Starting phenix.real_space_refine on Sun Aug 24 07:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ved_43170/08_2025/8ved_43170.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 84 5.16 5 C 11156 2.51 5 N 3010 2.21 5 O 3590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17840 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3907 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 21, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 960 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "C" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3907 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 21, 'TRANS': 469} Chain breaks: 1 Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 960 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "I" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3907 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 21, 'TRANS': 469} Chain breaks: 1 Chain: "J" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 960 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "K" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.22, per 1000 atoms: 0.24 Number of scatterers: 17840 At special positions: 0 Unit cell: (126.711, 116.964, 161.367, 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 84 16.00 O 3590 8.00 N 3010 7.00 C 11156 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=2.02 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=2.04 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=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1144 " - pdb=" SG CYS C1148 " 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 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E1144 " - pdb=" SG CYS E1148 " 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 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 ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA O 3 " - " MAN O 6 " " MAN O 6 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 7 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 7 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A2001 " - " ASN A 21 " " NAG A2002 " - " ASN A 33 " " NAG A2003 " - " ASN A 135 " " NAG A2004 " - " ASN A 296 " " NAG A2005 " - " ASN A1154 " " NAG C2001 " - " ASN C 33 " " NAG C2002 " - " ASN C 83 " " NAG C2003 " - " ASN C 135 " " NAG C2004 " - " ASN C 296 " " NAG C2005 " - " ASN C 21 " " NAG C2006 " - " ASN C1154 " " NAG E2001 " - " ASN E 164 " " NAG E2002 " - " ASN E 135 " " NAG E2003 " - " ASN E 296 " " NAG E2004 " - " ASN E 21 " " NAG E2005 " - " ASN E1154 " " NAG M 1 " - " ASN A 97 " " NAG N 1 " - " ASN A 83 " " NAG O 1 " - " ASN A 169 " " NAG P 1 " - " ASN C 97 " " NAG Q 1 " - " ASN C 169 " " NAG R 1 " - " ASN E 97 " " NAG S 1 " - " ASN E 33 " " NAG T 1 " - " ASN E 83 " " NAG U 1 " - " ASN E 169 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 762.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4038 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 43 sheets defined 20.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.298A pdb=" N SER A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 1037 through 1059 removed outlier: 3.635A pdb=" N THR A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1127 removed outlier: 3.696A pdb=" N LEU A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1154 removed outlier: 3.509A pdb=" N VAL A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1161 No H-bonds generated for 'chain 'A' and resid 1159 through 1161' Processing helix chain 'A' and resid 1162 through 1173 removed outlier: 3.550A pdb=" N SER A1166 " --> pdb=" O TYR A1162 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.778A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100B through 100G removed outlier: 3.544A pdb=" N TYR H 100E" --> pdb=" O THR H 100B" (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS H 100G" --> pdb=" O GLY H 100D" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.905A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.395A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 1039 through 1059 removed outlier: 3.921A pdb=" N MET C1059 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1127 removed outlier: 3.739A pdb=" N LEU C1089 " --> pdb=" O ASP C1085 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP C1090 " --> pdb=" O ASP C1086 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C1091 " --> pdb=" O GLY C1087 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1154 Processing helix chain 'C' and resid 1162 through 1173 removed outlier: 3.536A pdb=" N ILE C1173 " --> pdb=" O ASN C1169 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.728A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 100B through 100G removed outlier: 3.988A pdb=" N LYS G 100G" --> pdb=" O GLY G 100D" (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.909A pdb=" N VAL I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 107 through 117 removed outlier: 4.335A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.150A pdb=" N TRP E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.531A pdb=" N GLN E 197 " --> pdb=" O ASN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1037 through 1059 removed outlier: 3.551A pdb=" N THR E1041 " --> pdb=" O ASP E1037 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET E1059 " --> pdb=" O VAL E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1127 Processing helix chain 'E' and resid 1145 through 1154 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 1173 removed outlier: 3.566A pdb=" N ILE E1173 " --> pdb=" O ASN E1169 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.699A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 100B through 100G removed outlier: 3.897A pdb=" N LYS J 100G" --> pdb=" O GLY J 100D" (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.900A pdb=" N VAL K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.136A 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 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.272A pdb=" N LEU A 60 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.753A pdb=" N ARG A 84 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 121 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER A 267 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 121 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA A 265 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 123 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 263 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 264 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 294 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 11 through 12 removed outlier: 6.467A pdb=" N TRP H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 13 through 14 removed outlier: 6.620A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.449A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.449A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1032 through 1034 removed outlier: 3.616A pdb=" N GLY C1023 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.124A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.284A pdb=" N LEU C 60 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 118 through 125 removed outlier: 3.712A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 264 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 118 through 125 removed outlier: 3.712A pdb=" N SER C 120 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 264 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AC6, first strand: chain 'C' and resid 288 through 289 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.511A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 14 removed outlier: 3.902A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 14 removed outlier: 3.902A pdb=" N GLU I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1032 through 1036 Processing sheet with id=AD4, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.051A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.380A pdb=" N LEU E 60 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.743A pdb=" N ARG E 84 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 121 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER E 267 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE E 121 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA E 265 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 123 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 263 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE E 264 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU E 185 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.743A pdb=" N ARG E 84 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 121 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER E 267 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE E 121 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA E 265 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 123 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 263 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE E 264 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 170 through 175 Processing sheet with id=AE2, first strand: chain 'E' and resid 294 through 295 removed outlier: 3.510A pdb=" N ILE E 295 " --> pdb=" O CYS E 288 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS E 288 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.514A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.534A pdb=" N VAL J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.873A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.873A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3084 1.32 - 1.45: 5166 1.45 - 1.58: 9877 1.58 - 1.71: 1 1.71 - 1.84: 114 Bond restraints: 18242 Sorted by residual: bond pdb=" C TYR K 49 " pdb=" O TYR K 49 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.21e-02 6.83e+03 1.25e+01 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N ILE J 51 " pdb=" CA ILE J 51 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.17e-02 7.31e+03 1.08e+01 bond pdb=" CA SER H 59 " pdb=" CB SER H 59 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.51e-02 4.39e+03 1.02e+01 ... (remaining 18237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 24378 3.27 - 6.53: 331 6.53 - 9.80: 38 9.80 - 13.06: 8 13.06 - 16.33: 2 Bond angle restraints: 24757 Sorted by residual: angle pdb=" CB ARG L 46 " pdb=" CG ARG L 46 " pdb=" CD ARG L 46 " ideal model delta sigma weight residual 111.30 94.97 16.33 2.30e+00 1.89e-01 5.04e+01 angle pdb=" C LEU A 243 " pdb=" N GLU A 244 " pdb=" CA GLU A 244 " ideal model delta sigma weight residual 121.48 134.68 -13.20 2.04e+00 2.40e-01 4.19e+01 angle pdb=" N SER C 298 " pdb=" CA SER C 298 " pdb=" C SER C 298 " ideal model delta sigma weight residual 112.92 105.00 7.92 1.23e+00 6.61e-01 4.15e+01 angle pdb=" C LYS I 50 " pdb=" CA LYS I 50 " pdb=" CB LYS I 50 " ideal model delta sigma weight residual 110.42 122.96 -12.54 1.99e+00 2.53e-01 3.97e+01 angle pdb=" C LYS K 50 " pdb=" CA LYS K 50 " pdb=" CB LYS K 50 " ideal model delta sigma weight residual 110.42 122.44 -12.02 1.99e+00 2.53e-01 3.65e+01 ... (remaining 24752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 10858 21.58 - 43.15: 583 43.15 - 64.73: 75 64.73 - 86.30: 27 86.30 - 107.88: 13 Dihedral angle restraints: 11556 sinusoidal: 5241 harmonic: 6315 Sorted by residual: dihedral pdb=" C LYS K 50 " pdb=" N LYS K 50 " pdb=" CA LYS K 50 " pdb=" CB LYS K 50 " ideal model delta harmonic sigma weight residual -122.60 -140.77 18.17 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" C LYS I 50 " pdb=" N LYS I 50 " pdb=" CA LYS I 50 " pdb=" CB LYS I 50 " ideal model delta harmonic sigma weight residual -122.60 -139.96 17.36 0 2.50e+00 1.60e-01 4.82e+01 dihedral pdb=" C LYS L 50 " pdb=" N LYS L 50 " pdb=" CA LYS L 50 " pdb=" CB LYS L 50 " ideal model delta harmonic sigma weight residual -122.60 -139.90 17.30 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 11553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 2759 0.166 - 0.333: 55 0.333 - 0.499: 2 0.499 - 0.666: 3 0.666 - 0.832: 3 Chirality restraints: 2822 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.22e+02 chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.66e+02 chirality pdb=" C1 MAN U 6 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 6 " pdb=" O5 MAN U 6 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.59e+02 ... (remaining 2819 not shown) Planarity restraints: 3167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.313 2.00e-02 2.50e+03 2.64e-01 8.69e+02 pdb=" C7 NAG Q 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG U 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " 0.450 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.160 2.00e-02 2.50e+03 1.33e-01 2.20e+02 pdb=" C7 NAG T 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.119 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.214 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 3164 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4169 2.80 - 3.33: 14007 3.33 - 3.85: 28207 3.85 - 4.38: 31868 4.38 - 4.90: 58513 Nonbonded interactions: 136764 Sorted by model distance: nonbonded pdb=" O GLU E1147 " pdb=" OG SER E1151 " model vdw 2.277 3.040 nonbonded pdb=" O GLU C1147 " pdb=" OG SER C1151 " model vdw 2.292 3.040 nonbonded pdb=" OG SER A 120 " pdb=" OG SER A 267 " model vdw 2.304 3.040 nonbonded pdb=" NZ LYS C1123 " pdb=" OE2 GLU C1132 " model vdw 2.325 3.120 nonbonded pdb=" OG1 THR C 290 " pdb=" O GLY C 293 " model vdw 2.331 3.040 ... (remaining 136759 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' and resid 11 through 2005) selection = chain 'E' } 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 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'U' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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 0.103 18318 Z= 0.334 Angle : 1.062 19.114 24958 Z= 0.588 Chirality : 0.069 0.832 2822 Planarity : 0.011 0.264 3142 Dihedral : 13.369 107.876 7437 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.21 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.17), residues: 2163 helix: 0.85 (0.26), residues: 357 sheet: 1.17 (0.21), residues: 615 loop : -1.53 (0.15), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 46 TYR 0.042 0.002 TYR K 49 PHE 0.019 0.002 PHE C 121 TRP 0.016 0.002 TRP A 70 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00612 (18242) covalent geometry : angle 1.00709 (24757) SS BOND : bond 0.00594 ( 27) SS BOND : angle 1.89115 ( 54) hydrogen bonds : bond 0.16567 ( 653) hydrogen bonds : angle 7.43688 ( 1857) link_ALPHA1-2 : bond 0.00073 ( 3) link_ALPHA1-2 : angle 2.11376 ( 9) link_ALPHA1-3 : bond 0.00937 ( 3) link_ALPHA1-3 : angle 2.91933 ( 9) link_ALPHA1-6 : bond 0.01401 ( 6) link_ALPHA1-6 : angle 3.28720 ( 18) link_BETA1-4 : bond 0.01538 ( 12) link_BETA1-4 : angle 2.82551 ( 36) link_NAG-ASN : bond 0.01106 ( 25) link_NAG-ASN : angle 5.44749 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7067 (mttt) cc_final: 0.6524 (tptp) REVERT: A 61 GLN cc_start: 0.8149 (mt0) cc_final: 0.7881 (mt0) REVERT: A 85 SER cc_start: 0.8723 (t) cc_final: 0.8518 (m) REVERT: A 225 LYS cc_start: 0.7922 (mttt) cc_final: 0.7294 (tttm) REVERT: A 1059 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6723 (mtt) REVERT: H 69 MET cc_start: 0.8814 (mtt) cc_final: 0.8575 (mtm) REVERT: H 81 LYS cc_start: 0.6161 (mmtt) cc_final: 0.5713 (mppt) REVERT: L 74 LYS cc_start: 0.6792 (mttt) cc_final: 0.5793 (mtmp) REVERT: C 91 GLU cc_start: 0.7787 (tt0) cc_final: 0.7542 (tt0) REVERT: I 65 SER cc_start: 0.7614 (t) cc_final: 0.7025 (p) REVERT: I 74 LYS cc_start: 0.6735 (mttt) cc_final: 0.5650 (mtmm) REVERT: I 79 GLU cc_start: 0.6583 (mp0) cc_final: 0.6330 (mp0) REVERT: E 1077 MET cc_start: 0.7657 (mtm) cc_final: 0.7415 (mtp) REVERT: K 65 SER cc_start: 0.7425 (t) cc_final: 0.6946 (p) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.6417 time to fit residues: 224.1975 Evaluate side-chains 192 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 GLN L 53 ASN C 61 GLN C 278 ASN C 292 GLN C1129 ASN I 53 ASN E 61 GLN E 278 ASN E 292 GLN E1117 ASN E1129 ASN J 56 ASN K 53 ASN K 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.184966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135957 restraints weight = 17649.620| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.78 r_work: 0.3227 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18318 Z= 0.133 Angle : 0.640 15.919 24958 Z= 0.316 Chirality : 0.047 0.670 2822 Planarity : 0.005 0.059 3142 Dihedral : 8.465 78.936 3381 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.68 % Allowed : 7.72 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2163 helix: 2.28 (0.27), residues: 366 sheet: 1.24 (0.20), residues: 630 loop : -1.26 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 46 TYR 0.016 0.001 TYR H 52 PHE 0.011 0.001 PHE G 33 TRP 0.010 0.001 TRP L 94 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00289 (18242) covalent geometry : angle 0.58083 (24757) SS BOND : bond 0.00420 ( 27) SS BOND : angle 1.53395 ( 54) hydrogen bonds : bond 0.05815 ( 653) hydrogen bonds : angle 5.25598 ( 1857) link_ALPHA1-2 : bond 0.00514 ( 3) link_ALPHA1-2 : angle 2.21591 ( 9) link_ALPHA1-3 : bond 0.01464 ( 3) link_ALPHA1-3 : angle 1.98801 ( 9) link_ALPHA1-6 : bond 0.00737 ( 6) link_ALPHA1-6 : angle 1.79977 ( 18) link_BETA1-4 : bond 0.00734 ( 12) link_BETA1-4 : angle 1.40054 ( 36) link_NAG-ASN : bond 0.00653 ( 25) link_NAG-ASN : angle 4.52087 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7743 (mttt) REVERT: A 57 LYS cc_start: 0.6975 (mttt) cc_final: 0.6530 (mmpt) REVERT: A 92 THR cc_start: 0.8607 (m) cc_final: 0.8382 (m) REVERT: A 119 SER cc_start: 0.8424 (m) cc_final: 0.8211 (m) REVERT: A 225 LYS cc_start: 0.7773 (mttt) cc_final: 0.6891 (tttm) REVERT: A 311 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 1082 LYS cc_start: 0.8255 (mttp) cc_final: 0.7178 (mmtt) REVERT: L 74 LYS cc_start: 0.7762 (mttt) cc_final: 0.6559 (mtmp) REVERT: C 53 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7374 (mtp-110) REVERT: C 122 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 195 GLU cc_start: 0.6581 (mp0) cc_final: 0.6192 (mp0) REVERT: C 196 ASP cc_start: 0.7248 (t0) cc_final: 0.6871 (m-30) REVERT: C 1018 MET cc_start: 0.8539 (mtm) cc_final: 0.7829 (mmp) REVERT: C 1138 PHE cc_start: 0.8067 (m-80) cc_final: 0.7806 (m-80) REVERT: C 1165 GLU cc_start: 0.6085 (tm-30) cc_final: 0.5753 (tm-30) REVERT: G 81 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6857 (mmmt) REVERT: I 61 ARG cc_start: 0.6570 (ptt-90) cc_final: 0.6190 (ptt-90) REVERT: I 65 SER cc_start: 0.8049 (t) cc_final: 0.7694 (p) REVERT: I 74 LYS cc_start: 0.7716 (mttt) cc_final: 0.6443 (mtmm) REVERT: E 57 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7423 (mtpp) REVERT: E 122 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8269 (mt-10) REVERT: E 252 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: E 311 GLU cc_start: 0.7241 (tt0) cc_final: 0.6434 (mp0) REVERT: K 65 SER cc_start: 0.7857 (t) cc_final: 0.7497 (p) outliers start: 32 outliers final: 11 residues processed: 222 average time/residue: 0.5709 time to fit residues: 141.7744 Evaluate side-chains 192 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 71 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 104 optimal weight: 0.0970 chunk 128 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 214 ASN A1025 HIS A1125 GLN H 60 ASN C 61 GLN C 278 ASN E1129 ASN K 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.184840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135804 restraints weight = 17844.722| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.15 r_work: 0.3227 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18318 Z= 0.107 Angle : 0.569 15.392 24958 Z= 0.279 Chirality : 0.044 0.569 2822 Planarity : 0.004 0.050 3142 Dihedral : 7.279 70.836 3378 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.05 % Allowed : 9.82 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2163 helix: 2.90 (0.27), residues: 366 sheet: 1.39 (0.20), residues: 615 loop : -1.18 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 84 TYR 0.014 0.001 TYR G 52 PHE 0.012 0.001 PHE G 33 TRP 0.008 0.001 TRP A1092 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00226 (18242) covalent geometry : angle 0.52086 (24757) SS BOND : bond 0.00437 ( 27) SS BOND : angle 1.29454 ( 54) hydrogen bonds : bond 0.05086 ( 653) hydrogen bonds : angle 4.67631 ( 1857) link_ALPHA1-2 : bond 0.00625 ( 3) link_ALPHA1-2 : angle 1.70103 ( 9) link_ALPHA1-3 : bond 0.01224 ( 3) link_ALPHA1-3 : angle 1.65305 ( 9) link_ALPHA1-6 : bond 0.00683 ( 6) link_ALPHA1-6 : angle 1.83410 ( 18) link_BETA1-4 : bond 0.00720 ( 12) link_BETA1-4 : angle 1.24497 ( 36) link_NAG-ASN : bond 0.00619 ( 25) link_NAG-ASN : angle 3.84863 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7731 (mttp) REVERT: A 57 LYS cc_start: 0.6991 (mttt) cc_final: 0.6475 (mmpt) REVERT: A 119 SER cc_start: 0.8416 (m) cc_final: 0.8198 (m) REVERT: A 196 ASP cc_start: 0.7356 (t0) cc_final: 0.6761 (m-30) REVERT: A 225 LYS cc_start: 0.7727 (mttt) cc_final: 0.6825 (tttm) REVERT: L 74 LYS cc_start: 0.7705 (mttt) cc_final: 0.6494 (mtmp) REVERT: C 122 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7871 (mt-10) REVERT: C 139 ARG cc_start: 0.7332 (ptt90) cc_final: 0.6889 (mpp-170) REVERT: C 195 GLU cc_start: 0.6729 (mp0) cc_final: 0.6296 (mp0) REVERT: C 196 ASP cc_start: 0.7495 (t0) cc_final: 0.6966 (m-30) REVERT: C 1150 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6352 (mm-30) REVERT: C 1165 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5627 (tm-30) REVERT: G 81 LYS cc_start: 0.6928 (mmtt) cc_final: 0.6528 (mmmt) REVERT: I 61 ARG cc_start: 0.6400 (ptt-90) cc_final: 0.6199 (ptt-90) REVERT: I 65 SER cc_start: 0.8325 (t) cc_final: 0.7885 (p) REVERT: I 74 LYS cc_start: 0.7680 (mttt) cc_final: 0.6291 (mtmm) REVERT: I 89 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7654 (ppp) REVERT: E 48 ASN cc_start: 0.7465 (m-40) cc_final: 0.7245 (m110) REVERT: E 122 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8336 (mt-10) REVERT: E 202 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7888 (mmm160) REVERT: E 252 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: E 317 ARG cc_start: 0.8786 (ptp-170) cc_final: 0.8566 (ptp90) REVERT: K 65 SER cc_start: 0.8033 (t) cc_final: 0.7642 (p) outliers start: 39 outliers final: 14 residues processed: 214 average time/residue: 0.5622 time to fit residues: 133.8889 Evaluate side-chains 190 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 1125 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1057 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 61 GLN C 278 ASN C1026 HIS C1125 GLN C1129 ASN E 189 HIS E1125 GLN K 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131018 restraints weight = 17870.244| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.78 r_work: 0.3194 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18318 Z= 0.133 Angle : 0.606 15.359 24958 Z= 0.296 Chirality : 0.046 0.594 2822 Planarity : 0.004 0.046 3142 Dihedral : 6.792 65.134 3378 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.73 % Allowed : 11.18 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2163 helix: 2.89 (0.27), residues: 366 sheet: 1.37 (0.20), residues: 618 loop : -1.15 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 139 TYR 0.016 0.001 TYR G 52 PHE 0.011 0.001 PHE H 33 TRP 0.011 0.001 TRP I 94 HIS 0.004 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00307 (18242) covalent geometry : angle 0.56150 (24757) SS BOND : bond 0.00772 ( 27) SS BOND : angle 1.50140 ( 54) hydrogen bonds : bond 0.05382 ( 653) hydrogen bonds : angle 4.64973 ( 1857) link_ALPHA1-2 : bond 0.00615 ( 3) link_ALPHA1-2 : angle 1.67711 ( 9) link_ALPHA1-3 : bond 0.01193 ( 3) link_ALPHA1-3 : angle 1.92644 ( 9) link_ALPHA1-6 : bond 0.00680 ( 6) link_ALPHA1-6 : angle 1.78082 ( 18) link_BETA1-4 : bond 0.00673 ( 12) link_BETA1-4 : angle 1.26202 ( 36) link_NAG-ASN : bond 0.00523 ( 25) link_NAG-ASN : angle 3.76431 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7652 (mttp) REVERT: A 57 LYS cc_start: 0.6969 (mttt) cc_final: 0.6446 (mmpt) REVERT: A 196 ASP cc_start: 0.7633 (t0) cc_final: 0.6974 (m-30) REVERT: A 225 LYS cc_start: 0.7816 (mttt) cc_final: 0.6878 (tttm) REVERT: A 1059 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6462 (mtt) REVERT: L 74 LYS cc_start: 0.7706 (mttt) cc_final: 0.6468 (mtmp) REVERT: C 122 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 195 GLU cc_start: 0.6649 (mp0) cc_final: 0.6313 (mp0) REVERT: C 196 ASP cc_start: 0.7502 (t0) cc_final: 0.6915 (m-30) REVERT: C 317 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8051 (ptp-170) REVERT: C 1072 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7788 (pttt) REVERT: C 1101 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 1150 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6351 (mm-30) REVERT: C 1165 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5748 (tm-30) REVERT: G 46 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: G 81 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6419 (mmmt) REVERT: I 65 SER cc_start: 0.8389 (t) cc_final: 0.8040 (p) REVERT: I 89 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7615 (ppp) REVERT: E 202 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7914 (mmm160) REVERT: E 252 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: E 317 ARG cc_start: 0.8786 (ptp-170) cc_final: 0.8585 (ptp90) REVERT: K 65 SER cc_start: 0.8232 (t) cc_final: 0.7850 (p) outliers start: 52 outliers final: 26 residues processed: 219 average time/residue: 0.5496 time to fit residues: 134.4457 Evaluate side-chains 215 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1125 GLN Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1057 GLU Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 214 ASN C 278 ASN C 289 GLN ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E1125 GLN E1128 ASN K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128233 restraints weight = 17820.997| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.73 r_work: 0.3169 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18318 Z= 0.158 Angle : 0.635 16.389 24958 Z= 0.312 Chirality : 0.047 0.615 2822 Planarity : 0.004 0.045 3142 Dihedral : 6.612 61.310 3378 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.62 % Allowed : 12.65 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), residues: 2163 helix: 2.74 (0.27), residues: 366 sheet: 1.45 (0.20), residues: 573 loop : -1.17 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 112 TYR 0.017 0.002 TYR G 52 PHE 0.016 0.002 PHE A1138 TRP 0.014 0.001 TRP L 94 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00379 (18242) covalent geometry : angle 0.58945 (24757) SS BOND : bond 0.00660 ( 27) SS BOND : angle 1.65689 ( 54) hydrogen bonds : bond 0.05739 ( 653) hydrogen bonds : angle 4.71154 ( 1857) link_ALPHA1-2 : bond 0.00606 ( 3) link_ALPHA1-2 : angle 1.60788 ( 9) link_ALPHA1-3 : bond 0.01183 ( 3) link_ALPHA1-3 : angle 1.83977 ( 9) link_ALPHA1-6 : bond 0.00682 ( 6) link_ALPHA1-6 : angle 1.76426 ( 18) link_BETA1-4 : bond 0.00693 ( 12) link_BETA1-4 : angle 1.29376 ( 36) link_NAG-ASN : bond 0.00465 ( 25) link_NAG-ASN : angle 3.89813 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7654 (mttp) REVERT: A 57 LYS cc_start: 0.7037 (mttt) cc_final: 0.6486 (mmpt) REVERT: A 196 ASP cc_start: 0.7680 (t0) cc_final: 0.7023 (m-30) REVERT: A 225 LYS cc_start: 0.8059 (mttt) cc_final: 0.7150 (tttm) REVERT: A 1032 SER cc_start: 0.8254 (p) cc_final: 0.8014 (t) REVERT: A 1059 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6526 (mtt) REVERT: L 65 SER cc_start: 0.8556 (t) cc_final: 0.8098 (p) REVERT: L 74 LYS cc_start: 0.7708 (mttt) cc_final: 0.6442 (mtmp) REVERT: C 122 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 195 GLU cc_start: 0.6544 (mp0) cc_final: 0.6163 (mp0) REVERT: C 196 ASP cc_start: 0.7208 (t0) cc_final: 0.6599 (m-30) REVERT: C 1072 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7775 (pttt) REVERT: C 1101 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8340 (mp) REVERT: C 1165 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5740 (tm-30) REVERT: G 46 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: I 61 ARG cc_start: 0.6299 (ptt-90) cc_final: 0.6079 (ptt-90) REVERT: I 65 SER cc_start: 0.8498 (t) cc_final: 0.8168 (p) REVERT: I 89 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7602 (ppp) REVERT: E 202 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7944 (mmm160) REVERT: E 252 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: E 330 ILE cc_start: 0.7678 (mt) cc_final: 0.7374 (mm) REVERT: K 65 SER cc_start: 0.8312 (t) cc_final: 0.7941 (p) outliers start: 50 outliers final: 28 residues processed: 222 average time/residue: 0.5699 time to fit residues: 141.6939 Evaluate side-chains 221 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 60 optimal weight: 0.0030 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 292 GLN C 278 ASN ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1125 GLN K 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.179384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130265 restraints weight = 17815.894| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.87 r_work: 0.3165 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18318 Z= 0.123 Angle : 0.594 15.831 24958 Z= 0.290 Chirality : 0.045 0.588 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.328 57.150 3378 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.31 % Allowed : 13.86 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2163 helix: 2.91 (0.27), residues: 366 sheet: 1.21 (0.20), residues: 627 loop : -1.15 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 50 TYR 0.014 0.001 TYR A 17 PHE 0.015 0.001 PHE A1138 TRP 0.011 0.001 TRP I 94 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00278 (18242) covalent geometry : angle 0.54694 (24757) SS BOND : bond 0.00635 ( 27) SS BOND : angle 1.58550 ( 54) hydrogen bonds : bond 0.05263 ( 653) hydrogen bonds : angle 4.57144 ( 1857) link_ALPHA1-2 : bond 0.00674 ( 3) link_ALPHA1-2 : angle 1.56197 ( 9) link_ALPHA1-3 : bond 0.01138 ( 3) link_ALPHA1-3 : angle 1.82368 ( 9) link_ALPHA1-6 : bond 0.00715 ( 6) link_ALPHA1-6 : angle 1.75759 ( 18) link_BETA1-4 : bond 0.00640 ( 12) link_BETA1-4 : angle 1.23482 ( 36) link_NAG-ASN : bond 0.00490 ( 25) link_NAG-ASN : angle 3.81029 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7616 (mttp) REVERT: A 57 LYS cc_start: 0.7017 (mttt) cc_final: 0.6505 (mmpt) REVERT: A 196 ASP cc_start: 0.7659 (t0) cc_final: 0.7012 (m-30) REVERT: A 225 LYS cc_start: 0.7976 (mttt) cc_final: 0.7085 (tttm) REVERT: A 1032 SER cc_start: 0.8185 (p) cc_final: 0.7915 (t) REVERT: A 1059 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6652 (mtt) REVERT: L 65 SER cc_start: 0.8576 (t) cc_final: 0.8137 (p) REVERT: C 122 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 195 GLU cc_start: 0.6538 (mp0) cc_final: 0.6139 (mp0) REVERT: C 196 ASP cc_start: 0.7205 (t0) cc_final: 0.6639 (m-30) REVERT: C 1072 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7769 (pttt) REVERT: C 1101 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 1165 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5712 (tm-30) REVERT: G 46 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: I 61 ARG cc_start: 0.6241 (ptt-90) cc_final: 0.5939 (ptt-90) REVERT: I 65 SER cc_start: 0.8500 (t) cc_final: 0.8173 (p) REVERT: I 89 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7674 (ppp) REVERT: E 202 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7954 (mmm160) REVERT: E 252 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: E 330 ILE cc_start: 0.7681 (mt) cc_final: 0.7382 (mm) REVERT: E 1117 ASN cc_start: 0.7096 (m-40) cc_final: 0.6875 (m-40) REVERT: K 65 SER cc_start: 0.8333 (t) cc_final: 0.7958 (p) outliers start: 44 outliers final: 28 residues processed: 217 average time/residue: 0.5617 time to fit residues: 136.0797 Evaluate side-chains 221 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1032 SER Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 188 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 292 GLN C 278 ASN C1125 GLN E 232 GLN E1125 GLN K 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114786 restraints weight = 17809.036| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.55 r_work: 0.3069 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18318 Z= 0.181 Angle : 0.690 17.180 24958 Z= 0.338 Chirality : 0.048 0.644 2822 Planarity : 0.005 0.047 3142 Dihedral : 6.450 55.415 3378 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.99 % Allowed : 13.39 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2163 helix: 2.66 (0.27), residues: 366 sheet: 1.24 (0.21), residues: 567 loop : -1.18 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 317 TYR 0.017 0.002 TYR H 52 PHE 0.016 0.002 PHE A1138 TRP 0.016 0.002 TRP L 94 HIS 0.007 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00442 (18242) covalent geometry : angle 0.63862 (24757) SS BOND : bond 0.00629 ( 27) SS BOND : angle 2.61135 ( 54) hydrogen bonds : bond 0.06120 ( 653) hydrogen bonds : angle 4.79287 ( 1857) link_ALPHA1-2 : bond 0.00632 ( 3) link_ALPHA1-2 : angle 1.52260 ( 9) link_ALPHA1-3 : bond 0.01135 ( 3) link_ALPHA1-3 : angle 1.80901 ( 9) link_ALPHA1-6 : bond 0.00654 ( 6) link_ALPHA1-6 : angle 1.68607 ( 18) link_BETA1-4 : bond 0.00678 ( 12) link_BETA1-4 : angle 1.36262 ( 36) link_NAG-ASN : bond 0.00479 ( 25) link_NAG-ASN : angle 4.09324 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 189 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7375 (mttt) REVERT: A 57 LYS cc_start: 0.6891 (mttt) cc_final: 0.6380 (mmpt) REVERT: A 196 ASP cc_start: 0.7603 (t0) cc_final: 0.6868 (m-30) REVERT: A 225 LYS cc_start: 0.7956 (mttt) cc_final: 0.6958 (tttm) REVERT: A 311 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: A 1032 SER cc_start: 0.8110 (p) cc_final: 0.7817 (t) REVERT: A 1059 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6516 (mtt) REVERT: A 1101 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 1117 ASN cc_start: 0.7073 (m-40) cc_final: 0.6825 (m-40) REVERT: A 1150 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5711 (mp0) REVERT: L 65 SER cc_start: 0.8596 (t) cc_final: 0.8124 (p) REVERT: C 122 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 195 GLU cc_start: 0.6370 (mp0) cc_final: 0.5968 (mp0) REVERT: C 196 ASP cc_start: 0.7096 (t0) cc_final: 0.6865 (t0) REVERT: C 1101 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 1165 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5832 (tm-30) REVERT: G 46 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6736 (tp30) REVERT: I 65 SER cc_start: 0.8538 (t) cc_final: 0.8176 (p) REVERT: I 89 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7626 (ppp) REVERT: E 15 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7785 (mp) REVERT: E 200 LEU cc_start: 0.8014 (mt) cc_final: 0.7704 (tp) REVERT: E 202 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7850 (mmm160) REVERT: E 311 GLU cc_start: 0.7438 (tt0) cc_final: 0.7237 (pt0) REVERT: E 330 ILE cc_start: 0.7637 (mt) cc_final: 0.7316 (mm) REVERT: E 1075 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7888 (tttm) REVERT: E 1117 ASN cc_start: 0.6880 (m-40) cc_final: 0.6657 (m-40) REVERT: K 24 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6701 (ttt-90) REVERT: K 54 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7877 (ttp-110) REVERT: K 65 SER cc_start: 0.8406 (t) cc_final: 0.7995 (p) outliers start: 57 outliers final: 30 residues processed: 225 average time/residue: 0.5584 time to fit residues: 139.8550 Evaluate side-chains 223 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1032 SER Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 292 GLN C 278 ASN C1125 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.168181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113391 restraints weight = 17640.548| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.53 r_work: 0.3048 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18318 Z= 0.168 Angle : 0.677 17.337 24958 Z= 0.329 Chirality : 0.047 0.634 2822 Planarity : 0.004 0.048 3142 Dihedral : 6.382 59.516 3378 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.83 % Allowed : 14.07 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2163 helix: 2.69 (0.27), residues: 366 sheet: 1.04 (0.20), residues: 612 loop : -1.23 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 317 TYR 0.018 0.002 TYR A 17 PHE 0.017 0.002 PHE A1138 TRP 0.016 0.001 TRP L 94 HIS 0.005 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00407 (18242) covalent geometry : angle 0.62108 (24757) SS BOND : bond 0.00651 ( 27) SS BOND : angle 2.63287 ( 54) hydrogen bonds : bond 0.05927 ( 653) hydrogen bonds : angle 4.76273 ( 1857) link_ALPHA1-2 : bond 0.00640 ( 3) link_ALPHA1-2 : angle 1.48882 ( 9) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 1.73694 ( 9) link_ALPHA1-6 : bond 0.00685 ( 6) link_ALPHA1-6 : angle 1.68597 ( 18) link_BETA1-4 : bond 0.00651 ( 12) link_BETA1-4 : angle 1.31954 ( 36) link_NAG-ASN : bond 0.00521 ( 25) link_NAG-ASN : angle 4.26385 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7528 (mttp) REVERT: A 57 LYS cc_start: 0.6926 (mttt) cc_final: 0.6334 (mmpt) REVERT: A 196 ASP cc_start: 0.7691 (t0) cc_final: 0.6887 (m-30) REVERT: A 225 LYS cc_start: 0.7798 (mttt) cc_final: 0.6772 (tttm) REVERT: A 311 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 1032 SER cc_start: 0.8056 (p) cc_final: 0.7753 (t) REVERT: A 1059 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6640 (mtt) REVERT: A 1117 ASN cc_start: 0.7208 (m-40) cc_final: 0.6972 (m-40) REVERT: A 1150 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5700 (mp0) REVERT: L 65 SER cc_start: 0.8701 (t) cc_final: 0.8240 (p) REVERT: C 122 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 195 GLU cc_start: 0.6377 (mp0) cc_final: 0.6009 (mp0) REVERT: C 1072 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7768 (pttt) REVERT: C 1101 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 1165 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5781 (tm-30) REVERT: G 46 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: I 65 SER cc_start: 0.8650 (t) cc_final: 0.8276 (p) REVERT: I 89 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7667 (ppp) REVERT: E 15 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7784 (mp) REVERT: E 200 LEU cc_start: 0.8102 (mt) cc_final: 0.7736 (tp) REVERT: E 202 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7799 (mmm160) REVERT: E 330 ILE cc_start: 0.7677 (mt) cc_final: 0.7322 (mm) REVERT: E 1075 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7846 (tttm) REVERT: E 1117 ASN cc_start: 0.6942 (m-40) cc_final: 0.6714 (m-40) REVERT: K 24 ARG cc_start: 0.7386 (ttt180) cc_final: 0.6598 (ttt-90) REVERT: K 54 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7790 (ttp-110) REVERT: K 65 SER cc_start: 0.8532 (t) cc_final: 0.8137 (p) outliers start: 54 outliers final: 31 residues processed: 219 average time/residue: 0.5433 time to fit residues: 133.0915 Evaluate side-chains 223 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1125 GLN Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1032 SER Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C1125 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1129 ASN K 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122108 restraints weight = 17640.892| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.15 r_work: 0.3014 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18318 Z= 0.143 Angle : 0.648 16.994 24958 Z= 0.318 Chirality : 0.047 0.626 2822 Planarity : 0.004 0.048 3142 Dihedral : 6.227 55.486 3378 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.52 % Allowed : 14.44 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2163 helix: 2.74 (0.27), residues: 366 sheet: 1.05 (0.20), residues: 612 loop : -1.22 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 50 TYR 0.019 0.001 TYR C 17 PHE 0.016 0.002 PHE A1138 TRP 0.014 0.001 TRP L 94 HIS 0.004 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00334 (18242) covalent geometry : angle 0.59069 (24757) SS BOND : bond 0.00583 ( 27) SS BOND : angle 2.63987 ( 54) hydrogen bonds : bond 0.05665 ( 653) hydrogen bonds : angle 4.70538 ( 1857) link_ALPHA1-2 : bond 0.00642 ( 3) link_ALPHA1-2 : angle 1.48310 ( 9) link_ALPHA1-3 : bond 0.01094 ( 3) link_ALPHA1-3 : angle 1.72594 ( 9) link_ALPHA1-6 : bond 0.00696 ( 6) link_ALPHA1-6 : angle 1.68387 ( 18) link_BETA1-4 : bond 0.00630 ( 12) link_BETA1-4 : angle 1.29882 ( 36) link_NAG-ASN : bond 0.00534 ( 25) link_NAG-ASN : angle 4.18931 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7456 (mttp) REVERT: A 57 LYS cc_start: 0.6971 (mttt) cc_final: 0.6513 (mmpt) REVERT: A 196 ASP cc_start: 0.7707 (t0) cc_final: 0.6993 (m-30) REVERT: A 225 LYS cc_start: 0.7913 (mttt) cc_final: 0.6945 (tttm) REVERT: A 311 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 1032 SER cc_start: 0.8131 (p) cc_final: 0.7844 (t) REVERT: A 1059 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6749 (mtt) REVERT: A 1101 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 1150 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5780 (mp0) REVERT: L 65 SER cc_start: 0.8627 (t) cc_final: 0.8207 (p) REVERT: C 122 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 195 GLU cc_start: 0.6481 (mp0) cc_final: 0.6124 (mp0) REVERT: C 1072 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7755 (pttt) REVERT: C 1101 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 1165 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5899 (tm-30) REVERT: G 46 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: I 61 ARG cc_start: 0.6146 (mtp180) cc_final: 0.5822 (ptp-170) REVERT: I 65 SER cc_start: 0.8584 (t) cc_final: 0.8249 (p) REVERT: I 89 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7713 (ppp) REVERT: E 200 LEU cc_start: 0.8153 (mt) cc_final: 0.7828 (tp) REVERT: E 202 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7950 (mmm160) REVERT: E 330 ILE cc_start: 0.7795 (mt) cc_final: 0.7440 (mm) REVERT: E 1075 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7859 (tttt) REVERT: E 1117 ASN cc_start: 0.6967 (m-40) cc_final: 0.6732 (m-40) REVERT: K 24 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6781 (ttt-90) REVERT: K 54 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.7844 (ttp-110) REVERT: K 65 SER cc_start: 0.8473 (t) cc_final: 0.8109 (p) outliers start: 48 outliers final: 35 residues processed: 213 average time/residue: 0.5296 time to fit residues: 126.5725 Evaluate side-chains 227 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1125 GLN Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1032 SER Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 184 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 197 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 214 ASN A 292 GLN C 278 ASN C1125 GLN E1125 GLN E1129 ASN K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115807 restraints weight = 17502.435| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.52 r_work: 0.3081 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18318 Z= 0.121 Angle : 0.666 16.400 24958 Z= 0.324 Chirality : 0.046 0.600 2822 Planarity : 0.004 0.048 3142 Dihedral : 6.092 59.252 3378 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.26 % Allowed : 15.01 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2163 helix: 2.89 (0.27), residues: 366 sheet: 1.09 (0.20), residues: 612 loop : -1.17 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 139 TYR 0.017 0.001 TYR C 17 PHE 0.016 0.001 PHE A1138 TRP 0.011 0.001 TRP L 94 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00268 (18242) covalent geometry : angle 0.60157 (24757) SS BOND : bond 0.00546 ( 27) SS BOND : angle 3.71318 ( 54) hydrogen bonds : bond 0.05318 ( 653) hydrogen bonds : angle 4.62612 ( 1857) link_ALPHA1-2 : bond 0.00639 ( 3) link_ALPHA1-2 : angle 1.46777 ( 9) link_ALPHA1-3 : bond 0.01175 ( 3) link_ALPHA1-3 : angle 1.69534 ( 9) link_ALPHA1-6 : bond 0.00688 ( 6) link_ALPHA1-6 : angle 1.66329 ( 18) link_BETA1-4 : bond 0.00614 ( 12) link_BETA1-4 : angle 1.26548 ( 36) link_NAG-ASN : bond 0.00542 ( 25) link_NAG-ASN : angle 4.02004 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7448 (mttp) REVERT: A 57 LYS cc_start: 0.7005 (mttt) cc_final: 0.6303 (mmpt) REVERT: A 196 ASP cc_start: 0.7662 (t0) cc_final: 0.6917 (m-30) REVERT: A 225 LYS cc_start: 0.7726 (mttt) cc_final: 0.6710 (tttm) REVERT: A 1032 SER cc_start: 0.8037 (p) cc_final: 0.7737 (t) REVERT: A 1059 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6697 (mtt) REVERT: A 1150 GLU cc_start: 0.6343 (mm-30) cc_final: 0.5668 (mp0) REVERT: L 65 SER cc_start: 0.8706 (t) cc_final: 0.8238 (p) REVERT: C 122 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 175 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8268 (t) REVERT: C 195 GLU cc_start: 0.6419 (mp0) cc_final: 0.6043 (mp0) REVERT: C 196 ASP cc_start: 0.7517 (t0) cc_final: 0.7256 (t0) REVERT: C 1072 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: C 1101 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 1165 GLU cc_start: 0.6318 (tm-30) cc_final: 0.5809 (tm-30) REVERT: G 46 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: I 61 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5874 (ptp-170) REVERT: I 65 SER cc_start: 0.8625 (t) cc_final: 0.8251 (p) REVERT: I 89 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7742 (ppp) REVERT: E 200 LEU cc_start: 0.8045 (mt) cc_final: 0.7680 (tp) REVERT: E 202 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7794 (mmm160) REVERT: E 330 ILE cc_start: 0.7642 (mt) cc_final: 0.7287 (mm) REVERT: E 1117 ASN cc_start: 0.6916 (m-40) cc_final: 0.6710 (m-40) REVERT: K 24 ARG cc_start: 0.7365 (ttt180) cc_final: 0.6566 (ttt-90) REVERT: K 54 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7789 (ttp-110) REVERT: K 65 SER cc_start: 0.8512 (t) cc_final: 0.8118 (p) outliers start: 43 outliers final: 28 residues processed: 214 average time/residue: 0.5828 time to fit residues: 138.5786 Evaluate side-chains 211 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 1057 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1137 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 284 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1032 SER Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain E residue 1125 GLN Chi-restraints excluded: chain J residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1117 ASN C 278 ASN C1125 GLN C1129 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115379 restraints weight = 17632.927| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 18318 Z= 0.177 Angle : 0.835 59.200 24958 Z= 0.451 Chirality : 0.049 0.717 2822 Planarity : 0.004 0.049 3142 Dihedral : 6.109 59.301 3378 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 15.28 % Favored : 82.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2163 helix: 2.82 (0.27), residues: 366 sheet: 1.09 (0.20), residues: 612 loop : -1.17 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 50 TYR 0.017 0.001 TYR C 17 PHE 0.014 0.002 PHE A1138 TRP 0.011 0.001 TRP L 94 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00397 (18242) covalent geometry : angle 0.78283 (24757) SS BOND : bond 0.00467 ( 27) SS BOND : angle 4.00000 ( 54) hydrogen bonds : bond 0.05490 ( 653) hydrogen bonds : angle 4.63240 ( 1857) link_ALPHA1-2 : bond 0.00639 ( 3) link_ALPHA1-2 : angle 1.44784 ( 9) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.63872 ( 9) link_ALPHA1-6 : bond 0.00711 ( 6) link_ALPHA1-6 : angle 1.67704 ( 18) link_BETA1-4 : bond 0.00636 ( 12) link_BETA1-4 : angle 1.27136 ( 36) link_NAG-ASN : bond 0.00542 ( 25) link_NAG-ASN : angle 4.02976 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.01 seconds wall clock time: 90 minutes 21.84 seconds (5421.84 seconds total)