Starting phenix.real_space_refine on Sun Jun 15 16:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vef_43172/06_2025/8vef_43172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vef_43172/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vef_43172/06_2025/8vef_43172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vef_43172/06_2025/8vef_43172.map" model { file = "/net/cci-nas-00/data/ceres_data/8vef_43172/06_2025/8vef_43172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vef_43172/06_2025/8vef_43172.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.50, per 1000 atoms: 0.60 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: 4.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.52 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: 5.55 Time building geometry restraints manager: 5.38 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 1173 or resid 2001 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.160 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 TRP 0.018 0.002 TRP C 86 HIS 0.006 0.001 HIS E 18 PHE 0.032 0.003 PHE J 97 TYR 0.051 0.003 TYR J 53 ARG 0.014 0.001 ARG E 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 18) link_NAG-ASN : angle 2.89302 ( 54) 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_ALPHA1-3 : bond 0.00387 ( 3) link_ALPHA1-3 : angle 1.54933 ( 9) hydrogen bonds : bond 0.16786 ( 643) hydrogen bonds : angle 7.26745 ( 1818) SS BOND : bond 0.00672 ( 27) SS BOND : angle 1.54004 ( 54) covalent geometry : bond 0.00605 (17962) covalent geometry : angle 0.97127 (24365) *********************** 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 : 1.877 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: 0.6900 (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: 0.3173 time to fit residues: 132.3428 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 : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A1026 HIS A1117 ASN A1125 GLN H 76 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103325 restraints weight = 20784.616| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.92 r_work: 0.3062 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18030 Z= 0.215 Angle : 0.637 10.148 24542 Z= 0.333 Chirality : 0.046 0.196 2716 Planarity : 0.005 0.063 3101 Dihedral : 8.188 76.969 3192 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.59 % Allowed : 6.88 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2127 helix: 1.88 (0.27), residues: 363 sheet: 0.97 (0.21), residues: 561 loop : -1.58 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1092 HIS 0.007 0.002 HIS A1026 PHE 0.025 0.003 PHE G 78 TYR 0.025 0.002 TYR J 35 ARG 0.007 0.001 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 18) link_NAG-ASN : angle 2.17862 ( 54) link_ALPHA1-6 : bond 0.00532 ( 6) link_ALPHA1-6 : angle 1.82648 ( 18) link_BETA1-4 : bond 0.00563 ( 14) link_BETA1-4 : angle 1.38869 ( 42) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 2.61408 ( 9) hydrogen bonds : bond 0.06565 ( 643) hydrogen bonds : angle 5.40185 ( 1818) SS BOND : bond 0.00576 ( 27) SS BOND : angle 1.06887 ( 54) covalent geometry : bond 0.00524 (17962) covalent geometry : angle 0.62261 (24365) *********************** 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 180 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7322 (mmp) cc_final: 0.6941 (mmp) REVERT: C 53 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7200 (ttm110) REVERT: E 281 LEU cc_start: 0.8709 (tp) cc_final: 0.8470 (tp) REVERT: E 1017 MET cc_start: 0.8915 (ttp) cc_final: 0.8551 (ttm) REVERT: E 1077 MET cc_start: 0.8595 (tpp) cc_final: 0.8174 (ttm) REVERT: I 33 LEU cc_start: 0.8531 (tp) cc_final: 0.8172 (tp) REVERT: I 49 TYR cc_start: 0.7527 (m-80) cc_final: 0.7210 (m-80) outliers start: 11 outliers final: 7 residues processed: 176 average time/residue: 0.3971 time to fit residues: 107.8362 Evaluate side-chains 158 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 91 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 92 ASN C1125 GLN K 55 GLN K 92 ASN E 214 ASN I 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.160140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108446 restraints weight = 20889.906| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.97 r_work: 0.3039 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18030 Z= 0.123 Angle : 0.536 6.776 24542 Z= 0.281 Chirality : 0.043 0.187 2716 Planarity : 0.004 0.041 3101 Dihedral : 7.442 69.545 3192 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.07 % Allowed : 8.05 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2127 helix: 2.48 (0.27), residues: 369 sheet: 1.36 (0.22), residues: 528 loop : -1.49 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1092 HIS 0.003 0.001 HIS C 18 PHE 0.019 0.001 PHE H 78 TYR 0.020 0.001 TYR J 35 ARG 0.006 0.000 ARG E 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 18) link_NAG-ASN : angle 1.85871 ( 54) link_ALPHA1-6 : bond 0.00627 ( 6) link_ALPHA1-6 : angle 1.55883 ( 18) link_BETA1-4 : bond 0.00517 ( 14) link_BETA1-4 : angle 1.19835 ( 42) link_ALPHA1-3 : bond 0.01426 ( 3) link_ALPHA1-3 : angle 1.73717 ( 9) hydrogen bonds : bond 0.05392 ( 643) hydrogen bonds : angle 4.91588 ( 1818) SS BOND : bond 0.00397 ( 27) SS BOND : angle 1.48290 ( 54) covalent geometry : bond 0.00276 (17962) covalent geometry : angle 0.52053 (24365) *********************** 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 177 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6409 (m) cc_final: 0.5827 (m) REVERT: A 1121 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7219 (ttpp) REVERT: C 30 CYS cc_start: 0.6831 (m) cc_final: 0.6235 (m) REVERT: C 202 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8209 (mmm160) REVERT: C 287 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7539 (mttt) REVERT: E 30 CYS cc_start: 0.6786 (m) cc_final: 0.6170 (m) REVERT: E 162 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: E 1077 MET cc_start: 0.8540 (tpp) cc_final: 0.8128 (ttm) REVERT: I 24 ARG cc_start: 0.6655 (tpt170) cc_final: 0.6340 (mtm180) REVERT: I 33 LEU cc_start: 0.8356 (tp) cc_final: 0.7957 (tp) REVERT: I 49 TYR cc_start: 0.7530 (m-80) cc_final: 0.7216 (m-80) outliers start: 20 outliers final: 11 residues processed: 169 average time/residue: 0.3725 time to fit residues: 94.4474 Evaluate side-chains 157 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 139 ARG Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 1029 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN E 214 ASN I 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108686 restraints weight = 20886.257| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.89 r_work: 0.3063 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18030 Z= 0.125 Angle : 0.521 6.766 24542 Z= 0.271 Chirality : 0.043 0.195 2716 Planarity : 0.004 0.039 3101 Dihedral : 6.981 64.169 3192 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.91 % Allowed : 9.33 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2127 helix: 2.78 (0.27), residues: 369 sheet: 1.39 (0.22), residues: 528 loop : -1.43 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1092 HIS 0.003 0.001 HIS C 18 PHE 0.019 0.001 PHE H 78 TYR 0.018 0.001 TYR J 35 ARG 0.006 0.000 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 1.78774 ( 54) link_ALPHA1-6 : bond 0.00611 ( 6) link_ALPHA1-6 : angle 1.52306 ( 18) link_BETA1-4 : bond 0.00476 ( 14) link_BETA1-4 : angle 1.18562 ( 42) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 1.84175 ( 9) hydrogen bonds : bond 0.05190 ( 643) hydrogen bonds : angle 4.74653 ( 1818) SS BOND : bond 0.00415 ( 27) SS BOND : angle 1.50028 ( 54) covalent geometry : bond 0.00288 (17962) covalent geometry : angle 0.50616 (24365) *********************** 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 167 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1019 ASP cc_start: 0.8693 (p0) cc_final: 0.8094 (p0) REVERT: A 1121 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6998 (ttpp) REVERT: C 202 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8171 (mmm160) REVERT: C 1150 GLU cc_start: 0.7009 (tp30) cc_final: 0.6148 (mm-30) REVERT: K 24 ARG cc_start: 0.6742 (tpp-160) cc_final: 0.5852 (mtm180) REVERT: E 162 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: E 1077 MET cc_start: 0.8649 (tpp) cc_final: 0.8375 (ttm) REVERT: E 1121 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6834 (ttpp) REVERT: E 1150 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6290 (mm-30) REVERT: I 33 LEU cc_start: 0.8308 (tp) cc_final: 0.7868 (tp) REVERT: I 49 TYR cc_start: 0.7533 (m-80) cc_final: 0.7253 (m-80) outliers start: 17 outliers final: 12 residues processed: 158 average time/residue: 0.3674 time to fit residues: 86.0433 Evaluate side-chains 157 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 139 ARG Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 162 GLU 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 168 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** C 302 GLN 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 = 0.3852 r_free = 0.3852 target = 0.155944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100628 restraints weight = 21208.464| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.93 r_work: 0.3020 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18030 Z= 0.205 Angle : 0.605 7.336 24542 Z= 0.313 Chirality : 0.046 0.200 2716 Planarity : 0.004 0.047 3101 Dihedral : 6.995 62.190 3192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.60 % Allowed : 9.97 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2127 helix: 2.60 (0.27), residues: 369 sheet: 1.31 (0.22), residues: 528 loop : -1.51 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 70 HIS 0.004 0.001 HIS E 136 PHE 0.023 0.002 PHE H 78 TYR 0.026 0.002 TYR J 35 ARG 0.006 0.001 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 1.98251 ( 54) link_ALPHA1-6 : bond 0.00608 ( 6) link_ALPHA1-6 : angle 1.53038 ( 18) link_BETA1-4 : bond 0.00541 ( 14) link_BETA1-4 : angle 1.33982 ( 42) link_ALPHA1-3 : bond 0.01277 ( 3) link_ALPHA1-3 : angle 1.99964 ( 9) hydrogen bonds : bond 0.06113 ( 643) hydrogen bonds : angle 4.94704 ( 1818) SS BOND : bond 0.00558 ( 27) SS BOND : angle 1.65589 ( 54) covalent geometry : bond 0.00504 (17962) covalent geometry : angle 0.58955 (24365) *********************** 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 174 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8059 (mp) REVERT: A 1019 ASP cc_start: 0.8819 (p0) cc_final: 0.8300 (p0) REVERT: A 1047 CYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8322 (t) REVERT: A 1121 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7196 (ttpp) REVERT: A 1150 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: L 4 MET cc_start: 0.7294 (mmp) cc_final: 0.6946 (mmp) REVERT: C 1019 ASP cc_start: 0.8685 (p0) cc_final: 0.8183 (p0) REVERT: C 1047 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 1150 GLU cc_start: 0.7056 (tp30) cc_final: 0.6212 (mm-30) REVERT: E 162 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: E 1029 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: E 1047 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8277 (t) REVERT: E 1077 MET cc_start: 0.8709 (tpp) cc_final: 0.8428 (ttm) REVERT: I 49 TYR cc_start: 0.7786 (m-80) cc_final: 0.7509 (m-80) outliers start: 30 outliers final: 16 residues processed: 160 average time/residue: 0.4155 time to fit residues: 100.1343 Evaluate side-chains 161 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 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 139 ARG Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1006 ILE Chi-restraints excluded: chain C residue 1047 CYS 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 287 LYS Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1047 CYS Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain G residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 118 optimal weight: 0.0170 chunk 66 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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 6 GLN I 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106500 restraints weight = 21000.449| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.95 r_work: 0.3015 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18030 Z= 0.115 Angle : 0.515 9.004 24542 Z= 0.267 Chirality : 0.042 0.199 2716 Planarity : 0.004 0.039 3101 Dihedral : 6.415 55.899 3192 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.44 % Allowed : 10.67 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2127 helix: 2.93 (0.27), residues: 366 sheet: 1.40 (0.22), residues: 522 loop : -1.41 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1092 HIS 0.003 0.001 HIS C 18 PHE 0.016 0.001 PHE H 78 TYR 0.014 0.001 TYR J 35 ARG 0.004 0.000 ARG C 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 18) link_NAG-ASN : angle 1.66911 ( 54) link_ALPHA1-6 : bond 0.00699 ( 6) link_ALPHA1-6 : angle 1.47273 ( 18) link_BETA1-4 : bond 0.00495 ( 14) link_BETA1-4 : angle 1.17890 ( 42) link_ALPHA1-3 : bond 0.01214 ( 3) link_ALPHA1-3 : angle 1.61151 ( 9) hydrogen bonds : bond 0.05083 ( 643) hydrogen bonds : angle 4.67115 ( 1818) SS BOND : bond 0.00357 ( 27) SS BOND : angle 1.30959 ( 54) covalent geometry : bond 0.00259 (17962) covalent geometry : angle 0.50264 (24365) *********************** 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 170 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 1019 ASP cc_start: 0.8756 (p0) cc_final: 0.8197 (p0) REVERT: A 1047 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7998 (t) REVERT: A 1121 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7154 (ttpp) REVERT: A 1150 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: L 4 MET cc_start: 0.7131 (mmp) cc_final: 0.6805 (mmp) REVERT: C 29 VAL cc_start: 0.6771 (m) cc_final: 0.6324 (m) REVERT: C 1019 ASP cc_start: 0.8653 (p0) cc_final: 0.8046 (p0) REVERT: C 1022 TYR cc_start: 0.9560 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: C 1029 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: C 1105 GLU cc_start: 0.7854 (tp30) cc_final: 0.7602 (tt0) REVERT: C 1150 GLU cc_start: 0.6987 (tp30) cc_final: 0.6135 (mm-30) REVERT: K 24 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6115 (mtm180) REVERT: E 162 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: E 1077 MET cc_start: 0.8549 (tpp) cc_final: 0.8302 (ttm) REVERT: E 1121 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6880 (ttpp) REVERT: G 63 LEU cc_start: 0.5950 (mt) cc_final: 0.5597 (mp) REVERT: I 49 TYR cc_start: 0.7773 (m-80) cc_final: 0.7541 (m-80) outliers start: 27 outliers final: 13 residues processed: 161 average time/residue: 0.3461 time to fit residues: 83.5968 Evaluate side-chains 158 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU 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 139 ARG 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 E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 139 ARG 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 1118 LEU Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain I residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN K 92 ASN E 94 ASN E 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108004 restraints weight = 20890.973| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.95 r_work: 0.3034 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18030 Z= 0.099 Angle : 0.491 7.272 24542 Z= 0.254 Chirality : 0.042 0.207 2716 Planarity : 0.003 0.038 3101 Dihedral : 5.951 52.094 3192 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.28 % Allowed : 11.20 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2127 helix: 3.13 (0.27), residues: 366 sheet: 1.43 (0.22), residues: 522 loop : -1.36 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.002 0.001 HIS C 18 PHE 0.015 0.001 PHE J 78 TYR 0.012 0.001 TYR G 35 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 18) link_NAG-ASN : angle 1.55972 ( 54) link_ALPHA1-6 : bond 0.00805 ( 6) link_ALPHA1-6 : angle 1.37250 ( 18) link_BETA1-4 : bond 0.00494 ( 14) link_BETA1-4 : angle 1.13093 ( 42) link_ALPHA1-3 : bond 0.01165 ( 3) link_ALPHA1-3 : angle 1.65805 ( 9) hydrogen bonds : bond 0.04687 ( 643) hydrogen bonds : angle 4.51038 ( 1818) SS BOND : bond 0.00364 ( 27) SS BOND : angle 1.39482 ( 54) covalent geometry : bond 0.00211 (17962) covalent geometry : angle 0.47817 (24365) *********************** 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 168 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6777 (m) cc_final: 0.6269 (m) REVERT: A 200 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 1047 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7916 (t) REVERT: A 1120 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 1121 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.7043 (ttpt) REVERT: A 1150 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: L 4 MET cc_start: 0.7252 (mmp) cc_final: 0.6984 (mmp) REVERT: L 69 THR cc_start: 0.5976 (OUTLIER) cc_final: 0.5672 (t) REVERT: C 138 THR cc_start: 0.8712 (p) cc_final: 0.8440 (p) REVERT: C 287 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7553 (mttt) REVERT: C 1019 ASP cc_start: 0.8773 (p0) cc_final: 0.8157 (p0) REVERT: C 1022 TYR cc_start: 0.9554 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: C 1105 GLU cc_start: 0.7790 (tp30) cc_final: 0.7576 (tt0) REVERT: C 1150 GLU cc_start: 0.7000 (tp30) cc_final: 0.6151 (mm-30) REVERT: J 53 TYR cc_start: 0.8809 (t80) cc_final: 0.8505 (t80) REVERT: K 24 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6089 (mtm180) REVERT: E 162 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: E 1029 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: E 1077 MET cc_start: 0.8602 (tpp) cc_final: 0.8301 (ttm) REVERT: E 1121 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6882 (ttpp) REVERT: G 22 CYS cc_start: 0.5620 (t) cc_final: 0.5373 (t) REVERT: G 63 LEU cc_start: 0.5954 (mt) cc_final: 0.5597 (mp) REVERT: I 22 THR cc_start: 0.6889 (m) cc_final: 0.6587 (t) outliers start: 24 outliers final: 10 residues processed: 160 average time/residue: 0.3354 time to fit residues: 79.7064 Evaluate side-chains 154 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 139 ARG 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 1121 LYS Chi-restraints excluded: chain G residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN K 92 ASN E 94 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 = 0.3864 r_free = 0.3864 target = 0.157150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105460 restraints weight = 21093.887| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.95 r_work: 0.2992 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2797 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= 0.170 Angle : 0.550 7.166 24542 Z= 0.283 Chirality : 0.044 0.197 2716 Planarity : 0.004 0.039 3101 Dihedral : 6.157 53.083 3192 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.65 % Allowed : 11.04 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2127 helix: 2.93 (0.27), residues: 369 sheet: 1.32 (0.22), residues: 528 loop : -1.42 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.001 HIS E 136 PHE 0.018 0.002 PHE G 78 TYR 0.020 0.002 TYR J 35 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 18) link_NAG-ASN : angle 1.73364 ( 54) link_ALPHA1-6 : bond 0.00734 ( 6) link_ALPHA1-6 : angle 1.40130 ( 18) link_BETA1-4 : bond 0.00457 ( 14) link_BETA1-4 : angle 1.21817 ( 42) link_ALPHA1-3 : bond 0.01148 ( 3) link_ALPHA1-3 : angle 1.78813 ( 9) hydrogen bonds : bond 0.05470 ( 643) hydrogen bonds : angle 4.68594 ( 1818) SS BOND : bond 0.00384 ( 27) SS BOND : angle 1.55549 ( 54) covalent geometry : bond 0.00415 (17962) covalent geometry : angle 0.53578 (24365) *********************** 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: 31 poor density : 141 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6781 (m) cc_final: 0.6250 (m) REVERT: A 139 ARG cc_start: 0.7686 (ptp90) cc_final: 0.7476 (ptt-90) REVERT: A 200 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 1019 ASP cc_start: 0.8822 (p0) cc_final: 0.8210 (p0) REVERT: A 1047 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7967 (t) REVERT: A 1121 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7130 (ttpp) REVERT: A 1150 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: L 4 MET cc_start: 0.7223 (mmp) cc_final: 0.6921 (mmp) REVERT: L 69 THR cc_start: 0.6047 (OUTLIER) cc_final: 0.5770 (t) REVERT: C 138 THR cc_start: 0.8810 (p) cc_final: 0.8535 (p) REVERT: C 287 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7595 (mttt) REVERT: C 1019 ASP cc_start: 0.8784 (p0) cc_final: 0.8132 (p0) REVERT: C 1022 TYR cc_start: 0.9590 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: C 1029 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5761 (mp0) REVERT: C 1105 GLU cc_start: 0.7885 (tp30) cc_final: 0.7585 (tt0) REVERT: C 1150 GLU cc_start: 0.7032 (tp30) cc_final: 0.6158 (mm-30) REVERT: K 24 ARG cc_start: 0.7017 (tpp-160) cc_final: 0.6111 (mtm180) REVERT: E 162 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: E 282 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: E 1029 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: E 1077 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8324 (ttm) REVERT: E 1121 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6871 (ttpp) REVERT: G 63 LEU cc_start: 0.6007 (mt) cc_final: 0.5658 (mp) REVERT: I 22 THR cc_start: 0.6908 (m) cc_final: 0.6605 (t) outliers start: 31 outliers final: 16 residues processed: 162 average time/residue: 0.3577 time to fit residues: 86.2001 Evaluate side-chains 168 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 1121 LYS Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 275 ILE 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 E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 139 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 282 ASP 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 1077 MET Chi-restraints excluded: chain E residue 1098 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN I 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106020 restraints weight = 21249.290| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.92 r_work: 0.3037 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18030 Z= 0.158 Angle : 0.540 7.435 24542 Z= 0.279 Chirality : 0.044 0.201 2716 Planarity : 0.004 0.039 3101 Dihedral : 6.101 51.684 3192 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.60 % Allowed : 11.20 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2127 helix: 2.93 (0.27), residues: 366 sheet: 1.38 (0.22), residues: 522 loop : -1.42 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1092 HIS 0.004 0.001 HIS E 136 PHE 0.018 0.002 PHE G 78 TYR 0.017 0.001 TYR J 35 ARG 0.004 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 18) link_NAG-ASN : angle 1.69958 ( 54) link_ALPHA1-6 : bond 0.00766 ( 6) link_ALPHA1-6 : angle 1.45243 ( 18) link_BETA1-4 : bond 0.00526 ( 14) link_BETA1-4 : angle 1.19278 ( 42) link_ALPHA1-3 : bond 0.01122 ( 3) link_ALPHA1-3 : angle 1.63609 ( 9) hydrogen bonds : bond 0.05415 ( 643) hydrogen bonds : angle 4.70193 ( 1818) SS BOND : bond 0.00423 ( 27) SS BOND : angle 1.47099 ( 54) covalent geometry : bond 0.00382 (17962) covalent geometry : angle 0.52641 (24365) *********************** 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 : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 CYS cc_start: 0.7228 (m) cc_final: 0.6705 (m) REVERT: A 200 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 1019 ASP cc_start: 0.8904 (p0) cc_final: 0.8296 (p0) REVERT: A 1047 CYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 1121 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7101 (ttpp) REVERT: A 1150 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: L 4 MET cc_start: 0.7226 (mmp) cc_final: 0.6908 (mmp) REVERT: L 24 ARG cc_start: 0.6921 (tpp-160) cc_final: 0.6167 (mtm180) REVERT: C 138 THR cc_start: 0.8833 (p) cc_final: 0.8557 (p) REVERT: C 287 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7548 (mttt) REVERT: C 1019 ASP cc_start: 0.8888 (p0) cc_final: 0.8157 (p0) REVERT: C 1022 TYR cc_start: 0.9618 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: C 1029 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: C 1105 GLU cc_start: 0.7997 (tp30) cc_final: 0.7696 (tt0) REVERT: C 1150 GLU cc_start: 0.7035 (tp30) cc_final: 0.6182 (mm-30) REVERT: K 24 ARG cc_start: 0.6605 (tpp-160) cc_final: 0.5868 (mtm180) REVERT: E 162 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: E 1029 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: E 1077 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: E 1116 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6765 (mttp) REVERT: E 1121 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6848 (ttpp) REVERT: E 1150 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6211 (mm-30) REVERT: G 63 LEU cc_start: 0.5902 (mt) cc_final: 0.5557 (mp) REVERT: I 22 THR cc_start: 0.6858 (m) cc_final: 0.6569 (t) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 0.3271 time to fit residues: 79.4675 Evaluate side-chains 168 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 H residue 67 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 275 ILE 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 E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP 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 287 LYS Chi-restraints excluded: chain E residue 1022 TYR Chi-restraints excluded: chain E residue 1029 GLU Chi-restraints excluded: chain E residue 1077 MET 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 73 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 135 optimal weight: 0.0060 chunk 102 optimal weight: 0.0050 chunk 97 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.160433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109180 restraints weight = 21085.846| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.99 r_work: 0.3053 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18030 Z= 0.095 Angle : 0.477 7.671 24542 Z= 0.247 Chirality : 0.042 0.219 2716 Planarity : 0.003 0.038 3101 Dihedral : 5.545 46.475 3192 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.33 % Allowed : 11.52 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2127 helix: 3.15 (0.26), residues: 369 sheet: 1.43 (0.22), residues: 522 loop : -1.29 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1092 HIS 0.002 0.000 HIS E 136 PHE 0.015 0.001 PHE J 78 TYR 0.011 0.001 TYR G 35 ARG 0.005 0.000 ARG A 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 18) link_NAG-ASN : angle 1.45153 ( 54) link_ALPHA1-6 : bond 0.00897 ( 6) link_ALPHA1-6 : angle 1.34726 ( 18) link_BETA1-4 : bond 0.00502 ( 14) link_BETA1-4 : angle 1.08928 ( 42) link_ALPHA1-3 : bond 0.01205 ( 3) link_ALPHA1-3 : angle 1.53575 ( 9) hydrogen bonds : bond 0.04498 ( 643) hydrogen bonds : angle 4.44090 ( 1818) SS BOND : bond 0.00314 ( 27) SS BOND : angle 1.20884 ( 54) covalent geometry : bond 0.00197 (17962) covalent geometry : angle 0.46621 (24365) ********************** 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 170 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 30 CYS cc_start: 0.6883 (m) cc_final: 0.6341 (m) REVERT: A 96 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7528 (pm20) REVERT: A 200 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 1047 CYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7871 (t) REVERT: A 1150 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: L 4 MET cc_start: 0.7259 (mmp) cc_final: 0.6980 (mmp) REVERT: L 24 ARG cc_start: 0.6744 (tpp-160) cc_final: 0.6111 (mtm180) REVERT: C 29 VAL cc_start: 0.6709 (OUTLIER) cc_final: 0.6199 (m) REVERT: C 138 THR cc_start: 0.8674 (p) cc_final: 0.8399 (p) REVERT: C 287 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7544 (mttt) REVERT: C 1019 ASP cc_start: 0.8719 (p0) cc_final: 0.8068 (p0) REVERT: C 1022 TYR cc_start: 0.9582 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: C 1029 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: C 1150 GLU cc_start: 0.7020 (tp30) cc_final: 0.6179 (mm-30) REVERT: K 24 ARG cc_start: 0.6617 (tpp-160) cc_final: 0.5848 (mtm180) REVERT: E 162 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: E 202 ARG cc_start: 0.8371 (mmm160) cc_final: 0.8066 (mmm160) REVERT: E 1029 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: E 1077 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8281 (ttm) REVERT: E 1116 LYS cc_start: 0.7030 (mmtp) cc_final: 0.6710 (mttp) REVERT: E 1121 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6690 (ttpt) REVERT: E 1150 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6211 (mm-30) REVERT: G 22 CYS cc_start: 0.5876 (t) cc_final: 0.5642 (t) REVERT: G 63 LEU cc_start: 0.5982 (mt) cc_final: 0.5634 (mp) REVERT: I 22 THR cc_start: 0.6870 (m) cc_final: 0.6564 (t) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 0.3470 time to fit residues: 81.0420 Evaluate side-chains 164 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP 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 1150 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 139 ARG 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 J residue 67 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 139 ARG 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 1077 MET 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 201 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN I 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106023 restraints weight = 21233.171| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.07 r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18030 Z= 0.153 Angle : 0.533 7.697 24542 Z= 0.274 Chirality : 0.044 0.206 2716 Planarity : 0.004 0.038 3101 Dihedral : 5.760 48.258 3192 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.28 % Allowed : 11.47 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2127 helix: 3.00 (0.27), residues: 369 sheet: 1.34 (0.22), residues: 528 loop : -1.36 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1092 HIS 0.003 0.001 HIS E 136 PHE 0.017 0.002 PHE G 78 TYR 0.018 0.001 TYR J 35 ARG 0.005 0.000 ARG E 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 18) link_NAG-ASN : angle 1.64322 ( 54) link_ALPHA1-6 : bond 0.00828 ( 6) link_ALPHA1-6 : angle 1.37706 ( 18) link_BETA1-4 : bond 0.00511 ( 14) link_BETA1-4 : angle 1.17362 ( 42) link_ALPHA1-3 : bond 0.01068 ( 3) link_ALPHA1-3 : angle 1.68138 ( 9) hydrogen bonds : bond 0.05232 ( 643) hydrogen bonds : angle 4.59869 ( 1818) SS BOND : bond 0.00415 ( 27) SS BOND : angle 1.44151 ( 54) covalent geometry : bond 0.00369 (17962) covalent geometry : angle 0.52016 (24365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9358.95 seconds wall clock time: 165 minutes 31.31 seconds (9931.31 seconds total)