Starting phenix.real_space_refine on Thu Sep 18 14:38:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vef_43172/09_2025/8vef_43172.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 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 81 5.16 5 C 10990 2.51 5 N 2954 2.21 5 O 3529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17554 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "J" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3868 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "E" 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 Time building chain proxies: 4.53, per 1000 atoms: 0.26 Number of scatterers: 17554 At special positions: 0 Unit cell: (125.628, 129.96, 154.869, 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 81 16.00 O 3529 8.00 N 2954 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C1047 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.02 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A1047 " - pdb=" SG CYS E 30 " distance=2.04 Simple disulfide: pdb=" SG CYS A1144 " - pdb=" SG CYS A1148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS E1047 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.02 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C1144 " - pdb=" SG CYS C1148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E1137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 284 " distance=2.02 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E1144 " - pdb=" SG CYS E1148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 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 O 3 " - " MAN O 6 " " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 6 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 5 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 5 " BETA1-4 " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " 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 A2001 " - " ASN A 21 " " NAG A2002 " - " ASN A 33 " " NAG C2001 " - " ASN C 21 " " NAG C2002 " - " ASN C 33 " " NAG E2001 " - " ASN E 21 " " NAG E2002 " - " ASN E 33 " " NAG E2003 " - " ASN E 83 " " NAG M 1 " - " ASN A 97 " " NAG N 1 " - " ASN A 83 " " NAG O 1 " - " ASN A 169 " " NAG P 1 " - " ASN A1154 " " NAG Q 1 " - " ASN C 97 " " NAG R 1 " - " ASN C 83 " " NAG S 1 " - " ASN C 169 " " NAG T 1 " - " ASN C1154 " " NAG U 1 " - " ASN E 97 " " NAG V 1 " - " ASN E 169 " " NAG W 1 " - " ASN E1154 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 741.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 42 sheets defined 21.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.535A pdb=" N LEU A 80 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.183A pdb=" N SER A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.937A pdb=" N TRP A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.571A pdb=" N GLN A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1059 removed outlier: 3.715A pdb=" N MET A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1127 removed outlier: 3.703A pdb=" N LEU A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1155 removed outlier: 3.672A pdb=" N GLY A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1172 removed outlier: 3.910A pdb=" N SER A1166 " --> pdb=" O TYR A1162 " (cutoff:3.500A) Processing helix chain 'H' and resid 100H through 100M removed outlier: 3.900A pdb=" N ALA H 100L" --> pdb=" O ALA H 100I" (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE H 100M" --> pdb=" O ASP H 100J" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.293A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.092A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 1037 through 1059 removed outlier: 3.804A pdb=" N MET C1059 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1127 removed outlier: 3.675A pdb=" N LEU C1089 " --> pdb=" O ASP C1085 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C1090 " --> pdb=" O ASP C1086 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C1091 " --> pdb=" O GLY C1087 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1155 removed outlier: 3.654A pdb=" N GLY C1155 " --> pdb=" O SER C1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 1162 through 1172 removed outlier: 3.828A pdb=" N SER C1166 " --> pdb=" O TYR C1162 " (cutoff:3.500A) Processing helix chain 'J' and resid 100I through 100M Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.142A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 107 through 117 removed outlier: 4.245A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.156A pdb=" N TRP E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.559A pdb=" N GLN E 197 " --> pdb=" O ASN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1037 through 1059 removed outlier: 3.733A pdb=" N MET E1059 " --> pdb=" O VAL E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1127 removed outlier: 3.749A pdb=" N LEU E1089 " --> pdb=" O ASP E1085 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP E1090 " --> pdb=" O ASP E1086 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E1091 " --> pdb=" O GLY E1087 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU E1105 " --> pdb=" O LEU E1101 " (cutoff:3.500A) Processing helix chain 'E' and resid 1145 through 1155 removed outlier: 3.718A pdb=" N GLY E1155 " --> pdb=" O SER E1151 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1161 No H-bonds generated for 'chain 'E' and resid 1159 through 1161' Processing helix chain 'E' and resid 1162 through 1172 removed outlier: 3.927A pdb=" N SER E1166 " --> pdb=" O TYR E1162 " (cutoff:3.500A) Processing helix chain 'G' and resid 100H through 100M removed outlier: 3.850A pdb=" N ALA G 100L" --> pdb=" O ALA G 100I" (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE G 100M" --> pdb=" O ASP G 100J" (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.134A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1032 through 1034 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.190A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.348A pdb=" N LEU A 60 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.848A pdb=" N ARG A 84 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 121 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 120 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.063A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.828A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.680A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1032 through 1034 removed outlier: 3.503A pdb=" N GLY C 16 " --> pdb=" O GLY C1023 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.208A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.699A pdb=" N LEU C 60 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 89 " --> pdb=" O ILE C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.949A pdb=" N ARG C 84 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 121 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AC4, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AC5, first strand: chain 'C' and resid 293 through 295 removed outlier: 3.534A pdb=" N ILE C 295 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS C 288 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.736A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.830A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.545A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1032 through 1034 Processing sheet with id=AD2, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.111A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.612A pdb=" N LEU E 60 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 89 " --> pdb=" O ILE E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.959A pdb=" N ARG E 84 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 121 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER E 267 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E 121 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA E 265 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG E 123 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 263 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU E 181 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.563A pdb=" N CYS E 145 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AD8, first strand: chain 'E' and resid 170 through 175 Processing sheet with id=AD9, first strand: chain 'E' and resid 293 through 295 removed outlier: 4.088A pdb=" N CYS E 288 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.813A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.509A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1818 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: 3.32 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5390 1.34 - 1.46: 4289 1.46 - 1.58: 8175 1.58 - 1.70: 0 1.70 - 1.83: 108 Bond restraints: 17962 Sorted by residual: bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.10e-02 8.26e+03 1.34e+01 bond pdb=" N ILE I 29 " pdb=" CA ILE I 29 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.10e-02 8.26e+03 1.30e+01 bond pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.23e+01 bond pdb=" N ILE K 29 " pdb=" CA ILE K 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.10e-02 8.26e+03 1.18e+01 bond pdb=" N LYS J 64 " pdb=" CA LYS J 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.12e-02 7.97e+03 1.15e+01 ... (remaining 17957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 23431 2.36 - 4.71: 806 4.71 - 7.07: 104 7.07 - 9.43: 22 9.43 - 11.78: 2 Bond angle restraints: 24365 Sorted by residual: angle pdb=" C TYR J 35 " pdb=" CA TYR J 35 " pdb=" CB TYR J 35 " ideal model delta sigma weight residual 110.19 98.41 11.78 1.64e+00 3.72e-01 5.16e+01 angle pdb=" C TYR J 53 " pdb=" CA TYR J 53 " pdb=" CB TYR J 53 " ideal model delta sigma weight residual 110.88 101.51 9.37 1.57e+00 4.06e-01 3.56e+01 angle pdb=" CA TYR J 100F" pdb=" C TYR J 100F" pdb=" O TYR J 100F" ideal model delta sigma weight residual 120.49 113.95 6.54 1.16e+00 7.43e-01 3.18e+01 angle pdb=" N GLY H 100G" pdb=" CA GLY H 100G" pdb=" C GLY H 100G" ideal model delta sigma weight residual 112.49 118.71 -6.22 1.21e+00 6.83e-01 2.65e+01 angle pdb=" CA TYR J 35 " pdb=" C TYR J 35 " pdb=" O TYR J 35 " ideal model delta sigma weight residual 120.32 114.72 5.60 1.10e+00 8.26e-01 2.59e+01 ... (remaining 24360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.56: 10479 20.56 - 41.13: 605 41.13 - 61.69: 80 61.69 - 82.26: 33 82.26 - 102.82: 14 Dihedral angle restraints: 11211 sinusoidal: 4980 harmonic: 6231 Sorted by residual: dihedral pdb=" C TYR J 35 " pdb=" N TYR J 35 " pdb=" CA TYR J 35 " pdb=" CB TYR J 35 " ideal model delta harmonic sigma weight residual -122.60 -105.22 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C TYR H 100D" pdb=" N TYR H 100D" pdb=" CA TYR H 100D" pdb=" CB TYR H 100D" ideal model delta harmonic sigma weight residual -122.60 -136.55 13.95 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C GLU E 283 " pdb=" N GLU E 283 " pdb=" CA GLU E 283 " pdb=" CB GLU E 283 " ideal model delta harmonic sigma weight residual -122.60 -135.68 13.08 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 11208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2367 0.093 - 0.186: 301 0.186 - 0.279: 33 0.279 - 0.372: 9 0.372 - 0.465: 6 Chirality restraints: 2716 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.03e+01 chirality pdb=" CA TYR J 35 " pdb=" N TYR J 35 " pdb=" C TYR J 35 " pdb=" CB TYR J 35 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 2713 not shown) Planarity restraints: 3119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.243 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG R 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.347 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.133 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" C7 NAG N 1 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.181 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E2003 " -0.085 2.00e-02 2.50e+03 7.02e-02 6.16e+01 pdb=" C7 NAG E2003 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG E2003 " -0.064 2.00e-02 2.50e+03 pdb=" N2 NAG E2003 " 0.112 2.00e-02 2.50e+03 pdb=" O7 NAG E2003 " 0.014 2.00e-02 2.50e+03 ... (remaining 3116 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4954 2.82 - 3.34: 13592 3.34 - 3.86: 27839 3.86 - 4.38: 31064 4.38 - 4.90: 56622 Nonbonded interactions: 134071 Sorted by model distance: nonbonded pdb=" OE1 GLU C 44 " pdb=" OG SER C 297 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLU A 44 " pdb=" OG SER A 297 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR K 69 " pdb=" OE1 GLU K 70 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR I 69 " pdb=" OE1 GLU I 70 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR L 69 " pdb=" OE1 GLU L 70 " model vdw 2.328 3.040 ... (remaining 134066 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 'C' selection = (chain 'E' and resid 11 through 2002) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'V' } 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: 2.660 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.890 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.006 0.054 18030 Z= 0.326 Angle : 0.984 11.783 24542 Z= 0.571 Chirality : 0.066 0.465 2716 Planarity : 0.009 0.208 3101 Dihedral : 13.574 102.822 7164 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2127 helix: 0.78 (0.26), residues: 360 sheet: 1.42 (0.22), residues: 519 loop : -1.59 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 317 TYR 0.051 0.003 TYR J 53 PHE 0.032 0.003 PHE J 97 TRP 0.018 0.002 TRP C 86 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00605 (17962) covalent geometry : angle 0.97127 (24365) SS BOND : bond 0.00672 ( 27) SS BOND : angle 1.54004 ( 54) hydrogen bonds : bond 0.16786 ( 643) hydrogen bonds : angle 7.26745 ( 1818) link_ALPHA1-3 : bond 0.00387 ( 3) link_ALPHA1-3 : angle 1.54933 ( 9) link_ALPHA1-6 : bond 0.00553 ( 6) link_ALPHA1-6 : angle 1.22677 ( 18) link_BETA1-4 : bond 0.00858 ( 14) link_BETA1-4 : angle 1.74397 ( 42) link_NAG-ASN : bond 0.00506 ( 18) link_NAG-ASN : angle 2.89302 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7126 (tpp80) cc_final: 0.6771 (mtt90) REVERT: E 270 PRO cc_start: 0.7100 (Cg_endo) cc_final: 0.6896 (Cg_exo) REVERT: E 1027 GLN cc_start: 0.7992 (tp40) cc_final: 0.7701 (tt0) REVERT: G 22 CYS cc_start: 0.5783 (t) cc_final: 0.5560 (t) REVERT: I 33 LEU cc_start: 0.9065 (tp) cc_final: 0.8864 (tp) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1585 time to fit residues: 66.2052 Evaluate side-chains 163 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 178 GLN A1026 HIS A1117 ASN A1125 GLN H 76 ASN L 92 ASN C1026 HIS C1125 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 214 ASN E1026 HIS E1124 ASN I 92 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110038 restraints weight = 20597.580| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.93 r_work: 0.3048 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18030 Z= 0.159 Angle : 0.585 9.446 24542 Z= 0.306 Chirality : 0.044 0.204 2716 Planarity : 0.005 0.062 3101 Dihedral : 8.126 76.830 3192 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.48 % Allowed : 6.61 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2127 helix: 2.12 (0.27), residues: 363 sheet: 1.09 (0.21), residues: 555 loop : -1.53 (0.15), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 53 TYR 0.023 0.002 TYR J 35 PHE 0.021 0.002 PHE J 78 TRP 0.008 0.001 TRP J 35A HIS 0.007 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00373 (17962) covalent geometry : angle 0.57032 (24365) SS BOND : bond 0.00447 ( 27) SS BOND : angle 0.93761 ( 54) hydrogen bonds : bond 0.06022 ( 643) hydrogen bonds : angle 5.31211 ( 1818) link_ALPHA1-3 : bond 0.00993 ( 3) link_ALPHA1-3 : angle 2.30672 ( 9) link_ALPHA1-6 : bond 0.00467 ( 6) link_ALPHA1-6 : angle 1.80449 ( 18) link_BETA1-4 : bond 0.00618 ( 14) link_BETA1-4 : angle 1.33203 ( 42) link_NAG-ASN : bond 0.00394 ( 18) link_NAG-ASN : angle 2.12124 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7305 (mmp) cc_final: 0.6913 (mmp) REVERT: E 1017 MET cc_start: 0.8844 (ttp) cc_final: 0.8607 (ttm) REVERT: I 33 LEU cc_start: 0.8533 (tp) cc_final: 0.8192 (tp) outliers start: 9 outliers final: 4 residues processed: 174 average time/residue: 0.1542 time to fit residues: 40.2559 Evaluate side-chains 154 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain J residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 148 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 0.0020 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 0.0070 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 GLN K 55 GLN K 92 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN I 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112244 restraints weight = 20778.285| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.94 r_work: 0.3091 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18030 Z= 0.104 Angle : 0.504 6.021 24542 Z= 0.265 Chirality : 0.042 0.184 2716 Planarity : 0.004 0.042 3101 Dihedral : 7.275 69.042 3192 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.75 % Allowed : 7.84 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2127 helix: 2.74 (0.27), residues: 369 sheet: 1.17 (0.21), residues: 558 loop : -1.43 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 53 TYR 0.018 0.001 TYR J 35 PHE 0.018 0.001 PHE H 78 TRP 0.009 0.001 TRP C1092 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00212 (17962) covalent geometry : angle 0.48838 (24365) SS BOND : bond 0.00524 ( 27) SS BOND : angle 1.49017 ( 54) hydrogen bonds : bond 0.05018 ( 643) hydrogen bonds : angle 4.82912 ( 1818) link_ALPHA1-3 : bond 0.01253 ( 3) link_ALPHA1-3 : angle 1.59584 ( 9) link_ALPHA1-6 : bond 0.00624 ( 6) link_ALPHA1-6 : angle 1.52968 ( 18) link_BETA1-4 : bond 0.00600 ( 14) link_BETA1-4 : angle 1.22223 ( 42) link_NAG-ASN : bond 0.00213 ( 18) link_NAG-ASN : angle 1.83442 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 1121 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6978 (ttpp) REVERT: C 131 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7437 (mtm180) REVERT: C 138 THR cc_start: 0.8521 (p) cc_final: 0.8258 (p) REVERT: C 287 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7521 (mttt) REVERT: E 30 CYS cc_start: 0.6935 (m) cc_final: 0.6314 (m) REVERT: E 162 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: G 22 CYS cc_start: 0.5631 (t) cc_final: 0.5375 (t) REVERT: I 24 ARG cc_start: 0.6644 (tpt170) cc_final: 0.6220 (mtm180) REVERT: I 33 LEU cc_start: 0.8536 (tp) cc_final: 0.8224 (tp) REVERT: I 49 TYR cc_start: 0.7337 (m-80) cc_final: 0.7071 (m-80) outliers start: 14 outliers final: 9 residues processed: 172 average time/residue: 0.1593 time to fit residues: 40.5599 Evaluate side-chains 156 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN L 92 ASN K 92 ASN E 214 ASN I 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108359 restraints weight = 21132.932| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.91 r_work: 0.3062 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18030 Z= 0.134 Angle : 0.525 6.885 24542 Z= 0.273 Chirality : 0.043 0.196 2716 Planarity : 0.004 0.038 3101 Dihedral : 6.815 63.750 3192 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.12 % Allowed : 8.53 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2127 helix: 2.89 (0.27), residues: 369 sheet: 1.51 (0.22), residues: 522 loop : -1.39 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 172 TYR 0.020 0.001 TYR J 35 PHE 0.021 0.002 PHE H 78 TRP 0.007 0.001 TRP A1092 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00316 (17962) covalent geometry : angle 0.51059 (24365) SS BOND : bond 0.00297 ( 27) SS BOND : angle 1.41802 ( 54) hydrogen bonds : bond 0.05267 ( 643) hydrogen bonds : angle 4.75193 ( 1818) link_ALPHA1-3 : bond 0.01199 ( 3) link_ALPHA1-3 : angle 1.85771 ( 9) link_ALPHA1-6 : bond 0.00626 ( 6) link_ALPHA1-6 : angle 1.49842 ( 18) link_BETA1-4 : bond 0.00481 ( 14) link_BETA1-4 : angle 1.18864 ( 42) link_NAG-ASN : bond 0.00155 ( 18) link_NAG-ASN : angle 1.81515 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 1019 ASP cc_start: 0.8588 (p0) cc_final: 0.7985 (p0) REVERT: A 1121 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6987 (ttpp) REVERT: C 30 CYS cc_start: 0.6512 (m) cc_final: 0.5804 (m) REVERT: K 22 THR cc_start: 0.7284 (m) cc_final: 0.6961 (m) REVERT: K 24 ARG cc_start: 0.6779 (tpp-160) cc_final: 0.5885 (mtm180) REVERT: E 162 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: E 1121 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6786 (ttpp) REVERT: E 1150 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6173 (mm-30) REVERT: G 22 CYS cc_start: 0.5689 (t) cc_final: 0.5433 (t) REVERT: I 33 LEU cc_start: 0.8308 (tp) cc_final: 0.7875 (tp) REVERT: I 49 TYR cc_start: 0.7464 (m-80) cc_final: 0.7248 (m-80) outliers start: 21 outliers final: 13 residues processed: 170 average time/residue: 0.1597 time to fit residues: 40.0377 Evaluate side-chains 161 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 102 optimal weight: 0.0570 chunk 171 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN E 214 ASN I 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107311 restraints weight = 20958.980| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.02 r_work: 0.3026 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18030 Z= 0.122 Angle : 0.511 7.309 24542 Z= 0.266 Chirality : 0.042 0.192 2716 Planarity : 0.004 0.045 3101 Dihedral : 6.527 59.246 3192 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.07 % Allowed : 9.55 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2127 helix: 2.99 (0.27), residues: 369 sheet: 1.50 (0.22), residues: 522 loop : -1.35 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.017 0.001 TYR J 35 PHE 0.018 0.001 PHE G 78 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00279 (17962) covalent geometry : angle 0.49685 (24365) SS BOND : bond 0.00347 ( 27) SS BOND : angle 1.49355 ( 54) hydrogen bonds : bond 0.05052 ( 643) hydrogen bonds : angle 4.66530 ( 1818) link_ALPHA1-3 : bond 0.01241 ( 3) link_ALPHA1-3 : angle 1.73932 ( 9) link_ALPHA1-6 : bond 0.00657 ( 6) link_ALPHA1-6 : angle 1.47436 ( 18) link_BETA1-4 : bond 0.00483 ( 14) link_BETA1-4 : angle 1.15913 ( 42) link_NAG-ASN : bond 0.00161 ( 18) link_NAG-ASN : angle 1.73299 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6306 (m) cc_final: 0.5705 (m) REVERT: A 1019 ASP cc_start: 0.8603 (p0) cc_final: 0.7999 (p0) REVERT: A 1047 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8016 (t) REVERT: A 1121 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7163 (ttpp) REVERT: A 1150 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: L 4 MET cc_start: 0.7303 (mmp) cc_final: 0.6975 (mmp) REVERT: C 287 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7570 (mttt) REVERT: C 1105 GLU cc_start: 0.7866 (tp30) cc_final: 0.7588 (tt0) REVERT: C 1150 GLU cc_start: 0.6994 (tp30) cc_final: 0.6127 (mm-30) REVERT: K 22 THR cc_start: 0.7226 (m) cc_final: 0.6886 (m) REVERT: K 24 ARG cc_start: 0.6816 (tpp-160) cc_final: 0.5870 (mtm180) REVERT: E 162 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: E 202 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8157 (mmm160) REVERT: E 1047 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8019 (t) REVERT: E 1121 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (ttpp) REVERT: E 1150 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6280 (mm-30) REVERT: G 22 CYS cc_start: 0.5688 (t) cc_final: 0.5444 (t) REVERT: I 33 LEU cc_start: 0.8344 (tp) cc_final: 0.7922 (tp) outliers start: 20 outliers final: 12 residues processed: 159 average time/residue: 0.1669 time to fit residues: 38.8415 Evaluate side-chains 160 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 60 optimal weight: 30.0000 chunk 44 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN K 92 ASN E 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100168 restraints weight = 21192.135| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.93 r_work: 0.3018 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 18030 Z= 0.229 Angle : 0.625 6.872 24542 Z= 0.323 Chirality : 0.046 0.207 2716 Planarity : 0.005 0.055 3101 Dihedral : 6.915 60.608 3192 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.49 % Allowed : 9.60 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2127 helix: 2.66 (0.27), residues: 369 sheet: 1.33 (0.22), residues: 528 loop : -1.50 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 172 TYR 0.028 0.002 TYR J 35 PHE 0.023 0.002 PHE H 78 TRP 0.008 0.001 TRP E 70 HIS 0.005 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00566 (17962) covalent geometry : angle 0.60850 (24365) SS BOND : bond 0.00504 ( 27) SS BOND : angle 1.89652 ( 54) hydrogen bonds : bond 0.06268 ( 643) hydrogen bonds : angle 4.97939 ( 1818) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.90370 ( 9) link_ALPHA1-6 : bond 0.00653 ( 6) link_ALPHA1-6 : angle 1.51669 ( 18) link_BETA1-4 : bond 0.00525 ( 14) link_BETA1-4 : angle 1.38342 ( 42) link_NAG-ASN : bond 0.00172 ( 18) link_NAG-ASN : angle 2.00229 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 1019 ASP cc_start: 0.8822 (p0) cc_final: 0.8308 (p0) REVERT: A 1047 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8284 (t) REVERT: A 1121 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7224 (ttpp) REVERT: A 1150 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: L 4 MET cc_start: 0.7170 (mmp) cc_final: 0.6833 (mmp) REVERT: C 1019 ASP cc_start: 0.8675 (p0) cc_final: 0.8171 (p0) REVERT: C 1150 GLU cc_start: 0.7060 (tp30) cc_final: 0.6215 (mm-30) REVERT: E 139 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7844 (ptp90) REVERT: E 162 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: E 1029 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: E 1047 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8242 (t) REVERT: G 63 LEU cc_start: 0.6016 (mt) cc_final: 0.5681 (mp) outliers start: 28 outliers final: 13 residues processed: 166 average time/residue: 0.1614 time to fit residues: 39.7632 Evaluate side-chains 156 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1006 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 189 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN E 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104894 restraints weight = 21113.356| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.96 r_work: 0.2991 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18030 Z= 0.150 Angle : 0.542 8.509 24542 Z= 0.282 Chirality : 0.043 0.196 2716 Planarity : 0.004 0.039 3101 Dihedral : 6.459 55.662 3192 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.28 % Allowed : 10.61 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2127 helix: 2.90 (0.27), residues: 366 sheet: 1.40 (0.22), residues: 522 loop : -1.45 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 131 TYR 0.018 0.001 TYR J 35 PHE 0.018 0.002 PHE G 78 TRP 0.006 0.001 TRP A1092 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00358 (17962) covalent geometry : angle 0.52828 (24365) SS BOND : bond 0.00383 ( 27) SS BOND : angle 1.45499 ( 54) hydrogen bonds : bond 0.05459 ( 643) hydrogen bonds : angle 4.76875 ( 1818) link_ALPHA1-3 : bond 0.01163 ( 3) link_ALPHA1-3 : angle 1.60816 ( 9) link_ALPHA1-6 : bond 0.00705 ( 6) link_ALPHA1-6 : angle 1.49404 ( 18) link_BETA1-4 : bond 0.00522 ( 14) link_BETA1-4 : angle 1.20709 ( 42) link_NAG-ASN : bond 0.00163 ( 18) link_NAG-ASN : angle 1.72376 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6485 (m) cc_final: 0.5998 (m) REVERT: A 96 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7519 (pm20) REVERT: A 200 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 1019 ASP cc_start: 0.8897 (p0) cc_final: 0.8300 (p0) REVERT: A 1047 CYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8044 (t) REVERT: A 1121 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7099 (ttpp) REVERT: A 1150 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: L 4 MET cc_start: 0.7199 (mmp) cc_final: 0.6832 (mmp) REVERT: C 287 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7557 (mttt) REVERT: C 1019 ASP cc_start: 0.8642 (p0) cc_final: 0.8126 (p0) REVERT: C 1022 TYR cc_start: 0.9581 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: C 1105 GLU cc_start: 0.7860 (tp30) cc_final: 0.7548 (tt0) REVERT: C 1147 GLU cc_start: 0.6264 (mt-10) cc_final: 0.6021 (tt0) REVERT: C 1150 GLU cc_start: 0.7009 (tp30) cc_final: 0.6152 (mm-30) REVERT: K 24 ARG cc_start: 0.6986 (tpp-160) cc_final: 0.6124 (mtm180) REVERT: E 139 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7650 (mtm110) REVERT: E 162 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: E 1029 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: E 1047 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7986 (t) REVERT: E 1121 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7051 (ttpp) REVERT: G 63 LEU cc_start: 0.6024 (mt) cc_final: 0.5686 (mp) REVERT: I 33 LEU cc_start: 0.8129 (tp) cc_final: 0.7866 (tp) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.1654 time to fit residues: 38.2129 Evaluate side-chains 161 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 176 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN E 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104887 restraints weight = 21147.474| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.23 r_work: 0.3013 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18030 Z= 0.143 Angle : 0.535 7.068 24542 Z= 0.277 Chirality : 0.043 0.200 2716 Planarity : 0.004 0.038 3101 Dihedral : 6.187 53.148 3192 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.33 % Allowed : 10.93 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2127 helix: 2.92 (0.27), residues: 366 sheet: 1.37 (0.22), residues: 522 loop : -1.44 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.018 0.001 TYR J 35 PHE 0.018 0.002 PHE G 78 TRP 0.006 0.001 TRP A1092 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00340 (17962) covalent geometry : angle 0.52195 (24365) SS BOND : bond 0.00377 ( 27) SS BOND : angle 1.36203 ( 54) hydrogen bonds : bond 0.05336 ( 643) hydrogen bonds : angle 4.69304 ( 1818) link_ALPHA1-3 : bond 0.01126 ( 3) link_ALPHA1-3 : angle 1.71931 ( 9) link_ALPHA1-6 : bond 0.00772 ( 6) link_ALPHA1-6 : angle 1.43367 ( 18) link_BETA1-4 : bond 0.00507 ( 14) link_BETA1-4 : angle 1.20122 ( 42) link_NAG-ASN : bond 0.00134 ( 18) link_NAG-ASN : angle 1.68107 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6566 (m) cc_final: 0.6009 (m) REVERT: A 96 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7528 (pm20) REVERT: A 200 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 1019 ASP cc_start: 0.8892 (p0) cc_final: 0.8303 (p0) REVERT: A 1047 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 1121 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7186 (ttpt) REVERT: A 1150 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: L 4 MET cc_start: 0.7207 (mmp) cc_final: 0.6909 (mmp) REVERT: C 29 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6288 (m) REVERT: C 287 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7523 (mttt) REVERT: C 1019 ASP cc_start: 0.8793 (p0) cc_final: 0.8276 (p0) REVERT: C 1022 TYR cc_start: 0.9590 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: C 1029 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: C 1105 GLU cc_start: 0.7821 (tp30) cc_final: 0.7615 (tt0) REVERT: C 1150 GLU cc_start: 0.7002 (tp30) cc_final: 0.6122 (mm-30) REVERT: K 24 ARG cc_start: 0.6938 (tpp-160) cc_final: 0.5989 (mtm180) REVERT: E 162 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: E 202 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8048 (mmm160) REVERT: E 1029 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: E 1047 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7990 (t) REVERT: E 1121 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6858 (ttpp) REVERT: E 1150 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6123 (mm-30) REVERT: G 63 LEU cc_start: 0.6062 (mt) cc_final: 0.5731 (mp) REVERT: I 33 LEU cc_start: 0.8126 (tp) cc_final: 0.7865 (tp) outliers start: 25 outliers final: 14 residues processed: 164 average time/residue: 0.1663 time to fit residues: 39.9191 Evaluate side-chains 167 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1022 TYR Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain G residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 54 optimal weight: 0.0030 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 1.1952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN E 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106043 restraints weight = 21225.001| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.99 r_work: 0.3004 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18030 Z= 0.131 Angle : 0.520 7.257 24542 Z= 0.269 Chirality : 0.043 0.206 2716 Planarity : 0.004 0.038 3101 Dihedral : 6.006 50.857 3192 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.60 % Allowed : 10.67 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.18), residues: 2127 helix: 3.01 (0.27), residues: 366 sheet: 1.39 (0.22), residues: 522 loop : -1.41 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 131 TYR 0.016 0.001 TYR J 35 PHE 0.017 0.001 PHE G 78 TRP 0.007 0.001 TRP A1092 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00306 (17962) covalent geometry : angle 0.50749 (24365) SS BOND : bond 0.00330 ( 27) SS BOND : angle 1.28412 ( 54) hydrogen bonds : bond 0.05146 ( 643) hydrogen bonds : angle 4.62680 ( 1818) link_ALPHA1-3 : bond 0.01072 ( 3) link_ALPHA1-3 : angle 1.56255 ( 9) link_ALPHA1-6 : bond 0.00813 ( 6) link_ALPHA1-6 : angle 1.42346 ( 18) link_BETA1-4 : bond 0.00537 ( 14) link_BETA1-4 : angle 1.15586 ( 42) link_NAG-ASN : bond 0.00147 ( 18) link_NAG-ASN : angle 1.63773 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6596 (m) cc_final: 0.6043 (m) REVERT: A 96 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7532 (pm20) REVERT: A 139 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7489 (ptt-90) REVERT: A 200 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 1019 ASP cc_start: 0.8868 (p0) cc_final: 0.8287 (p0) REVERT: A 1047 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7969 (t) REVERT: A 1121 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7238 (ttpt) REVERT: A 1150 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: L 4 MET cc_start: 0.7227 (mmp) cc_final: 0.6931 (mmp) REVERT: L 24 ARG cc_start: 0.6966 (tpp-160) cc_final: 0.6275 (mtm180) REVERT: C 29 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6473 (m) REVERT: C 287 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7542 (mttt) REVERT: C 1019 ASP cc_start: 0.8791 (p0) cc_final: 0.8261 (p0) REVERT: C 1022 TYR cc_start: 0.9592 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: C 1029 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: C 1150 GLU cc_start: 0.7028 (tp30) cc_final: 0.6154 (mm-30) REVERT: K 24 ARG cc_start: 0.6924 (tpp-160) cc_final: 0.5992 (mtm180) REVERT: E 1029 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: E 1047 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (t) REVERT: E 1077 MET cc_start: 0.8683 (mmm) cc_final: 0.8151 (ttm) REVERT: E 1116 LYS cc_start: 0.7018 (mmtp) cc_final: 0.6643 (mttp) REVERT: E 1121 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6908 (ttpp) REVERT: E 1150 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6236 (mm-30) REVERT: G 63 LEU cc_start: 0.6065 (mt) cc_final: 0.5730 (mp) REVERT: I 33 LEU cc_start: 0.8117 (tp) cc_final: 0.7859 (tp) outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.1672 time to fit residues: 40.2080 Evaluate side-chains 166 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1022 TYR Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain G residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN E 94 ASN I 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.158921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106883 restraints weight = 21008.717| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.24 r_work: 0.3042 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18030 Z= 0.109 Angle : 0.497 7.448 24542 Z= 0.257 Chirality : 0.042 0.212 2716 Planarity : 0.003 0.038 3101 Dihedral : 5.706 48.086 3192 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.33 % Allowed : 10.99 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2127 helix: 3.13 (0.27), residues: 366 sheet: 1.41 (0.22), residues: 522 loop : -1.36 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 131 TYR 0.013 0.001 TYR G 35 PHE 0.016 0.001 PHE J 78 TRP 0.013 0.001 TRP E1092 HIS 0.002 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00245 (17962) covalent geometry : angle 0.48550 (24365) SS BOND : bond 0.00296 ( 27) SS BOND : angle 1.17888 ( 54) hydrogen bonds : bond 0.04798 ( 643) hydrogen bonds : angle 4.51489 ( 1818) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 1.56363 ( 9) link_ALPHA1-6 : bond 0.00861 ( 6) link_ALPHA1-6 : angle 1.36019 ( 18) link_BETA1-4 : bond 0.00494 ( 14) link_BETA1-4 : angle 1.10254 ( 42) link_NAG-ASN : bond 0.00157 ( 18) link_NAG-ASN : angle 1.53005 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6610 (m) cc_final: 0.6046 (m) REVERT: A 96 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7547 (pm20) REVERT: A 200 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 1047 CYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7861 (t) REVERT: A 1121 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6942 (ttpt) REVERT: A 1150 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: L 24 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6291 (mtm180) REVERT: C 29 VAL cc_start: 0.6493 (OUTLIER) cc_final: 0.6136 (m) REVERT: C 287 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7515 (mttt) REVERT: C 1019 ASP cc_start: 0.8757 (p0) cc_final: 0.8248 (p0) REVERT: C 1022 TYR cc_start: 0.9580 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: C 1150 GLU cc_start: 0.6961 (tp30) cc_final: 0.6166 (mm-30) REVERT: K 24 ARG cc_start: 0.6909 (tpp-160) cc_final: 0.6010 (mtm180) REVERT: E 1029 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: E 1047 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8055 (t) REVERT: E 1077 MET cc_start: 0.8640 (mmm) cc_final: 0.8110 (ttm) REVERT: E 1116 LYS cc_start: 0.7055 (mmtp) cc_final: 0.6728 (mttp) REVERT: E 1121 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6797 (ttpp) REVERT: E 1150 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6187 (mm-30) REVERT: G 22 CYS cc_start: 0.5918 (t) cc_final: 0.5685 (t) REVERT: G 63 LEU cc_start: 0.6035 (mt) cc_final: 0.5707 (mp) REVERT: I 33 LEU cc_start: 0.8120 (tp) cc_final: 0.7873 (tp) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 0.1630 time to fit residues: 37.4951 Evaluate side-chains 160 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain E residue 1022 TYR Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain I residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 208 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103311 restraints weight = 21169.151| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.02 r_work: 0.2962 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18030 Z= 0.221 Angle : 0.600 7.061 24542 Z= 0.309 Chirality : 0.046 0.198 2716 Planarity : 0.004 0.048 3101 Dihedral : 6.188 51.339 3192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.28 % Allowed : 11.25 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2127 helix: 2.79 (0.27), residues: 369 sheet: 1.32 (0.22), residues: 522 loop : -1.47 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.021 0.002 TYR H 35 PHE 0.020 0.002 PHE H 78 TRP 0.007 0.001 TRP J 47 HIS 0.005 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00545 (17962) covalent geometry : angle 0.58627 (24365) SS BOND : bond 0.00440 ( 27) SS BOND : angle 1.54333 ( 54) hydrogen bonds : bond 0.05928 ( 643) hydrogen bonds : angle 4.80684 ( 1818) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 1.76766 ( 9) link_ALPHA1-6 : bond 0.00767 ( 6) link_ALPHA1-6 : angle 1.46657 ( 18) link_BETA1-4 : bond 0.00532 ( 14) link_BETA1-4 : angle 1.34952 ( 42) link_NAG-ASN : bond 0.00148 ( 18) link_NAG-ASN : angle 1.81408 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4545.49 seconds wall clock time: 78 minutes 47.43 seconds (4727.43 seconds total)