Starting phenix.real_space_refine on Sun Jun 15 22:51:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ved_43170/06_2025/8ved_43170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ved_43170/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ved_43170/06_2025/8ved_43170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ved_43170/06_2025/8ved_43170.map" model { file = "/net/cci-nas-00/data/ceres_data/8ved_43170/06_2025/8ved_43170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ved_43170/06_2025/8ved_43170.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.47, per 1000 atoms: 0.59 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: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.38 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: 5.73 Time building geometry restraints manager: 5.35 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 1173 or resid 2001 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 40.600 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (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 TRP 0.016 0.002 TRP A 70 HIS 0.007 0.001 HIS C 18 PHE 0.019 0.002 PHE C 121 TYR 0.042 0.002 TYR K 49 ARG 0.011 0.001 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.01106 ( 25) link_NAG-ASN : angle 5.44749 ( 75) 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_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) hydrogen bonds : bond 0.16567 ( 653) hydrogen bonds : angle 7.43688 ( 1857) SS BOND : bond 0.00594 ( 27) SS BOND : angle 1.89115 ( 54) covalent geometry : bond 0.00612 (18242) covalent geometry : angle 1.00709 (24757) *********************** 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 : 2.088 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: 0.7295 (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: 0.8574 (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: 0.7024 (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: 1.3244 time to fit residues: 466.4017 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 : 1.906 ------------------------------------------------------------------------------- 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 182 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A1025 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133992 restraints weight = 17619.666| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.75 r_work: 0.3225 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18318 Z= 0.144 Angle : 0.653 16.119 24958 Z= 0.322 Chirality : 0.047 0.692 2822 Planarity : 0.005 0.060 3142 Dihedral : 8.490 78.218 3381 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.05 % Allowed : 7.19 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2163 helix: 2.24 (0.27), residues: 366 sheet: 1.19 (0.20), residues: 630 loop : -1.33 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.006 0.001 HIS C 18 PHE 0.012 0.002 PHE G 33 TYR 0.016 0.001 TYR H 52 ARG 0.004 0.001 ARG C1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00933 ( 25) link_NAG-ASN : angle 4.55757 ( 75) link_ALPHA1-6 : bond 0.00711 ( 6) link_ALPHA1-6 : angle 1.75876 ( 18) link_BETA1-4 : bond 0.00692 ( 12) link_BETA1-4 : angle 1.46571 ( 36) link_ALPHA1-2 : bond 0.00542 ( 3) link_ALPHA1-2 : angle 2.13758 ( 9) link_ALPHA1-3 : bond 0.01256 ( 3) link_ALPHA1-3 : angle 1.96572 ( 9) hydrogen bonds : bond 0.06067 ( 653) hydrogen bonds : angle 5.28027 ( 1857) SS BOND : bond 0.00890 ( 27) SS BOND : angle 1.59691 ( 54) covalent geometry : bond 0.00318 (18242) covalent geometry : angle 0.59464 (24757) *********************** 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 238 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7760 (mttt) REVERT: A 57 LYS cc_start: 0.7064 (mttt) cc_final: 0.6628 (mmpt) REVERT: A 92 THR cc_start: 0.8665 (m) cc_final: 0.8443 (m) REVERT: A 119 SER cc_start: 0.8454 (m) cc_final: 0.8252 (m) REVERT: A 225 LYS cc_start: 0.7816 (mttt) cc_final: 0.6916 (tttm) REVERT: A 311 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 1082 LYS cc_start: 0.8321 (mttp) cc_final: 0.7329 (mmtt) REVERT: L 65 SER cc_start: 0.8207 (t) cc_final: 0.7746 (p) REVERT: L 74 LYS cc_start: 0.7749 (mttt) cc_final: 0.6550 (mtmp) REVERT: C 53 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7443 (mtp-110) REVERT: C 122 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7909 (mt-10) REVERT: C 195 GLU cc_start: 0.6473 (mp0) cc_final: 0.6099 (mp0) REVERT: C 196 ASP cc_start: 0.7284 (t0) cc_final: 0.6852 (m-30) REVERT: C 1138 PHE cc_start: 0.8066 (m-80) cc_final: 0.7801 (m-80) REVERT: C 1165 GLU cc_start: 0.6070 (tm-30) cc_final: 0.5764 (tm-30) REVERT: G 81 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6797 (mmmt) REVERT: I 61 ARG cc_start: 0.6525 (ptt-90) cc_final: 0.6177 (ptt-90) REVERT: I 65 SER cc_start: 0.8138 (t) cc_final: 0.7792 (p) REVERT: I 74 LYS cc_start: 0.7726 (mttt) cc_final: 0.6395 (mtmm) REVERT: E 57 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7456 (mtpp) REVERT: E 122 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8324 (mt-10) REVERT: E 252 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: K 65 SER cc_start: 0.7907 (t) cc_final: 0.7552 (p) outliers start: 39 outliers final: 15 residues processed: 223 average time/residue: 1.2528 time to fit residues: 313.7852 Evaluate side-chains 198 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 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 323 MET Chi-restraints excluded: chain E residue 23 THR 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 Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 88 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A1125 GLN C 61 GLN C 278 ASN C 289 GLN C1026 HIS E 189 HIS E1128 ASN E1129 ASN K 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.178653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128801 restraints weight = 17746.325| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.76 r_work: 0.3185 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18318 Z= 0.154 Angle : 0.643 17.310 24958 Z= 0.316 Chirality : 0.047 0.656 2822 Planarity : 0.005 0.050 3142 Dihedral : 7.479 70.914 3378 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.73 % Allowed : 9.76 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2163 helix: 2.59 (0.27), residues: 366 sheet: 1.43 (0.20), residues: 564 loop : -1.28 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 94 HIS 0.005 0.001 HIS A 47 PHE 0.012 0.002 PHE G 33 TYR 0.018 0.002 TYR H 52 ARG 0.003 0.000 ARG C 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 25) link_NAG-ASN : angle 4.16075 ( 75) link_ALPHA1-6 : bond 0.00650 ( 6) link_ALPHA1-6 : angle 1.78398 ( 18) link_BETA1-4 : bond 0.00763 ( 12) link_BETA1-4 : angle 1.39113 ( 36) link_ALPHA1-2 : bond 0.00580 ( 3) link_ALPHA1-2 : angle 1.75011 ( 9) link_ALPHA1-3 : bond 0.01247 ( 3) link_ALPHA1-3 : angle 1.63997 ( 9) hydrogen bonds : bond 0.05963 ( 653) hydrogen bonds : angle 4.91036 ( 1857) SS BOND : bond 0.00437 ( 27) SS BOND : angle 1.48162 ( 54) covalent geometry : bond 0.00362 (18242) covalent geometry : angle 0.59331 (24757) *********************** 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 250 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 1.763 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: 0.8388 (OUTLIER) cc_final: 0.7691 (mttt) REVERT: A 57 LYS cc_start: 0.6972 (mttt) cc_final: 0.6449 (mmpt) REVERT: A 196 ASP cc_start: 0.7379 (t0) cc_final: 0.6723 (m-30) REVERT: A 225 LYS cc_start: 0.7909 (mttt) cc_final: 0.6987 (tttm) REVERT: A 311 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: L 74 LYS cc_start: 0.7706 (mttt) cc_final: 0.6453 (mtmp) REVERT: C 122 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 195 GLU cc_start: 0.6457 (mp0) cc_final: 0.6018 (mp0) REVERT: C 196 ASP cc_start: 0.7116 (t0) cc_final: 0.6595 (m-30) REVERT: C 1165 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5634 (tm-30) REVERT: G 46 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: I 65 SER cc_start: 0.8449 (t) cc_final: 0.8109 (p) REVERT: E 202 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7923 (mmm160) REVERT: E 252 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: K 65 SER cc_start: 0.8357 (t) cc_final: 0.8021 (p) outliers start: 52 outliers final: 24 residues processed: 228 average time/residue: 1.2421 time to fit residues: 318.1639 Evaluate side-chains 212 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 252 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1125 GLN 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 131 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 317 ARG 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 E residue 22 SER 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 J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 178 GLN A 214 ASN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN C 278 ASN C1125 GLN C1129 ASN 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 = 0.3997 r_free = 0.3997 target = 0.179809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130378 restraints weight = 17723.646| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.77 r_work: 0.3197 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2333 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= 0.116 Angle : 0.590 16.184 24958 Z= 0.288 Chirality : 0.045 0.617 2822 Planarity : 0.004 0.046 3142 Dihedral : 6.864 65.087 3378 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.26 % Allowed : 12.39 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2163 helix: 2.85 (0.27), residues: 366 sheet: 1.29 (0.20), residues: 618 loop : -1.20 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.003 0.001 HIS C 18 PHE 0.011 0.001 PHE H 33 TYR 0.013 0.001 TYR G 52 ARG 0.004 0.000 ARG G 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 25) link_NAG-ASN : angle 3.93040 ( 75) link_ALPHA1-6 : bond 0.00660 ( 6) link_ALPHA1-6 : angle 1.78338 ( 18) link_BETA1-4 : bond 0.00672 ( 12) link_BETA1-4 : angle 1.27175 ( 36) link_ALPHA1-2 : bond 0.00585 ( 3) link_ALPHA1-2 : angle 1.70250 ( 9) link_ALPHA1-3 : bond 0.01217 ( 3) link_ALPHA1-3 : angle 1.89535 ( 9) hydrogen bonds : bond 0.05300 ( 653) hydrogen bonds : angle 4.68710 ( 1857) SS BOND : bond 0.00574 ( 27) SS BOND : angle 1.41676 ( 54) covalent geometry : bond 0.00254 (18242) covalent geometry : angle 0.54128 (24757) *********************** 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 233 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 1.806 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: 0.8372 (OUTLIER) cc_final: 0.7715 (mttp) REVERT: A 57 LYS cc_start: 0.7044 (mttt) cc_final: 0.6500 (mmpt) REVERT: A 196 ASP cc_start: 0.7363 (t0) cc_final: 0.6722 (m-30) REVERT: A 225 LYS cc_start: 0.7874 (mttt) cc_final: 0.6903 (tttm) REVERT: A 311 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 1059 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6598 (mtt) REVERT: L 74 LYS cc_start: 0.7702 (mttt) cc_final: 0.6423 (mtmp) REVERT: C 122 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 195 GLU cc_start: 0.6585 (mp0) cc_final: 0.6162 (mp0) REVERT: C 196 ASP cc_start: 0.7282 (t0) cc_final: 0.6735 (m-30) REVERT: C 317 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7976 (ptp-170) REVERT: C 1101 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 1129 ASN cc_start: 0.6994 (m-40) cc_final: 0.6741 (m-40) REVERT: C 1165 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5797 (tm-30) REVERT: G 46 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6698 (tp30) REVERT: I 65 SER cc_start: 0.8433 (t) cc_final: 0.8110 (p) REVERT: E 202 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7935 (mmm160) REVERT: E 252 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: E 330 ILE cc_start: 0.7692 (mt) cc_final: 0.7366 (mm) REVERT: K 65 SER cc_start: 0.8250 (t) cc_final: 0.7889 (p) outliers start: 43 outliers final: 19 residues processed: 217 average time/residue: 1.2687 time to fit residues: 307.9694 Evaluate side-chains 208 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 282 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 223 ILE 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 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 50 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** E 214 ASN E1125 GLN K 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124505 restraints weight = 18042.135| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.72 r_work: 0.3130 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18318 Z= 0.216 Angle : 0.715 18.484 24958 Z= 0.351 Chirality : 0.050 0.696 2822 Planarity : 0.005 0.048 3142 Dihedral : 6.835 62.614 3378 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.10 % Allowed : 12.70 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2163 helix: 2.48 (0.27), residues: 366 sheet: 1.25 (0.20), residues: 573 loop : -1.30 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 94 HIS 0.008 0.002 HIS E 305 PHE 0.012 0.002 PHE A1110 TYR 0.020 0.002 TYR H 52 ARG 0.004 0.001 ARG G 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 25) link_NAG-ASN : angle 4.27890 ( 75) link_ALPHA1-6 : bond 0.00632 ( 6) link_ALPHA1-6 : angle 1.73564 ( 18) link_BETA1-4 : bond 0.00728 ( 12) link_BETA1-4 : angle 1.42385 ( 36) link_ALPHA1-2 : bond 0.00622 ( 3) link_ALPHA1-2 : angle 1.63927 ( 9) link_ALPHA1-3 : bond 0.01147 ( 3) link_ALPHA1-3 : angle 1.83228 ( 9) hydrogen bonds : bond 0.06489 ( 653) hydrogen bonds : angle 4.94165 ( 1857) SS BOND : bond 0.00738 ( 27) SS BOND : angle 1.89099 ( 54) covalent geometry : bond 0.00538 (18242) covalent geometry : angle 0.66666 (24757) *********************** 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 249 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 1.965 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: 0.8378 (OUTLIER) cc_final: 0.7730 (mttp) REVERT: A 57 LYS cc_start: 0.7039 (mttt) cc_final: 0.6566 (mmpt) REVERT: A 139 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6624 (mpp-170) REVERT: A 196 ASP cc_start: 0.7532 (t0) cc_final: 0.6821 (m-30) REVERT: A 225 LYS cc_start: 0.8037 (mttt) cc_final: 0.7107 (tttm) REVERT: A 311 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 1032 SER cc_start: 0.8215 (p) cc_final: 0.7942 (t) REVERT: A 1059 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6650 (mtt) REVERT: A 1101 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8359 (tp) REVERT: L 65 SER cc_start: 0.8606 (t) cc_final: 0.8170 (p) REVERT: C 122 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 195 GLU cc_start: 0.6482 (mp0) cc_final: 0.6089 (mp0) REVERT: C 1072 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7829 (pttt) REVERT: C 1101 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8364 (mp) REVERT: C 1129 ASN cc_start: 0.7316 (m-40) cc_final: 0.7016 (m-40) REVERT: C 1165 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5744 (tm-30) REVERT: G 46 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: I 65 SER cc_start: 0.8591 (t) cc_final: 0.8279 (p) REVERT: E 202 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7953 (mmm160) REVERT: E 330 ILE cc_start: 0.7657 (mt) cc_final: 0.7368 (mm) REVERT: E 1075 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7988 (tttt) REVERT: K 24 ARG cc_start: 0.7313 (ttt180) cc_final: 0.6779 (ttt-90) REVERT: K 54 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7848 (ttp-110) REVERT: K 65 SER cc_start: 0.8563 (t) cc_final: 0.8091 (p) outliers start: 59 outliers final: 31 residues processed: 225 average time/residue: 1.2513 time to fit residues: 316.7688 Evaluate side-chains 223 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 319 THR 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 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 275 ILE Chi-restraints excluded: chain C residue 323 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 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 20 SER 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 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 80 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 210 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129596 restraints weight = 17905.531| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.19 r_work: 0.3168 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2763 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= 0.124 Angle : 0.614 17.020 24958 Z= 0.298 Chirality : 0.045 0.630 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.444 57.643 3378 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.05 % Allowed : 14.49 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2163 helix: 2.79 (0.27), residues: 366 sheet: 1.10 (0.20), residues: 621 loop : -1.23 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 94 HIS 0.003 0.001 HIS C 18 PHE 0.013 0.001 PHE A1138 TYR 0.014 0.001 TYR A 17 ARG 0.005 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 25) link_NAG-ASN : angle 4.26799 ( 75) link_ALPHA1-6 : bond 0.00692 ( 6) link_ALPHA1-6 : angle 1.75068 ( 18) link_BETA1-4 : bond 0.00651 ( 12) link_BETA1-4 : angle 1.28126 ( 36) link_ALPHA1-2 : bond 0.00626 ( 3) link_ALPHA1-2 : angle 1.57912 ( 9) link_ALPHA1-3 : bond 0.01168 ( 3) link_ALPHA1-3 : angle 1.84879 ( 9) hydrogen bonds : bond 0.05430 ( 653) hydrogen bonds : angle 4.68229 ( 1857) SS BOND : bond 0.00488 ( 27) SS BOND : angle 1.67561 ( 54) covalent geometry : bond 0.00279 (18242) covalent geometry : angle 0.55820 (24757) *********************** 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 226 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7487 (mttp) REVERT: A 57 LYS cc_start: 0.7076 (mttt) cc_final: 0.6650 (mmpt) REVERT: A 196 ASP cc_start: 0.7424 (t0) cc_final: 0.6832 (m-30) REVERT: A 225 LYS cc_start: 0.8004 (mttt) cc_final: 0.7129 (tttm) REVERT: A 311 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 1032 SER cc_start: 0.8242 (p) cc_final: 0.7978 (t) REVERT: A 1059 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6668 (mtt) REVERT: L 65 SER cc_start: 0.8579 (t) cc_final: 0.8166 (p) REVERT: C 122 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 195 GLU cc_start: 0.6563 (mp0) cc_final: 0.6181 (mp0) REVERT: C 1072 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7796 (pttt) REVERT: C 1101 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8457 (mp) REVERT: C 1129 ASN cc_start: 0.7331 (m-40) cc_final: 0.7072 (m-40) REVERT: C 1165 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5875 (tm-30) REVERT: G 46 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: I 65 SER cc_start: 0.8496 (t) cc_final: 0.8209 (p) REVERT: E 202 ARG cc_start: 0.8300 (mmm160) cc_final: 0.8036 (mmm160) REVERT: E 311 GLU cc_start: 0.7680 (tt0) cc_final: 0.7461 (pt0) REVERT: E 330 ILE cc_start: 0.7677 (mt) cc_final: 0.7395 (mm) REVERT: E 1075 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7958 (tttt) REVERT: E 1106 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7066 (mtm-85) REVERT: K 54 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.7894 (ttp-110) REVERT: K 65 SER cc_start: 0.8379 (t) cc_final: 0.8050 (p) outliers start: 39 outliers final: 21 residues processed: 210 average time/residue: 1.3387 time to fit residues: 313.1806 Evaluate side-chains 207 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 THR 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 119 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 267 SER 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 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 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 1118 LEU Chi-restraints excluded: chain J residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.170758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116396 restraints weight = 17681.113| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.55 r_work: 0.3092 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2866 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= 0.135 Angle : 0.634 16.976 24958 Z= 0.309 Chirality : 0.046 0.632 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.270 54.836 3378 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.57 % Allowed : 14.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2163 helix: 2.86 (0.27), residues: 366 sheet: 1.10 (0.20), residues: 621 loop : -1.21 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 94 HIS 0.005 0.001 HIS A 18 PHE 0.015 0.001 PHE A1138 TYR 0.014 0.001 TYR H 52 ARG 0.004 0.000 ARG G 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 25) link_NAG-ASN : angle 4.06326 ( 75) link_ALPHA1-6 : bond 0.00682 ( 6) link_ALPHA1-6 : angle 1.72046 ( 18) link_BETA1-4 : bond 0.00661 ( 12) link_BETA1-4 : angle 1.27058 ( 36) link_ALPHA1-2 : bond 0.00649 ( 3) link_ALPHA1-2 : angle 1.54092 ( 9) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 1.79817 ( 9) hydrogen bonds : bond 0.05496 ( 653) hydrogen bonds : angle 4.64748 ( 1857) SS BOND : bond 0.00642 ( 27) SS BOND : angle 2.57457 ( 54) covalent geometry : bond 0.00312 (18242) covalent geometry : angle 0.57781 (24757) *********************** 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 229 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 2.009 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: 0.8092 (OUTLIER) cc_final: 0.7442 (mttp) REVERT: A 57 LYS cc_start: 0.6988 (mttt) cc_final: 0.6395 (mmpt) REVERT: A 196 ASP cc_start: 0.7287 (t0) cc_final: 0.6627 (m-30) REVERT: A 225 LYS cc_start: 0.7897 (mttt) cc_final: 0.6934 (tttm) REVERT: A 311 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: A 1032 SER cc_start: 0.8096 (p) cc_final: 0.7801 (t) REVERT: A 1059 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6597 (mtt) REVERT: A 1117 ASN cc_start: 0.6994 (m-40) cc_final: 0.6699 (m-40) REVERT: H 100 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7785 (m) REVERT: L 65 SER cc_start: 0.8584 (t) cc_final: 0.8108 (p) REVERT: C 122 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 195 GLU cc_start: 0.6345 (mp0) cc_final: 0.5944 (mp0) REVERT: C 196 ASP cc_start: 0.7222 (t0) cc_final: 0.6927 (t0) REVERT: C 1072 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7709 (pttt) REVERT: C 1101 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 1129 ASN cc_start: 0.7270 (m-40) cc_final: 0.6981 (m-40) REVERT: C 1165 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5869 (tm-30) REVERT: G 46 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6606 (tp30) REVERT: I 61 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5910 (ptp-170) REVERT: I 65 SER cc_start: 0.8505 (t) cc_final: 0.8133 (p) REVERT: E 202 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7850 (mmm160) REVERT: E 311 GLU cc_start: 0.7503 (tt0) cc_final: 0.7262 (pt0) REVERT: E 330 ILE cc_start: 0.7601 (mt) cc_final: 0.7276 (mm) REVERT: E 1075 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7738 (tttt) REVERT: E 1117 ASN cc_start: 0.6783 (m-40) cc_final: 0.6523 (m-40) REVERT: K 54 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7736 (ttp-110) REVERT: K 65 SER cc_start: 0.8392 (t) cc_final: 0.8003 (p) outliers start: 49 outliers final: 31 residues processed: 211 average time/residue: 1.3761 time to fit residues: 323.6920 Evaluate side-chains 213 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 319 THR 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 H residue 100 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 323 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 50 ARG Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 67 SER 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 E residue 1120 GLU Chi-restraints excluded: chain J residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 211 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126074 restraints weight = 17871.144| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.38 r_work: 0.3114 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18318 Z= 0.216 Angle : 0.733 18.781 24958 Z= 0.359 Chirality : 0.050 0.698 2822 Planarity : 0.005 0.047 3142 Dihedral : 6.456 57.595 3378 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 14.17 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2163 helix: 2.44 (0.27), residues: 369 sheet: 0.99 (0.20), residues: 576 loop : -1.27 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 94 HIS 0.007 0.002 HIS E 305 PHE 0.017 0.002 PHE A1138 TYR 0.023 0.002 TYR C 17 ARG 0.006 0.001 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 25) link_NAG-ASN : angle 4.30648 ( 75) link_ALPHA1-6 : bond 0.00681 ( 6) link_ALPHA1-6 : angle 1.69209 ( 18) link_BETA1-4 : bond 0.00692 ( 12) link_BETA1-4 : angle 1.41091 ( 36) link_ALPHA1-2 : bond 0.00672 ( 3) link_ALPHA1-2 : angle 1.51620 ( 9) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.81570 ( 9) hydrogen bonds : bond 0.06436 ( 653) hydrogen bonds : angle 4.91380 ( 1857) SS BOND : bond 0.00673 ( 27) SS BOND : angle 2.76688 ( 54) covalent geometry : bond 0.00537 (18242) covalent geometry : angle 0.67980 (24757) *********************** 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: 55 poor density : 184 time to evaluate : 1.909 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: 0.8291 (OUTLIER) cc_final: 0.7663 (mttp) REVERT: A 57 LYS cc_start: 0.6984 (mttt) cc_final: 0.6517 (mmpt) REVERT: A 131 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6950 (ptm160) REVERT: A 196 ASP cc_start: 0.7492 (t0) cc_final: 0.7004 (t0) REVERT: A 225 LYS cc_start: 0.8026 (mttt) cc_final: 0.7063 (tttm) REVERT: A 311 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 1032 SER cc_start: 0.8187 (p) cc_final: 0.7898 (t) REVERT: A 1059 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6593 (mtt) REVERT: A 1117 ASN cc_start: 0.7404 (m-40) cc_final: 0.7154 (m-40) REVERT: A 1150 GLU cc_start: 0.6474 (mm-30) cc_final: 0.5861 (mp0) REVERT: H 100 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8048 (m) REVERT: L 65 SER cc_start: 0.8690 (t) cc_final: 0.8297 (p) REVERT: C 122 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7887 (mt-10) REVERT: C 195 GLU cc_start: 0.6588 (mp0) cc_final: 0.6248 (mp0) REVERT: C 1072 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7786 (pttt) REVERT: C 1101 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8423 (mp) REVERT: C 1129 ASN cc_start: 0.7384 (m-40) cc_final: 0.7181 (m-40) REVERT: C 1165 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5887 (tm-30) REVERT: G 46 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6793 (tp30) REVERT: I 65 SER cc_start: 0.8553 (t) cc_final: 0.8270 (p) REVERT: E 175 VAL cc_start: 0.8407 (p) cc_final: 0.8024 (t) REVERT: E 202 ARG cc_start: 0.8322 (mmm160) cc_final: 0.8029 (mmm160) REVERT: E 311 GLU cc_start: 0.7796 (tt0) cc_final: 0.7586 (pt0) REVERT: E 330 ILE cc_start: 0.7864 (mt) cc_final: 0.7528 (mm) REVERT: E 1075 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7930 (tttt) REVERT: K 24 ARG cc_start: 0.7475 (ttt180) cc_final: 0.6858 (ttt-90) REVERT: K 54 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7934 (ttp-110) REVERT: K 65 SER cc_start: 0.8672 (t) cc_final: 0.8243 (p) outliers start: 55 outliers final: 30 residues processed: 220 average time/residue: 1.4636 time to fit residues: 361.9468 Evaluate side-chains 218 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 131 ARG 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 H residue 100 THR 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 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 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 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 20 SER Chi-restraints excluded: chain I residue 61 ARG 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 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 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 0.0270 chunk 78 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 H 77 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132540 restraints weight = 17779.948| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.16 r_work: 0.3194 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18318 Z= 0.117 Angle : 0.629 17.061 24958 Z= 0.307 Chirality : 0.046 0.625 2822 Planarity : 0.004 0.049 3142 Dihedral : 6.146 54.440 3378 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.26 % Allowed : 15.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2163 helix: 2.92 (0.27), residues: 366 sheet: 1.03 (0.20), residues: 612 loop : -1.18 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.003 0.001 HIS A 18 PHE 0.017 0.001 PHE A1138 TYR 0.017 0.001 TYR C 17 ARG 0.006 0.000 ARG E 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 25) link_NAG-ASN : angle 4.14124 ( 75) link_ALPHA1-6 : bond 0.00715 ( 6) link_ALPHA1-6 : angle 1.70520 ( 18) link_BETA1-4 : bond 0.00624 ( 12) link_BETA1-4 : angle 1.27862 ( 36) link_ALPHA1-2 : bond 0.00650 ( 3) link_ALPHA1-2 : angle 1.48247 ( 9) link_ALPHA1-3 : bond 0.01116 ( 3) link_ALPHA1-3 : angle 1.71835 ( 9) hydrogen bonds : bond 0.05272 ( 653) hydrogen bonds : angle 4.63308 ( 1857) SS BOND : bond 0.00536 ( 27) SS BOND : angle 2.84353 ( 54) covalent geometry : bond 0.00257 (18242) covalent geometry : angle 0.56850 (24757) *********************** 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 230 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.812 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: symmetry clash REVERT: A 32 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7541 (mttp) REVERT: A 57 LYS cc_start: 0.7066 (mttt) cc_final: 0.6583 (mmpt) REVERT: A 131 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.6907 (ptm160) REVERT: A 196 ASP cc_start: 0.7333 (t0) cc_final: 0.6713 (m-30) REVERT: A 225 LYS cc_start: 0.7949 (mttt) cc_final: 0.7063 (tttm) REVERT: A 311 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: A 1032 SER cc_start: 0.8162 (p) cc_final: 0.7882 (t) REVERT: A 1059 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6609 (mtt) REVERT: H 100 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7868 (m) REVERT: L 65 SER cc_start: 0.8600 (t) cc_final: 0.8189 (p) REVERT: C 122 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7755 (mt-10) REVERT: C 175 VAL cc_start: 0.8648 (p) cc_final: 0.8288 (t) REVERT: C 195 GLU cc_start: 0.6573 (mp0) cc_final: 0.6214 (mp0) REVERT: C 196 ASP cc_start: 0.7368 (t0) cc_final: 0.7094 (t0) REVERT: C 1072 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7735 (pttt) REVERT: C 1101 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8409 (mp) REVERT: C 1165 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5950 (tm-30) REVERT: G 46 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6718 (tp30) REVERT: I 65 SER cc_start: 0.8419 (t) cc_final: 0.8119 (p) REVERT: E 202 ARG cc_start: 0.8282 (mmm160) cc_final: 0.8026 (mmm160) REVERT: E 311 GLU cc_start: 0.7716 (tt0) cc_final: 0.7515 (pt0) REVERT: E 330 ILE cc_start: 0.7840 (mt) cc_final: 0.7496 (mm) REVERT: E 1075 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7822 (tttt) REVERT: E 1117 ASN cc_start: 0.7065 (m-40) cc_final: 0.6811 (m-40) REVERT: E 1149 MET cc_start: 0.5129 (mmt) cc_final: 0.4904 (mmt) REVERT: K 54 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7882 (ttp-110) REVERT: K 65 SER cc_start: 0.8593 (t) cc_final: 0.8141 (p) outliers start: 43 outliers final: 23 residues processed: 217 average time/residue: 1.3196 time to fit residues: 319.5398 Evaluate side-chains 213 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 131 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 311 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 H residue 100 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 223 ILE 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 215 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN H 77 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.176218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129258 restraints weight = 17724.262| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.13 r_work: 0.3162 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3129 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= 0.173 Angle : 0.727 17.970 24958 Z= 0.354 Chirality : 0.049 0.661 2822 Planarity : 0.005 0.047 3142 Dihedral : 6.263 56.594 3378 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.26 % Allowed : 15.59 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2163 helix: 2.77 (0.27), residues: 366 sheet: 0.89 (0.20), residues: 621 loop : -1.25 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 94 HIS 0.005 0.001 HIS A 18 PHE 0.017 0.002 PHE A1138 TYR 0.020 0.002 TYR C 17 ARG 0.004 0.000 ARG G 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 25) link_NAG-ASN : angle 4.21789 ( 75) link_ALPHA1-6 : bond 0.00680 ( 6) link_ALPHA1-6 : angle 1.67438 ( 18) link_BETA1-4 : bond 0.00649 ( 12) link_BETA1-4 : angle 1.33059 ( 36) link_ALPHA1-2 : bond 0.00667 ( 3) link_ALPHA1-2 : angle 1.47333 ( 9) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 1.71678 ( 9) hydrogen bonds : bond 0.05956 ( 653) hydrogen bonds : angle 4.76994 ( 1857) SS BOND : bond 0.00602 ( 27) SS BOND : angle 4.01370 ( 54) covalent geometry : bond 0.00418 (18242) covalent geometry : angle 0.66161 (24757) ********************** 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 224 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 2.030 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: 0.8232 (OUTLIER) cc_final: 0.7620 (mttp) REVERT: A 57 LYS cc_start: 0.6960 (mttt) cc_final: 0.6544 (mmpt) REVERT: A 131 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: A 196 ASP cc_start: 0.7409 (t0) cc_final: 0.6966 (t0) REVERT: A 225 LYS cc_start: 0.7939 (mttt) cc_final: 0.7039 (tttm) REVERT: A 311 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: A 1032 SER cc_start: 0.8172 (p) cc_final: 0.7884 (t) REVERT: A 1059 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6635 (mtt) REVERT: A 1101 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 1150 GLU cc_start: 0.6488 (mm-30) cc_final: 0.5812 (mp0) REVERT: H 100 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7921 (m) REVERT: L 65 SER cc_start: 0.8626 (t) cc_final: 0.8235 (p) REVERT: C 122 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 195 GLU cc_start: 0.6600 (mp0) cc_final: 0.6245 (mp0) REVERT: C 196 ASP cc_start: 0.7418 (t0) cc_final: 0.7127 (t0) REVERT: C 1072 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7774 (pttt) REVERT: C 1101 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 1165 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5924 (tm-30) REVERT: G 46 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6742 (tp30) REVERT: I 65 SER cc_start: 0.8480 (t) cc_final: 0.8200 (p) REVERT: E 175 VAL cc_start: 0.8373 (p) cc_final: 0.8019 (t) REVERT: E 202 ARG cc_start: 0.8317 (mmm160) cc_final: 0.8053 (mmm160) REVERT: E 330 ILE cc_start: 0.7881 (mt) cc_final: 0.7542 (mm) REVERT: E 1075 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7816 (tttt) REVERT: E 1117 ASN cc_start: 0.7070 (m-40) cc_final: 0.6819 (m-40) REVERT: K 54 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: K 65 SER cc_start: 0.8620 (t) cc_final: 0.8176 (p) outliers start: 43 outliers final: 29 residues processed: 209 average time/residue: 1.2779 time to fit residues: 299.6204 Evaluate side-chains 216 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 131 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 311 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 H residue 100 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 223 ILE Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 CYS 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 50 ARG Chi-restraints excluded: chain G residue 100 THR 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 275 ILE 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 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN C 278 ASN C1125 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129933 restraints weight = 17713.175| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.48 r_work: 0.3136 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18318 Z= 0.127 Angle : 0.693 18.338 24958 Z= 0.338 Chirality : 0.047 0.646 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.201 57.251 3378 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 16.01 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2163 helix: 2.85 (0.26), residues: 366 sheet: 1.02 (0.20), residues: 606 loop : -1.23 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 94 HIS 0.004 0.001 HIS E 305 PHE 0.017 0.001 PHE A1138 TYR 0.016 0.001 TYR C 17 ARG 0.005 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 25) link_NAG-ASN : angle 4.13776 ( 75) link_ALPHA1-6 : bond 0.00686 ( 6) link_ALPHA1-6 : angle 1.67823 ( 18) link_BETA1-4 : bond 0.00631 ( 12) link_BETA1-4 : angle 1.31231 ( 36) link_ALPHA1-2 : bond 0.00624 ( 3) link_ALPHA1-2 : angle 1.48250 ( 9) link_ALPHA1-3 : bond 0.01102 ( 3) link_ALPHA1-3 : angle 1.72326 ( 9) hydrogen bonds : bond 0.05550 ( 653) hydrogen bonds : angle 4.71682 ( 1857) SS BOND : bond 0.00643 ( 27) SS BOND : angle 4.04150 ( 54) covalent geometry : bond 0.00284 (18242) covalent geometry : angle 0.62424 (24757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11799.56 seconds wall clock time: 205 minutes 20.03 seconds (12320.03 seconds total)