Starting phenix.real_space_refine on Mon May 19 03:03:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ved_43170/05_2025/8ved_43170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ved_43170/05_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_43170/05_2025/8ved_43170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ved_43170/05_2025/8ved_43170.map" model { file = "/net/cci-nas-00/data/ceres_data/8ved_43170/05_2025/8ved_43170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ved_43170/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.67, per 1000 atoms: 0.54 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: 4.34 Conformation dependent library (CDL) restraints added in 2.0 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: 2.29 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: 5.60 Time building geometry restraints manager: 5.08 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: 1.330 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.790 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.590 ------------------------------------------------------------------------------- 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 : 2.048 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: 1.2947 time to fit residues: 455.4168 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 : 1.862 ------------------------------------------------------------------------------- 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 = 0.133988 restraints weight = 17619.625| |-----------------------------------------------------------------------------| 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: 0.7717 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 78.219 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 0.00932 ( 25) link_NAG-ASN : angle 4.55768 ( 75) link_ALPHA1-6 : bond 0.00711 ( 6) link_ALPHA1-6 : angle 1.75873 ( 18) link_BETA1-4 : bond 0.00692 ( 12) link_BETA1-4 : angle 1.46575 ( 36) link_ALPHA1-2 : bond 0.00542 ( 3) link_ALPHA1-2 : angle 2.13762 ( 9) link_ALPHA1-3 : bond 0.01255 ( 3) link_ALPHA1-3 : angle 1.96543 ( 9) hydrogen bonds : bond 0.06067 ( 653) hydrogen bonds : angle 5.28028 ( 1857) SS BOND : bond 0.00889 ( 27) SS BOND : angle 1.59703 ( 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 : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7761 (mttt) REVERT: A 57 LYS cc_start: 0.7063 (mttt) cc_final: 0.6625 (mmpt) REVERT: A 92 THR cc_start: 0.8666 (m) cc_final: 0.8444 (m) REVERT: A 119 SER cc_start: 0.8455 (m) cc_final: 0.8253 (m) REVERT: A 225 LYS cc_start: 0.7815 (mttt) cc_final: 0.6916 (tttm) REVERT: A 311 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 1082 LYS cc_start: 0.8319 (mttp) cc_final: 0.7329 (mmtt) REVERT: L 65 SER cc_start: 0.8206 (t) cc_final: 0.7745 (p) REVERT: L 74 LYS cc_start: 0.7745 (mttt) cc_final: 0.6546 (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: 0.6474 (mp0) cc_final: 0.6100 (mp0) REVERT: C 196 ASP cc_start: 0.7282 (t0) cc_final: 0.6851 (m-30) REVERT: C 1138 PHE cc_start: 0.8062 (m-80) cc_final: 0.7795 (m-80) REVERT: C 1165 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5761 (tm-30) REVERT: G 81 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6787 (mmmt) REVERT: I 61 ARG cc_start: 0.6519 (ptt-90) cc_final: 0.6168 (ptt-90) REVERT: I 65 SER cc_start: 0.8135 (t) cc_final: 0.7789 (p) REVERT: I 74 LYS cc_start: 0.7720 (mttt) cc_final: 0.6388 (mtmm) REVERT: E 57 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (mtpp) REVERT: E 122 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8325 (mt-10) REVERT: E 252 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: K 65 SER cc_start: 0.7908 (t) cc_final: 0.7551 (p) outliers start: 39 outliers final: 15 residues processed: 223 average time/residue: 1.2317 time to fit residues: 308.8254 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 : 1.855 ------------------------------------------------------------------------------- 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: 0.0050 chunk 88 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- 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 E 189 HIS 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 = 0.4026 r_free = 0.4026 target = 0.182786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.133786 restraints weight = 17698.298| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.79 r_work: 0.3228 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18318 Z= 0.114 Angle : 0.582 15.942 24958 Z= 0.286 Chirality : 0.044 0.598 2822 Planarity : 0.004 0.050 3142 Dihedral : 7.435 71.731 3378 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.94 % Allowed : 9.97 % Favored : 88.08 % 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: 0.42 (0.17), residues: 2163 helix: 2.81 (0.27), residues: 366 sheet: 1.34 (0.20), residues: 615 loop : -1.22 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 94 HIS 0.003 0.001 HIS C 18 PHE 0.012 0.001 PHE G 33 TYR 0.014 0.001 TYR H 52 ARG 0.002 0.000 ARG E 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 25) link_NAG-ASN : angle 3.97632 ( 75) link_ALPHA1-6 : bond 0.00654 ( 6) link_ALPHA1-6 : angle 1.78409 ( 18) link_BETA1-4 : bond 0.00732 ( 12) link_BETA1-4 : angle 1.29560 ( 36) link_ALPHA1-2 : bond 0.00581 ( 3) link_ALPHA1-2 : angle 1.76359 ( 9) link_ALPHA1-3 : bond 0.01234 ( 3) link_ALPHA1-3 : angle 1.65476 ( 9) hydrogen bonds : bond 0.05281 ( 653) hydrogen bonds : angle 4.75612 ( 1857) SS BOND : bond 0.00458 ( 27) SS BOND : angle 1.28761 ( 54) covalent geometry : bond 0.00247 (18242) covalent geometry : angle 0.53150 (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 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.957 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: 0.8390 (OUTLIER) cc_final: 0.7766 (mttp) REVERT: A 57 LYS cc_start: 0.7028 (mttt) cc_final: 0.6562 (mmpt) REVERT: A 119 SER cc_start: 0.8494 (m) cc_final: 0.8290 (m) REVERT: A 196 ASP cc_start: 0.7384 (t0) cc_final: 0.6795 (m-30) REVERT: A 225 LYS cc_start: 0.7828 (mttt) cc_final: 0.6941 (tttm) REVERT: A 311 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: L 74 LYS cc_start: 0.7797 (mttt) cc_final: 0.6572 (mtmp) REVERT: C 122 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 139 ARG cc_start: 0.7307 (ptt90) cc_final: 0.6957 (mpp-170) REVERT: C 195 GLU cc_start: 0.6657 (mp0) cc_final: 0.6250 (mp0) REVERT: C 196 ASP cc_start: 0.7523 (t0) cc_final: 0.7059 (m-30) REVERT: C 1165 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5799 (tm-30) REVERT: I 61 ARG cc_start: 0.6564 (ptt-90) cc_final: 0.6283 (ptt-90) REVERT: I 65 SER cc_start: 0.8285 (t) cc_final: 0.7951 (p) REVERT: E 122 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8297 (mt-10) REVERT: E 202 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7953 (mmm160) REVERT: E 252 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: K 65 SER cc_start: 0.8093 (t) cc_final: 0.7747 (p) outliers start: 37 outliers final: 14 residues processed: 218 average time/residue: 1.2770 time to fit residues: 311.5470 Evaluate side-chains 198 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1125 GLN 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 1165 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1057 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR 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: 1.9990 chunk 176 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN C 61 GLN C 278 ASN C1026 HIS 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 = 0.4014 r_free = 0.4014 target = 0.181587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132351 restraints weight = 17694.915| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.80 r_work: 0.3216 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2162 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= 0.115 Angle : 0.582 15.573 24958 Z= 0.284 Chirality : 0.045 0.599 2822 Planarity : 0.004 0.046 3142 Dihedral : 6.857 65.883 3378 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.31 % Allowed : 11.50 % Favored : 86.19 % 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: 0.54 (0.17), residues: 2163 helix: 2.98 (0.27), residues: 366 sheet: 1.38 (0.20), residues: 615 loop : -1.15 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 94 HIS 0.003 0.001 HIS E 305 PHE 0.011 0.001 PHE G 33 TYR 0.014 0.001 TYR G 52 ARG 0.002 0.000 ARG G 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 25) link_NAG-ASN : angle 3.82416 ( 75) link_ALPHA1-6 : bond 0.00568 ( 6) link_ALPHA1-6 : angle 1.72591 ( 18) link_BETA1-4 : bond 0.00674 ( 12) link_BETA1-4 : angle 1.25071 ( 36) link_ALPHA1-2 : bond 0.00628 ( 3) link_ALPHA1-2 : angle 1.70259 ( 9) link_ALPHA1-3 : bond 0.01151 ( 3) link_ALPHA1-3 : angle 1.85244 ( 9) hydrogen bonds : bond 0.05139 ( 653) hydrogen bonds : angle 4.59897 ( 1857) SS BOND : bond 0.00447 ( 27) SS BOND : angle 1.41845 ( 54) covalent geometry : bond 0.00251 (18242) covalent geometry : angle 0.53515 (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 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.852 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: 0.8328 (OUTLIER) cc_final: 0.7712 (mttp) REVERT: A 54 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7072 (tp) REVERT: A 57 LYS cc_start: 0.7001 (mttt) cc_final: 0.6529 (mmpt) REVERT: A 196 ASP cc_start: 0.7641 (t0) cc_final: 0.7038 (m-30) REVERT: A 225 LYS cc_start: 0.7821 (mttt) cc_final: 0.6915 (tttm) REVERT: A 311 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 1059 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6574 (mtt) REVERT: L 74 LYS cc_start: 0.7767 (mttt) cc_final: 0.6541 (mtmp) REVERT: C 122 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 195 GLU cc_start: 0.6785 (mp0) cc_final: 0.6471 (mp0) REVERT: C 196 ASP cc_start: 0.7571 (t0) cc_final: 0.7019 (m-30) REVERT: C 317 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8017 (ptp-170) REVERT: C 1101 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 1165 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5886 (tm-30) REVERT: G 46 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6808 (tp30) REVERT: I 65 SER cc_start: 0.8338 (t) cc_final: 0.8007 (p) REVERT: I 89 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7639 (ppp) REVERT: E 139 ARG cc_start: 0.7360 (ptp-110) cc_final: 0.6867 (mpp80) REVERT: E 202 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7967 (mmm160) REVERT: E 252 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: K 65 SER cc_start: 0.8204 (t) cc_final: 0.7860 (p) outliers start: 44 outliers final: 24 residues processed: 215 average time/residue: 1.2633 time to fit residues: 304.2317 Evaluate side-chains 215 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 323 MET Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 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 89 MET Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 1057 GLU Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 176 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 214 ASN A 292 GLN C 278 ASN C 289 GLN ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E1125 GLN E1128 ASN K 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125945 restraints weight = 17964.507| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.82 r_work: 0.3115 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18318 Z= 0.242 Angle : 0.753 18.752 24958 Z= 0.370 Chirality : 0.051 0.711 2822 Planarity : 0.005 0.051 3142 Dihedral : 6.961 62.991 3378 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.25 % Allowed : 11.86 % Favored : 84.88 % 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: 0.12 (0.17), residues: 2163 helix: 2.33 (0.27), residues: 369 sheet: 1.28 (0.20), residues: 573 loop : -1.32 (0.15), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 94 HIS 0.009 0.002 HIS E 305 PHE 0.014 0.002 PHE A1138 TYR 0.021 0.002 TYR H 52 ARG 0.005 0.001 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 25) link_NAG-ASN : angle 4.31750 ( 75) link_ALPHA1-6 : bond 0.00660 ( 6) link_ALPHA1-6 : angle 1.74354 ( 18) link_BETA1-4 : bond 0.00803 ( 12) link_BETA1-4 : angle 1.51132 ( 36) link_ALPHA1-2 : bond 0.00632 ( 3) link_ALPHA1-2 : angle 1.63906 ( 9) link_ALPHA1-3 : bond 0.01154 ( 3) link_ALPHA1-3 : angle 1.82988 ( 9) hydrogen bonds : bond 0.06811 ( 653) hydrogen bonds : angle 5.02439 ( 1857) SS BOND : bond 0.01137 ( 27) SS BOND : angle 2.03096 ( 54) covalent geometry : bond 0.00602 (18242) covalent geometry : angle 0.70602 (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 255 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 1.904 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: 0.7683 (mttp) REVERT: A 57 LYS cc_start: 0.6973 (mttt) cc_final: 0.6413 (mmpt) REVERT: A 196 ASP cc_start: 0.7514 (t0) cc_final: 0.6814 (m-30) REVERT: A 225 LYS cc_start: 0.8002 (mttt) cc_final: 0.7065 (tttm) REVERT: A 311 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 1032 SER cc_start: 0.8215 (p) cc_final: 0.7942 (t) REVERT: A 1059 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6710 (mtt) REVERT: A 1101 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8319 (tp) REVERT: L 65 SER cc_start: 0.8611 (t) cc_final: 0.8177 (p) REVERT: C 122 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7823 (mt-10) REVERT: C 195 GLU cc_start: 0.6436 (mp0) cc_final: 0.6042 (mp0) REVERT: C 196 ASP cc_start: 0.7146 (t0) cc_final: 0.6933 (t0) REVERT: C 1072 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7821 (pttt) REVERT: C 1101 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8311 (mp) REVERT: C 1165 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5749 (tm-30) REVERT: G 46 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: G 50 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8426 (ptt-90) REVERT: I 61 ARG cc_start: 0.6296 (ptt-90) cc_final: 0.6063 (ptt-90) REVERT: I 65 SER cc_start: 0.8572 (t) cc_final: 0.8236 (p) REVERT: E 202 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7896 (mmm160) REVERT: E 330 ILE cc_start: 0.7612 (mt) cc_final: 0.7330 (mm) REVERT: E 1075 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7975 (tttt) REVERT: K 24 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6740 (ttt-90) REVERT: K 54 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7874 (ttp-110) REVERT: K 65 SER cc_start: 0.8471 (t) cc_final: 0.8092 (p) outliers start: 62 outliers final: 31 residues processed: 224 average time/residue: 1.2756 time to fit residues: 319.5582 Evaluate side-chains 222 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 A residue 1152 VAL 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 139 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 311 GLU 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 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 1032 SER Chi-restraints excluded: chain E residue 1057 GLU Chi-restraints excluded: chain E residue 1118 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain 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: 0.3980 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.177291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129957 restraints weight = 17889.490| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.34 r_work: 0.3175 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2736 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= 0.126 Angle : 0.615 16.980 24958 Z= 0.300 Chirality : 0.045 0.630 2822 Planarity : 0.004 0.048 3142 Dihedral : 6.510 57.959 3378 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.99 % Allowed : 13.91 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.17), residues: 2163 helix: 2.74 (0.27), residues: 366 sheet: 1.13 (0.20), residues: 621 loop : -1.24 (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 A 18 PHE 0.013 0.001 PHE A1138 TYR 0.015 0.001 TYR A 17 ARG 0.005 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 25) link_NAG-ASN : angle 4.24462 ( 75) link_ALPHA1-6 : bond 0.00698 ( 6) link_ALPHA1-6 : angle 1.75555 ( 18) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 1.29391 ( 36) link_ALPHA1-2 : bond 0.00610 ( 3) link_ALPHA1-2 : angle 1.58854 ( 9) link_ALPHA1-3 : bond 0.01165 ( 3) link_ALPHA1-3 : angle 1.84764 ( 9) hydrogen bonds : bond 0.05506 ( 653) hydrogen bonds : angle 4.69940 ( 1857) SS BOND : bond 0.00572 ( 27) SS BOND : angle 1.66341 ( 54) covalent geometry : bond 0.00284 (18242) covalent geometry : angle 0.55986 (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 227 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7707 (mttp) REVERT: A 57 LYS cc_start: 0.7070 (mttt) cc_final: 0.6638 (mmpt) REVERT: A 196 ASP cc_start: 0.7415 (t0) cc_final: 0.6803 (m-30) REVERT: A 225 LYS cc_start: 0.7996 (mttt) cc_final: 0.7129 (tttm) REVERT: A 311 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: A 1032 SER cc_start: 0.8236 (p) cc_final: 0.7979 (t) REVERT: A 1059 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6571 (mtt) REVERT: L 65 SER cc_start: 0.8575 (t) cc_final: 0.8162 (p) REVERT: C 122 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7763 (mt-10) REVERT: C 195 GLU cc_start: 0.6615 (mp0) cc_final: 0.6226 (mp0) REVERT: C 1072 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7784 (pttt) REVERT: C 1101 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 1165 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5865 (tm-30) REVERT: G 46 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: I 61 ARG cc_start: 0.6353 (ptt-90) cc_final: 0.6081 (ptt-90) REVERT: I 65 SER cc_start: 0.8484 (t) cc_final: 0.8188 (p) REVERT: E 202 ARG cc_start: 0.8298 (mmm160) cc_final: 0.8030 (mmm160) REVERT: E 330 ILE cc_start: 0.7614 (mt) cc_final: 0.7329 (mm) REVERT: E 1106 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.7018 (mtm-85) REVERT: K 24 ARG cc_start: 0.7316 (ttt180) cc_final: 0.6845 (ttt-90) REVERT: K 54 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7848 (ttp-110) REVERT: K 65 SER cc_start: 0.8375 (t) cc_final: 0.8035 (p) outliers start: 38 outliers final: 16 residues processed: 210 average time/residue: 1.3659 time to fit residues: 319.3025 Evaluate side-chains 201 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 C residue 139 ARG 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 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 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: 0.9980 chunk 102 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 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 = 0.3971 r_free = 0.3971 target = 0.176945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128909 restraints weight = 17883.616| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.66 r_work: 0.3172 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18318 Z= 0.135 Angle : 0.622 17.077 24958 Z= 0.303 Chirality : 0.046 0.631 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.289 54.907 3378 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.36 % Allowed : 14.28 % Favored : 83.36 % 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: 2.84 (0.27), residues: 366 sheet: 1.12 (0.20), residues: 621 loop : -1.23 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 94 HIS 0.004 0.001 HIS E 305 PHE 0.015 0.001 PHE A1138 TYR 0.015 0.001 TYR A 17 ARG 0.005 0.000 ARG C 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 25) link_NAG-ASN : angle 4.07950 ( 75) link_ALPHA1-6 : bond 0.00705 ( 6) link_ALPHA1-6 : angle 1.73167 ( 18) link_BETA1-4 : bond 0.00654 ( 12) link_BETA1-4 : angle 1.27069 ( 36) link_ALPHA1-2 : bond 0.00644 ( 3) link_ALPHA1-2 : angle 1.53682 ( 9) link_ALPHA1-3 : bond 0.01136 ( 3) link_ALPHA1-3 : angle 1.77944 ( 9) hydrogen bonds : bond 0.05496 ( 653) hydrogen bonds : angle 4.64367 ( 1857) SS BOND : bond 0.00556 ( 27) SS BOND : angle 1.70364 ( 54) covalent geometry : bond 0.00314 (18242) covalent geometry : angle 0.57159 (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 226 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.848 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: 0.8112 (OUTLIER) cc_final: 0.7440 (mttp) REVERT: A 57 LYS cc_start: 0.7085 (mttt) cc_final: 0.6529 (mmpt) REVERT: A 196 ASP cc_start: 0.7668 (t0) cc_final: 0.6994 (m-30) REVERT: A 225 LYS cc_start: 0.7975 (mttt) cc_final: 0.7070 (tttm) REVERT: A 311 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: A 1032 SER cc_start: 0.8148 (p) cc_final: 0.7880 (t) REVERT: A 1059 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6618 (mtt) REVERT: A 1117 ASN cc_start: 0.7232 (m-40) cc_final: 0.6950 (m-40) REVERT: L 65 SER cc_start: 0.8581 (t) cc_final: 0.8147 (p) REVERT: C 122 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C 195 GLU cc_start: 0.6446 (mp0) cc_final: 0.6043 (mp0) REVERT: C 196 ASP cc_start: 0.7223 (t0) cc_final: 0.6948 (t0) REVERT: C 1072 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7755 (pttt) REVERT: C 1101 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 1165 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5786 (tm-30) REVERT: G 46 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: I 61 ARG cc_start: 0.6197 (ptt-90) cc_final: 0.5922 (ptt-90) REVERT: I 65 SER cc_start: 0.8510 (t) cc_final: 0.8187 (p) REVERT: E 200 LEU cc_start: 0.8134 (mt) cc_final: 0.7881 (tp) REVERT: E 202 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7960 (mmm160) REVERT: E 311 GLU cc_start: 0.7586 (tt0) cc_final: 0.7367 (pt0) REVERT: E 330 ILE cc_start: 0.7700 (mt) cc_final: 0.7378 (mm) REVERT: E 1117 ASN cc_start: 0.7080 (m-40) cc_final: 0.6830 (m-40) REVERT: K 24 ARG cc_start: 0.7297 (ttt180) cc_final: 0.6838 (ttt-90) REVERT: K 65 SER cc_start: 0.8428 (t) cc_final: 0.8064 (p) outliers start: 45 outliers final: 24 residues processed: 209 average time/residue: 1.3519 time to fit residues: 315.2248 Evaluate side-chains 209 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain C residue 54 LEU 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 1125 GLN Chi-restraints excluded: chain C residue 1165 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 67 SER 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 1118 LEU 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: 5.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 278 ASN ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1129 ASN K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.165186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110068 restraints weight = 17773.385| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.56 r_work: 0.3002 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.006 0.045 18318 Z= 0.238 Angle : 0.744 19.020 24958 Z= 0.365 Chirality : 0.051 0.709 2822 Planarity : 0.005 0.047 3142 Dihedral : 6.535 57.128 3378 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.57 % Allowed : 14.70 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2163 helix: 2.34 (0.27), residues: 369 sheet: 0.99 (0.20), residues: 591 loop : -1.34 (0.15), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 94 HIS 0.008 0.002 HIS E 305 PHE 0.017 0.002 PHE A1138 TYR 0.018 0.002 TYR H 100F ARG 0.008 0.001 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 25) link_NAG-ASN : angle 4.36653 ( 75) link_ALPHA1-6 : bond 0.00683 ( 6) link_ALPHA1-6 : angle 1.68291 ( 18) link_BETA1-4 : bond 0.00702 ( 12) link_BETA1-4 : angle 1.45523 ( 36) link_ALPHA1-2 : bond 0.00672 ( 3) link_ALPHA1-2 : angle 1.51458 ( 9) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 1.79145 ( 9) hydrogen bonds : bond 0.06686 ( 653) hydrogen bonds : angle 4.97502 ( 1857) SS BOND : bond 0.00786 ( 27) SS BOND : angle 2.13048 ( 54) covalent geometry : bond 0.00593 (18242) covalent geometry : angle 0.69505 (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 236 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7564 (mttp) REVERT: A 57 LYS cc_start: 0.6849 (mttt) cc_final: 0.6213 (mmpt) REVERT: A 131 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6834 (ptm160) REVERT: A 196 ASP cc_start: 0.7510 (t0) cc_final: 0.7010 (t0) REVERT: A 225 LYS cc_start: 0.7758 (mttt) cc_final: 0.6709 (tttm) REVERT: A 311 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 1032 SER cc_start: 0.8075 (p) cc_final: 0.7762 (t) REVERT: A 1059 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6630 (mtt) REVERT: L 65 SER cc_start: 0.8737 (t) cc_final: 0.8277 (p) REVERT: C 122 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 195 GLU cc_start: 0.6464 (mp0) cc_final: 0.6115 (mp0) REVERT: C 1072 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7783 (pttt) REVERT: C 1101 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8241 (mp) REVERT: C 1165 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: G 46 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: G 50 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8542 (ptt-90) REVERT: I 61 ARG cc_start: 0.6299 (ptt-90) cc_final: 0.5848 (ptt-90) REVERT: I 65 SER cc_start: 0.8667 (t) cc_final: 0.8316 (p) REVERT: E 15 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7881 (mp) REVERT: E 175 VAL cc_start: 0.8360 (p) cc_final: 0.7998 (t) REVERT: E 200 LEU cc_start: 0.8160 (mt) cc_final: 0.7872 (tp) REVERT: E 202 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7751 (mmm160) REVERT: E 311 GLU cc_start: 0.7650 (tt0) cc_final: 0.7445 (pt0) REVERT: E 330 ILE cc_start: 0.7625 (mt) cc_final: 0.7277 (mm) REVERT: K 24 ARG cc_start: 0.7348 (ttt180) cc_final: 0.6576 (ttt-90) REVERT: K 54 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7798 (ttp-110) REVERT: K 65 SER cc_start: 0.8693 (t) cc_final: 0.8223 (p) outliers start: 49 outliers final: 26 residues processed: 217 average time/residue: 1.2735 time to fit residues: 311.7045 Evaluate side-chains 219 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 1059 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 1018 MET Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 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 15 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 298 SER 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: 0.5980 chunk 211 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 H 77 GLN C 164 ASN C 278 ASN C1125 GLN ** E1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.177159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130675 restraints weight = 17823.099| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.16 r_work: 0.3168 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3058 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= 0.142 Angle : 0.650 17.698 24958 Z= 0.317 Chirality : 0.046 0.649 2822 Planarity : 0.004 0.049 3142 Dihedral : 6.257 52.854 3378 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.31 % Allowed : 15.38 % Favored : 82.31 % 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: 0.19 (0.17), residues: 2163 helix: 2.72 (0.27), residues: 366 sheet: 0.99 (0.20), residues: 621 loop : -1.29 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 94 HIS 0.004 0.001 HIS E 305 PHE 0.015 0.002 PHE A1138 TYR 0.019 0.001 TYR C 17 ARG 0.004 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 25) link_NAG-ASN : angle 4.26497 ( 75) link_ALPHA1-6 : bond 0.00701 ( 6) link_ALPHA1-6 : angle 1.69593 ( 18) link_BETA1-4 : bond 0.00640 ( 12) link_BETA1-4 : angle 1.32573 ( 36) link_ALPHA1-2 : bond 0.00637 ( 3) link_ALPHA1-2 : angle 1.48685 ( 9) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.73363 ( 9) hydrogen bonds : bond 0.05697 ( 653) hydrogen bonds : angle 4.73315 ( 1857) SS BOND : bond 0.00604 ( 27) SS BOND : angle 2.22033 ( 54) covalent geometry : bond 0.00332 (18242) covalent geometry : angle 0.59445 (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 227 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.900 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: 0.8254 (OUTLIER) cc_final: 0.7631 (mttt) REVERT: A 57 LYS cc_start: 0.7058 (mttt) cc_final: 0.6595 (mmpt) REVERT: A 131 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.6910 (ptm160) REVERT: A 196 ASP cc_start: 0.7432 (t0) cc_final: 0.6777 (m-30) REVERT: A 225 LYS cc_start: 0.7981 (mttt) cc_final: 0.7092 (tttm) REVERT: A 311 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 1032 SER cc_start: 0.8199 (p) cc_final: 0.7924 (t) REVERT: A 1059 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6678 (mtt) REVERT: L 65 SER cc_start: 0.8612 (t) cc_final: 0.8239 (p) REVERT: C 122 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7826 (mt-10) REVERT: C 195 GLU cc_start: 0.6644 (mp0) cc_final: 0.6311 (mp0) REVERT: C 1072 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7769 (pttt) REVERT: C 1101 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8446 (mp) REVERT: C 1165 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5924 (tm-30) REVERT: G 46 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: G 50 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8207 (ptt-90) REVERT: I 61 ARG cc_start: 0.6405 (ptt-90) cc_final: 0.6094 (ptt-90) REVERT: I 65 SER cc_start: 0.8486 (t) cc_final: 0.8210 (p) REVERT: E 175 VAL cc_start: 0.8348 (p) cc_final: 0.8009 (t) REVERT: E 200 LEU cc_start: 0.8230 (mt) cc_final: 0.7980 (tp) REVERT: E 202 ARG cc_start: 0.8317 (mmm160) cc_final: 0.8029 (mmm160) REVERT: E 330 ILE cc_start: 0.7818 (mt) cc_final: 0.7472 (mm) REVERT: E 1117 ASN cc_start: 0.7184 (m-40) cc_final: 0.6942 (m-40) REVERT: K 24 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6911 (ttt-90) REVERT: K 54 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.7906 (ttp-110) REVERT: K 65 SER cc_start: 0.8630 (t) cc_final: 0.8211 (p) outliers start: 44 outliers final: 25 residues processed: 209 average time/residue: 1.3329 time to fit residues: 311.0752 Evaluate side-chains 215 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 252 GLU 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 54 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 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 284 CYS Chi-restraints excluded: chain C residue 1024 TYR 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 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: 0.6980 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 80 optimal weight: 0.0570 chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.179262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132597 restraints weight = 17660.931| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.12 r_work: 0.3201 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18318 Z= 0.114 Angle : 0.635 16.598 24958 Z= 0.310 Chirality : 0.046 0.605 2822 Planarity : 0.004 0.049 3142 Dihedral : 6.039 58.582 3378 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.63 % Allowed : 16.12 % Favored : 82.26 % 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: 2.98 (0.27), residues: 366 sheet: 0.94 (0.20), residues: 636 loop : -1.18 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.004 0.001 HIS C 136 PHE 0.015 0.001 PHE A1138 TYR 0.018 0.001 TYR C 17 ARG 0.005 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 25) link_NAG-ASN : angle 3.99334 ( 75) link_ALPHA1-6 : bond 0.00693 ( 6) link_ALPHA1-6 : angle 1.67899 ( 18) link_BETA1-4 : bond 0.00618 ( 12) link_BETA1-4 : angle 1.26995 ( 36) link_ALPHA1-2 : bond 0.00636 ( 3) link_ALPHA1-2 : angle 1.46085 ( 9) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.67521 ( 9) hydrogen bonds : bond 0.05153 ( 653) hydrogen bonds : angle 4.56726 ( 1857) SS BOND : bond 0.00557 ( 27) SS BOND : angle 3.37287 ( 54) covalent geometry : bond 0.00247 (18242) covalent geometry : angle 0.57248 (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 212 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.884 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: 0.8175 (OUTLIER) cc_final: 0.7575 (mttp) REVERT: A 57 LYS cc_start: 0.7110 (mttt) cc_final: 0.6638 (mmpt) REVERT: A 196 ASP cc_start: 0.7680 (t0) cc_final: 0.7071 (m-30) REVERT: A 225 LYS cc_start: 0.7906 (mttt) cc_final: 0.7058 (tttm) REVERT: A 311 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 1032 SER cc_start: 0.8169 (p) cc_final: 0.7891 (t) REVERT: A 1059 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6586 (mtt) REVERT: A 1165 GLU cc_start: 0.6575 (tt0) cc_final: 0.6130 (tm-30) REVERT: L 65 SER cc_start: 0.8628 (t) cc_final: 0.8248 (p) REVERT: C 122 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7794 (mt-10) REVERT: C 175 VAL cc_start: 0.8659 (p) cc_final: 0.8307 (t) REVERT: C 195 GLU cc_start: 0.6625 (mp0) cc_final: 0.6274 (mp0) REVERT: C 196 ASP cc_start: 0.7421 (t0) cc_final: 0.7161 (t0) REVERT: C 1072 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7760 (pttt) REVERT: C 1101 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 1165 GLU cc_start: 0.6504 (tm-30) cc_final: 0.5991 (tm-30) REVERT: G 46 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: I 61 ARG cc_start: 0.6286 (ptt-90) cc_final: 0.6041 (ptt-90) REVERT: I 65 SER cc_start: 0.8438 (t) cc_final: 0.8157 (p) REVERT: E 200 LEU cc_start: 0.8149 (mt) cc_final: 0.7856 (tp) REVERT: E 202 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7997 (mmm160) REVERT: E 330 ILE cc_start: 0.7851 (mt) cc_final: 0.7506 (mm) REVERT: K 24 ARG cc_start: 0.7428 (ttt180) cc_final: 0.6880 (ttt-90) REVERT: K 54 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7861 (ttp-110) REVERT: K 65 SER cc_start: 0.8583 (t) cc_final: 0.8174 (p) outliers start: 31 outliers final: 17 residues processed: 203 average time/residue: 1.3103 time to fit residues: 297.7310 Evaluate side-chains 196 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 311 GLU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1118 LEU 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 275 ILE Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 1057 GLU Chi-restraints excluded: chain C residue 1072 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain E residue 267 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 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 83 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN C 278 ASN C1125 GLN C1129 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.177913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130621 restraints weight = 17823.050| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.68 r_work: 0.3169 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3151 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= 0.137 Angle : 0.670 16.815 24958 Z= 0.326 Chirality : 0.046 0.616 2822 Planarity : 0.004 0.047 3142 Dihedral : 6.030 58.072 3378 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.73 % Allowed : 15.96 % Favored : 82.31 % 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: 0.29 (0.17), residues: 2163 helix: 2.90 (0.27), residues: 366 sheet: 0.91 (0.20), residues: 642 loop : -1.21 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 94 HIS 0.004 0.001 HIS A 18 PHE 0.016 0.002 PHE A1138 TYR 0.017 0.001 TYR C 17 ARG 0.005 0.000 ARG E1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 25) link_NAG-ASN : angle 3.98986 ( 75) link_ALPHA1-6 : bond 0.00672 ( 6) link_ALPHA1-6 : angle 1.64196 ( 18) link_BETA1-4 : bond 0.00621 ( 12) link_BETA1-4 : angle 1.29766 ( 36) link_ALPHA1-2 : bond 0.00639 ( 3) link_ALPHA1-2 : angle 1.45596 ( 9) link_ALPHA1-3 : bond 0.01088 ( 3) link_ALPHA1-3 : angle 1.68465 ( 9) hydrogen bonds : bond 0.05513 ( 653) hydrogen bonds : angle 4.64030 ( 1857) SS BOND : bond 0.00548 ( 27) SS BOND : angle 3.46674 ( 54) covalent geometry : bond 0.00319 (18242) covalent geometry : angle 0.61024 (24757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10945.47 seconds wall clock time: 189 minutes 43.83 seconds (11383.83 seconds total)