT: b 353 HIS cc_start: 0.7653 (t70) cc_final: 0.7318 (t-90) REVERT: b 409 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6621 (mpp) outliers start: 54 outliers final: 40 residues processed: 285 average time/residue: 0.2636 time to fit residues: 115.5135 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 : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 18 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 9 SER Chi-restraints excluded: chain L residue 25 SER 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 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 A residue 187 LEU Chi-restraints excluded: chain C residue 81 MET 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 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 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 60 optimal weight: 0.3980 chunk 106 optimal weight: 0.0870 chunk 82 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 92 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 91 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 = 0.4237 r_free = 0.4237 target = 0.174061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148738 restraints weight = 27822.756| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.44 r_work: 0.3815 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1668 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= 0.121 Angle : 0.659 11.259 23747 Z= 0.311 Chirality : 0.043 0.247 2812 Planarity : 0.004 0.053 2912 Dihedral : 8.878 106.558 3321 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.38 % Allowed : 19.84 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2046 helix: 0.70 (0.28), residues: 357 sheet: 0.53 (0.19), residues: 810 loop : -1.22 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 226 HIS 0.005 0.001 HIS A 92 PHE 0.021 0.001 PHE G 70 TYR 0.014 0.001 TYR a 277 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 24) link_NAG-ASN : angle 2.76167 ( 72) link_ALPHA1-6 : bond 0.01672 ( 3) link_ALPHA1-6 : angle 2.12769 ( 9) link_BETA1-4 : bond 0.00667 ( 20) link_BETA1-4 : angle 1.69717 ( 60) link_ALPHA1-3 : bond 0.02787 ( 6) link_ALPHA1-3 : angle 3.67796 ( 18) hydrogen bonds : bond 0.03244 ( 691) hydrogen bonds : angle 4.81805 ( 1941) SS BOND : bond 0.00554 ( 27) SS BOND : angle 1.75313 ( 54) covalent geometry : bond 0.00258 (17368) covalent geometry : angle 0.62306 (23534) ********************** 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 302 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 1.668 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: 0.7046 (OUTLIER) cc_final: 0.6813 (pp) REVERT: D 105 THR cc_start: 0.6119 (m) cc_final: 0.5865 (m) REVERT: D 132 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.3011 (tt) REVERT: H 110 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (tp) REVERT: H 153 TYR cc_start: 0.6350 (p90) cc_final: 0.4486 (p90) REVERT: H 177 VAL cc_start: 0.5571 (t) cc_final: 0.5184 (m) REVERT: G 3 MET cc_start: 0.7907 (mmt) cc_final: 0.7374 (mmm) REVERT: A 138 THR cc_start: 0.7836 (t) cc_final: 0.7541 (p) REVERT: C 95 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7278 (mtt-85) REVERT: a 286 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6830 (tm-30) REVERT: a 306 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6627 (mm-30) REVERT: a 307 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: a 350 MET cc_start: 0.7729 (mmm) cc_final: 0.7488 (mmm) REVERT: a 409 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6147 (mpp) REVERT: c 286 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6875 (tm-30) REVERT: c 338 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7920 (ptmt) REVERT: b 338 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7967 (ptmt) REVERT: b 350 MET cc_start: 0.7725 (mmm) cc_final: 0.7346 (mmm) REVERT: b 353 HIS cc_start: 0.7823 (t70) cc_final: 0.7540 (t-90) REVERT: b 409 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6853 (mpp) outliers start: 44 outliers final: 32 residues processed: 280 average time/residue: 0.2750 time to fit residues: 117.9681 Evaluate side-chains 293 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 70 VAL 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 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 140 HIS Chi-restraints excluded: chain C residue 81 MET 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 140 HIS 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 335 LEU Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain b 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 198 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.172214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147094 restraints weight = 27645.258| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.40 r_work: 0.3798 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17448 Z= 0.194 Angle : 0.733 11.901 23747 Z= 0.346 Chirality : 0.046 0.255 2812 Planarity : 0.005 0.052 2912 Dihedral : 9.002 104.978 3321 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.33 % Allowed : 20.22 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2046 helix: 0.61 (0.27), residues: 357 sheet: 0.61 (0.19), residues: 801 loop : -1.32 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP c 385 HIS 0.005 0.001 HIS A 92 PHE 0.023 0.002 PHE G 70 TYR 0.019 0.002 TYR L 48 ARG 0.007 0.001 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 24) link_NAG-ASN : angle 2.96108 ( 72) link_ALPHA1-6 : bond 0.01623 ( 3) link_ALPHA1-6 : angle 2.05530 ( 9) link_BETA1-4 : bond 0.00649 ( 20) link_BETA1-4 : angle 2.01391 ( 60) link_ALPHA1-3 : bond 0.02732 ( 6) link_ALPHA1-3 : angle 3.70609 ( 18) hydrogen bonds : bond 0.03882 ( 691) hydrogen bonds : angle 5.04611 ( 1941) SS BOND : bond 0.00812 ( 27) SS BOND : angle 2.11836 ( 54) covalent geometry : bond 0.00448 (17368) covalent geometry : angle 0.69467 (23534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10412.75 seconds wall clock time: 180 minutes 2.89 seconds (10802.89 seconds total)