Starting phenix.real_space_refine on Fri Sep 27 21:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_26458.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_26458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_26458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_26458.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/09_2024/7uds_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-5461/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: 10.77, per 1000 atoms: 0.63 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: 5.01 Conformation dependent library (CDL) restraints added in 2.1 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: 2.37 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: 5.72 Time building geometry restraints manager: 5.73 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: 7.370 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 40.140 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.270 ------------------------------------------------------------------------------- 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 17368 Z= 0.317 Angle : 0.743 11.743 23534 Z= 0.355 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.786 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: 0.2765 time to fit residues: 115.3005 Evaluate side-chains 254 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17368 Z= 0.292 Angle : 0.705 11.587 23534 Z= 0.345 Chirality : 0.047 0.275 2812 Planarity : 0.005 0.051 2912 Dihedral : 14.572 101.426 3321 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.92 % Allowed : 8.35 % Favored : 90.73 % 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: 0.59 (0.19), residues: 789 loop : -1.23 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 385 HIS 0.004 0.001 HIS c 353 PHE 0.017 0.002 PHE D 80 TYR 0.023 0.002 TYR F 94 ARG 0.008 0.001 ARG L 105 *********************** 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 274 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 257 time to evaluate : 1.690 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: 0.6087 (m) REVERT: H 153 TYR cc_start: 0.6099 (p90) cc_final: 0.5494 (p90) REVERT: B 81 MET cc_start: 0.6481 (mtp) cc_final: 0.6256 (mtp) REVERT: a 409 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5793 (mpp) REVERT: a 413 MET cc_start: 0.6659 (tmm) cc_final: 0.6259 (tmm) REVERT: c 286 GLU cc_start: 0.6139 (tm-30) cc_final: 0.5822 (tm-30) REVERT: c 335 LEU cc_start: 0.7658 (tt) cc_final: 0.7414 (tp) REVERT: c 338 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7662 (ptmt) REVERT: b 350 MET cc_start: 0.7310 (mmm) cc_final: 0.7095 (mpp) outliers start: 17 outliers final: 13 residues processed: 263 average time/residue: 0.2653 time to fit residues: 107.7025 Evaluate side-chains 264 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 197 optimal weight: 0.5980 chunk 162 optimal weight: 0.0050 chunk 181 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17368 Z= 0.207 Angle : 0.644 11.868 23534 Z= 0.311 Chirality : 0.044 0.261 2812 Planarity : 0.004 0.050 2912 Dihedral : 12.380 111.496 3321 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.61 % 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: 0.60 (0.27), residues: 357 sheet: 0.61 (0.19), residues: 795 loop : -1.17 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 385 HIS 0.006 0.001 HIS A 92 PHE 0.016 0.001 PHE D 80 TYR 0.017 0.001 TYR F 94 ARG 0.005 0.000 ARG L 105 *********************** 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 276 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.778 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: 0.6255 (t) cc_final: 0.5988 (m) REVERT: H 153 TYR cc_start: 0.6052 (p90) cc_final: 0.4511 (p90) REVERT: a 286 GLU cc_start: 0.6295 (tm-30) cc_final: 0.5962 (tm-30) REVERT: a 392 TYR cc_start: 0.8543 (m-80) cc_final: 0.8318 (m-80) REVERT: a 409 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5784 (mpp) REVERT: a 413 MET cc_start: 0.6681 (tmm) cc_final: 0.6335 (tmm) REVERT: c 286 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5784 (tm-30) REVERT: c 338 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7690 (ptmt) REVERT: b 364 ASN cc_start: 0.6266 (t0) cc_final: 0.6061 (t0) outliers start: 23 outliers final: 14 residues processed: 265 average time/residue: 0.2813 time to fit residues: 113.7873 Evaluate side-chains 262 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 247 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 A residue 140 HIS 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 409 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 180 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 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** C 231 GLN b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17368 Z= 0.248 Angle : 0.652 11.553 23534 Z= 0.317 Chirality : 0.045 0.264 2812 Planarity : 0.005 0.051 2912 Dihedral : 11.018 110.530 3321 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.84 % Allowed : 14.63 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2046 helix: 0.59 (0.27), residues: 357 sheet: 0.63 (0.19), residues: 780 loop : -1.17 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP a 385 HIS 0.005 0.001 HIS A 92 PHE 0.012 0.002 PHE b 398 TYR 0.019 0.002 TYR G 48 ARG 0.005 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.7007 (t) REVERT: D 64 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6446 (pp) REVERT: F 143 THR cc_start: 0.6320 (t) cc_final: 0.6064 (m) REVERT: H 153 TYR cc_start: 0.6049 (p90) cc_final: 0.4499 (p90) REVERT: a 286 GLU cc_start: 0.6304 (tm-30) cc_final: 0.5974 (tm-30) REVERT: a 409 MET cc_start: 0.6362 (mpp) cc_final: 0.5885 (mpp) REVERT: a 413 MET cc_start: 0.6717 (tmm) cc_final: 0.6378 (tmm) REVERT: c 286 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5821 (tm-30) REVERT: c 338 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7668 (ptmt) REVERT: b 409 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6575 (mpp) outliers start: 34 outliers final: 21 residues processed: 273 average time/residue: 0.2606 time to fit residues: 108.9999 Evaluate side-chains 271 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 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 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 409 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 91 HIS ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN b 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17368 Z= 0.249 Angle : 0.649 11.628 23534 Z= 0.315 Chirality : 0.045 0.269 2812 Planarity : 0.004 0.051 2912 Dihedral : 10.478 110.564 3321 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.11 % Allowed : 16.37 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.19), residues: 2046 helix: 0.62 (0.27), residues: 357 sheet: 0.61 (0.19), residues: 771 loop : -1.16 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 162 HIS 0.006 0.001 HIS a 353 PHE 0.011 0.001 PHE b 398 TYR 0.018 0.002 TYR G 48 ARG 0.005 0.000 ARG B 95 *********************** 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 287 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 1.877 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: 0.6861 (OUTLIER) cc_final: 0.6631 (pp) REVERT: F 105 THR cc_start: 0.6082 (OUTLIER) cc_final: 0.5758 (m) REVERT: F 143 THR cc_start: 0.6310 (t) cc_final: 0.6060 (m) REVERT: H 110 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8206 (tp) REVERT: H 153 TYR cc_start: 0.6057 (p90) cc_final: 0.4488 (p90) REVERT: C 95 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6911 (mtt-85) REVERT: a 286 GLU cc_start: 0.6318 (tm-30) cc_final: 0.5971 (tm-30) REVERT: a 409 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5796 (mpp) REVERT: a 413 MET cc_start: 0.6798 (tmm) cc_final: 0.6451 (tmm) REVERT: c 286 GLU cc_start: 0.6220 (tm-30) cc_final: 0.5845 (tm-30) REVERT: c 338 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7627 (ptmt) REVERT: b 350 MET cc_start: 0.7232 (mmm) cc_final: 0.6705 (mmm) REVERT: b 409 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6479 (mpp) outliers start: 39 outliers final: 26 residues processed: 270 average time/residue: 0.2617 time to fit residues: 108.9092 Evaluate side-chains 275 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 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 9 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 16 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17368 Z= 0.210 Angle : 0.626 11.332 23534 Z= 0.303 Chirality : 0.044 0.263 2812 Planarity : 0.004 0.051 2912 Dihedral : 9.844 109.382 3321 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.49 % Allowed : 16.69 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.19), residues: 2046 helix: 0.70 (0.27), residues: 357 sheet: 0.55 (0.19), residues: 798 loop : -1.13 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 111 HIS 0.005 0.001 HIS A 92 PHE 0.012 0.001 PHE b 398 TYR 0.016 0.001 TYR E 48 ARG 0.006 0.000 ARG B 95 *********************** 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 297 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 251 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 12 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6979 (t) REVERT: D 64 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6642 (pp) REVERT: D 132 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.2936 (tt) REVERT: F 143 THR cc_start: 0.6233 (t) cc_final: 0.5988 (m) REVERT: H 110 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8204 (tp) REVERT: H 153 TYR cc_start: 0.6053 (p90) cc_final: 0.4447 (p90) REVERT: G 3 MET cc_start: 0.7625 (mmt) cc_final: 0.7255 (mmm) REVERT: C 93 TYR cc_start: 0.7758 (m-80) cc_final: 0.7184 (m-80) REVERT: C 95 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6910 (mtt-85) REVERT: a 286 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5978 (tm-30) REVERT: a 307 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: a 409 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5855 (mpp) REVERT: a 413 MET cc_start: 0.6830 (tmm) cc_final: 0.6515 (tmm) REVERT: c 286 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5818 (tm-30) REVERT: c 338 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7618 (ptmt) REVERT: b 409 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6487 (mpp) outliers start: 46 outliers final: 29 residues processed: 279 average time/residue: 0.2584 time to fit residues: 111.1808 Evaluate side-chains 284 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 81 MET 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 B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 163 optimal weight: 0.0970 chunk 108 optimal weight: 0.0980 chunk 193 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 119 optimal weight: 0.2980 overall best weight: 0.2136 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17368 Z= 0.162 Angle : 0.597 10.451 23534 Z= 0.287 Chirality : 0.042 0.251 2812 Planarity : 0.004 0.051 2912 Dihedral : 9.127 107.219 3321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.95 % Allowed : 17.40 % 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: -0.09 (0.19), residues: 2046 helix: 0.86 (0.28), residues: 357 sheet: 0.60 (0.18), residues: 825 loop : -1.08 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 385 HIS 0.007 0.001 HIS a 353 PHE 0.013 0.001 PHE H 68 TYR 0.012 0.001 TYR H 94 ARG 0.007 0.000 ARG B 95 *********************** 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 283 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 2.074 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 132 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.2898 (tt) REVERT: F 143 THR cc_start: 0.6224 (t) cc_final: 0.5939 (m) REVERT: H 153 TYR cc_start: 0.5998 (p90) cc_final: 0.4298 (p90) REVERT: G 3 MET cc_start: 0.7549 (mmt) cc_final: 0.7320 (mmm) REVERT: C 93 TYR cc_start: 0.7741 (m-80) cc_final: 0.7047 (m-80) REVERT: C 95 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6831 (mtt-85) REVERT: a 286 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5961 (tm-30) REVERT: a 307 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: a 409 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5783 (mpp) REVERT: c 286 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5683 (tm-30) REVERT: c 338 LYS cc_start: 0.7874 (ptmt) cc_final: 0.7655 (ptmt) REVERT: b 353 HIS cc_start: 0.7401 (t70) cc_final: 0.7008 (t-90) REVERT: b 409 MET cc_start: 0.6811 (mpp) cc_final: 0.6469 (mpp) outliers start: 36 outliers final: 22 residues processed: 269 average time/residue: 0.2871 time to fit residues: 118.9246 Evaluate side-chains 268 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain 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 384 CYS Chi-restraints excluded: chain b residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 152 optimal weight: 0.0870 chunk 176 optimal weight: 0.8980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17368 Z= 0.220 Angle : 0.633 10.266 23534 Z= 0.303 Chirality : 0.044 0.248 2812 Planarity : 0.004 0.051 2912 Dihedral : 8.930 105.327 3321 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.22 % Allowed : 17.78 % Favored : 80.00 % 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: -0.05 (0.19), residues: 2046 helix: 0.86 (0.28), residues: 357 sheet: 0.64 (0.19), residues: 813 loop : -1.04 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 369 HIS 0.005 0.001 HIS A 92 PHE 0.027 0.001 PHE H 68 TYR 0.017 0.001 TYR G 48 ARG 0.006 0.000 ARG B 95 *********************** 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 287 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 246 time to evaluate : 1.623 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 132 LEU cc_start: 0.3486 (OUTLIER) cc_final: 0.2924 (tt) REVERT: F 38 ARG cc_start: 0.7621 (ttm170) cc_final: 0.5577 (ttm170) REVERT: F 143 THR cc_start: 0.6308 (t) cc_final: 0.6026 (m) REVERT: H 110 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8212 (tp) REVERT: H 153 TYR cc_start: 0.6053 (p90) cc_final: 0.4407 (p90) REVERT: G 3 MET cc_start: 0.7521 (mmt) cc_final: 0.7308 (mmm) REVERT: C 93 TYR cc_start: 0.7755 (m-80) cc_final: 0.7163 (m-80) REVERT: C 95 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6900 (mtt-85) REVERT: a 286 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5953 (tm-30) REVERT: a 307 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: a 409 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5856 (mpp) REVERT: c 286 GLU cc_start: 0.6257 (tm-30) cc_final: 0.5835 (tm-30) REVERT: c 338 LYS cc_start: 0.7870 (ptmt) cc_final: 0.7581 (ptmt) REVERT: b 350 MET cc_start: 0.7285 (mmm) cc_final: 0.7027 (mmm) REVERT: b 353 HIS cc_start: 0.7408 (t70) cc_final: 0.7053 (t-90) REVERT: b 409 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6493 (mpp) outliers start: 41 outliers final: 28 residues processed: 270 average time/residue: 0.2838 time to fit residues: 117.6600 Evaluate side-chains 277 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 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 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 0.0970 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17368 Z= 0.268 Angle : 0.663 10.954 23534 Z= 0.320 Chirality : 0.045 0.268 2812 Planarity : 0.004 0.051 2912 Dihedral : 8.948 104.332 3321 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.49 % Allowed : 17.83 % Favored : 79.67 % 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: -0.16 (0.19), residues: 2046 helix: 0.70 (0.28), residues: 357 sheet: 0.63 (0.19), residues: 801 loop : -1.13 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP a 369 HIS 0.005 0.001 HIS A 92 PHE 0.019 0.002 PHE H 68 TYR 0.021 0.002 TYR G 48 ARG 0.006 0.000 ARG B 95 *********************** 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 301 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 1.827 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 132 LEU cc_start: 0.3461 (OUTLIER) cc_final: 0.2846 (tt) REVERT: F 143 THR cc_start: 0.6295 (t) cc_final: 0.6058 (m) REVERT: H 110 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (tp) REVERT: H 153 TYR cc_start: 0.6063 (p90) cc_final: 0.4433 (p90) REVERT: C 95 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: a 286 GLU cc_start: 0.6377 (tm-30) cc_final: 0.5995 (tm-30) REVERT: a 307 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: a 409 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5879 (mpp) REVERT: c 286 GLU cc_start: 0.6278 (tm-30) cc_final: 0.5856 (tm-30) REVERT: c 338 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7610 (ptmt) REVERT: b 353 HIS cc_start: 0.7417 (t70) cc_final: 0.7071 (t-90) REVERT: b 409 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6476 (mpp) outliers start: 46 outliers final: 34 residues processed: 278 average time/residue: 0.2598 time to fit residues: 111.1555 Evaluate side-chains 287 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 247 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain H residue 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 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 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 138 THR Chi-restraints excluded: chain B residue 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 16 optimal weight: 0.0010 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 0.1980 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17368 Z= 0.199 Angle : 0.628 10.786 23534 Z= 0.303 Chirality : 0.044 0.274 2812 Planarity : 0.004 0.052 2912 Dihedral : 8.692 103.057 3321 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.01 % Allowed : 18.54 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2046 helix: 0.77 (0.28), residues: 357 sheet: 0.60 (0.19), residues: 813 loop : -1.10 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 369 HIS 0.005 0.001 HIS A 92 PHE 0.020 0.001 PHE H 68 TYR 0.015 0.001 TYR C 93 ARG 0.006 0.000 ARG B 95 ********************** 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 287 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 1.712 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 132 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.2951 (tt) REVERT: F 143 THR cc_start: 0.6195 (t) cc_final: 0.5961 (m) REVERT: H 110 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8200 (tp) REVERT: H 153 TYR cc_start: 0.6073 (p90) cc_final: 0.4455 (p90) REVERT: C 95 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6861 (mtt-85) REVERT: a 286 GLU cc_start: 0.6398 (tm-30) cc_final: 0.5996 (tm-30) REVERT: a 307 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: a 409 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5870 (mpp) REVERT: c 286 GLU cc_start: 0.6271 (tm-30) cc_final: 0.5836 (tm-30) REVERT: c 338 LYS cc_start: 0.7870 (ptmt) cc_final: 0.7613 (ptmt) REVERT: b 353 HIS cc_start: 0.7300 (t-170) cc_final: 0.7088 (t-90) REVERT: b 409 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6511 (mpp) outliers start: 37 outliers final: 30 residues processed: 271 average time/residue: 0.2638 time to fit residues: 109.7931 Evaluate side-chains 282 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 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 172 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 140 HIS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 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 140 HIS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 346 ASP Chi-restraints excluded: chain c residue 384 CYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 393 LEU Chi-restraints excluded: chain b residue 409 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.0040 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.172827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147666 restraints weight = 27711.405| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.41 r_work: 0.3796 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17368 Z= 0.273 Angle : 0.673 12.705 23534 Z= 0.325 Chirality : 0.046 0.270 2812 Planarity : 0.005 0.052 2912 Dihedral : 8.763 101.951 3321 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.17 % Allowed : 18.54 % Favored : 79.30 % 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: -0.19 (0.19), residues: 2046 helix: 0.69 (0.28), residues: 357 sheet: 0.66 (0.19), residues: 792 loop : -1.19 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP a 369 HIS 0.006 0.001 HIS A 92 PHE 0.017 0.002 PHE H 68 TYR 0.020 0.002 TYR G 48 ARG 0.007 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4117.80 seconds wall clock time: 74 minutes 16.69 seconds (4456.69 seconds total)