Starting phenix.real_space_refine on Sun May 18 22:34:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.cif Found real_map, /net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.map" model { file = "/net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8veb_43169/05_2025/8veb_43169.cif" } resolution = 2.97 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= 0.075 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 87 5.16 5 C 10986 2.51 5 N 2985 2.21 5 O 3513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17571 Number of models: 1 Model: "" Number of chains: 18 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: "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: "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: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "J" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.23, per 1000 atoms: 0.58 Number of scatterers: 17571 At special positions: 0 Unit cell: (131.272, 133.424, 151.716, 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 87 16.00 O 3513 8.00 N 2985 7.00 C 10986 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=2.07 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.02 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=2.05 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=2.08 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.03 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=2.06 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=2.04 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=2.02 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=2.06 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 6 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A2001 " - " ASN A 97 " " NAG A2002 " - " ASN A 21 " " NAG A2003 " - " ASN A 33 " " NAG A2004 " - " ASN A1154 " " NAG C2001 " - " ASN C 97 " " NAG C2002 " - " ASN C 21 " " NAG C2003 " - " ASN C 33 " " NAG C2004 " - " ASN C1154 " " NAG E2001 " - " ASN E 97 " " NAG E2002 " - " ASN E 21 " " NAG E2003 " - " ASN E 33 " " NAG E2004 " - " ASN E1154 " " NAG M 1 " - " ASN A 83 " " NAG N 1 " - " ASN A 169 " " NAG O 1 " - " ASN C 83 " " NAG P 1 " - " ASN C 169 " " NAG Q 1 " - " ASN E 83 " " NAG R 1 " - " ASN E 169 " Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3990 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 47 sheets defined 18.2% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.583A pdb=" N GLN A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1059 removed outlier: 3.593A pdb=" N CYS A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1127 removed outlier: 3.588A pdb=" N LEU A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A1112 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1162 through 1173 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.248A 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 1037 through 1059 removed outlier: 3.556A pdb=" N ASN C1050 " --> pdb=" O ASN C1046 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET C1059 " --> pdb=" O VAL C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1127 removed outlier: 3.917A pdb=" N LEU C1089 " --> pdb=" O ASP C1085 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C1090 " --> pdb=" O ASP C1086 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C1112 " --> pdb=" O LEU C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1154 Processing helix chain 'C' and resid 1162 through 1173 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.552A pdb=" N GLN E 197 " --> pdb=" O ASN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1037 through 1059 removed outlier: 3.546A pdb=" N ASN E1050 " --> pdb=" O ASN E1046 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET E1059 " --> pdb=" O VAL E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1127 removed outlier: 3.554A pdb=" N LEU E1089 " --> pdb=" O ASP E1085 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP E1090 " --> pdb=" O ASP E1086 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP E1112 " --> pdb=" O LEU E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1145 through 1154 removed outlier: 3.554A pdb=" N ASN E1154 " --> pdb=" O GLU E1150 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1173 Processing helix chain 'G' and resid 61 through 64 removed outlier: 4.184A pdb=" N ARG G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR G 87 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.182A pdb=" N ARG H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'J' and resid 61 through 64 removed outlier: 4.143A pdb=" N ARG J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 1032 through 1036 removed outlier: 3.669A pdb=" N GLY A1023 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 4.074A 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 63 removed outlier: 6.055A pdb=" N ILE A 89 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.879A pdb=" N ARG A 84 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 267 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 121 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA A 265 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.688A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 142 through 146 removed outlier: 4.344A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.787A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 309 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1032 through 1036 removed outlier: 3.608A pdb=" N GLY C1023 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.087A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.474A pdb=" N LEU C 51 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 286 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.073A pdb=" N ILE C 89 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.959A pdb=" N ARG C 84 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 121 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER C 267 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 121 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA C 265 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG C 123 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 263 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.959A pdb=" N ARG C 84 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 121 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER C 267 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 121 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA C 265 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG C 123 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 263 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C 181 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 142 through 146 removed outlier: 4.310A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AC3, first strand: chain 'C' and resid 294 through 295 removed outlier: 3.791A pdb=" N CYS C 288 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 309 " --> pdb=" O GLN C 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1032 through 1036 removed outlier: 3.517A pdb=" N GLY E1033 " --> pdb=" O HIS E1026 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY E1023 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 24 through 27 removed outlier: 4.094A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.739A pdb=" N LEU E 51 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS E 284 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 53 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 286 " --> pdb=" O ARG E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.108A pdb=" N ILE E 89 " --> pdb=" O ILE E 275 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 118 through 120 removed outlier: 6.914A pdb=" N SER E 267 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 181 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU E 185 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.688A pdb=" N TYR E 262 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU E 185 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 181 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.382A pdb=" N CYS E 145 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 170 through 175 Processing sheet with id=AD5, first strand: chain 'E' and resid 294 through 295 removed outlier: 3.850A pdb=" N CYS E 288 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 309 " --> pdb=" O GLN E 289 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.813A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.310A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.813A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.310A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 88 " --> pdb=" O ALA G 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.297A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA H 93 " --> pdb=" O THR H 35B" (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.297A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA H 93 " --> pdb=" O THR H 35B" (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.521A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ILE I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N SER I 65 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.694A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN I 37 " --> pdb=" O CYS I 46 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N CYS I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.592A pdb=" N SER J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.592A pdb=" N SER J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP J 35A" --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.510A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR K 69 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N GLN K 27 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N SER K 67 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE K 29 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N SER K 65 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.861A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.529A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.791A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1905 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: 6.10 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 90 1.22 - 1.38: 6634 1.38 - 1.54: 10948 1.54 - 1.70: 181 1.70 - 1.86: 117 Bond restraints: 17970 Sorted by residual: bond pdb=" C GLU C1150 " pdb=" O GLU C1150 " ideal model delta sigma weight residual 1.236 1.066 0.170 1.28e-02 6.10e+03 1.77e+02 bond pdb=" C THR A 290 " pdb=" O THR A 290 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.30e-02 5.92e+03 4.00e+01 bond pdb=" C LYS C1123 " pdb=" O LYS C1123 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.16e-02 7.43e+03 2.89e+01 bond pdb=" CA SER G 54 " pdb=" CB SER G 54 " ideal model delta sigma weight residual 1.528 1.444 0.084 1.59e-02 3.96e+03 2.80e+01 bond pdb=" C LYS A1123 " pdb=" O LYS A1123 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.16e-02 7.43e+03 2.73e+01 ... (remaining 17965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 23364 2.45 - 4.89: 841 4.89 - 7.34: 125 7.34 - 9.78: 37 9.78 - 12.23: 11 Bond angle restraints: 24378 Sorted by residual: angle pdb=" N MET C1149 " pdb=" CA MET C1149 " pdb=" C MET C1149 " ideal model delta sigma weight residual 111.07 101.77 9.30 1.07e+00 8.73e-01 7.56e+01 angle pdb=" CA ASN E1154 " pdb=" CB ASN E1154 " pdb=" CG ASN E1154 " ideal model delta sigma weight residual 112.60 120.91 -8.31 1.00e+00 1.00e+00 6.91e+01 angle pdb=" C THR A 290 " pdb=" CA THR A 290 " pdb=" CB THR A 290 " ideal model delta sigma weight residual 108.84 121.07 -12.23 1.51e+00 4.39e-01 6.56e+01 angle pdb=" CA GLU C1150 " pdb=" C GLU C1150 " pdb=" O GLU C1150 " ideal model delta sigma weight residual 119.49 109.72 9.77 1.21e+00 6.83e-01 6.52e+01 angle pdb=" CA ASN A1154 " pdb=" CB ASN A1154 " pdb=" CG ASN A1154 " ideal model delta sigma weight residual 112.60 120.67 -8.07 1.00e+00 1.00e+00 6.52e+01 ... (remaining 24373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 10340 21.31 - 42.63: 643 42.63 - 63.94: 114 63.94 - 85.25: 43 85.25 - 106.56: 17 Dihedral angle restraints: 11157 sinusoidal: 4902 harmonic: 6255 Sorted by residual: dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS E1047 " pdb=" CB CYS E1047 " ideal model delta sinusoidal sigma weight residual 93.00 31.41 61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS A 30 " pdb=" SG CYS A 30 " pdb=" SG CYS C1047 " pdb=" CB CYS C1047 " ideal model delta sinusoidal sigma weight residual 93.00 33.68 59.32 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS C1144 " pdb=" SG CYS C1144 " pdb=" SG CYS C1148 " pdb=" CB CYS C1148 " ideal model delta sinusoidal sigma weight residual 93.00 44.45 48.55 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 11154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2401 0.093 - 0.186: 278 0.186 - 0.279: 41 0.279 - 0.372: 6 0.372 - 0.465: 4 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA TYR H 100F" pdb=" N TYR H 100F" pdb=" C TYR H 100F" pdb=" CB TYR H 100F" both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CG LEU A 327 " pdb=" CB LEU A 327 " pdb=" CD1 LEU A 327 " pdb=" CD2 LEU A 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA THR A1015 " pdb=" N THR A1015 " pdb=" C THR A1015 " pdb=" CB THR A1015 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 2727 not shown) Planarity restraints: 3132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C1144 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C CYS C1144 " -0.081 2.00e-02 2.50e+03 pdb=" O CYS C1144 " 0.031 2.00e-02 2.50e+03 pdb=" N ASP C1145 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E1144 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C CYS E1144 " -0.080 2.00e-02 2.50e+03 pdb=" O CYS E1144 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP E1145 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C1149 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C MET C1149 " 0.071 2.00e-02 2.50e+03 pdb=" O MET C1149 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU C1150 " -0.024 2.00e-02 2.50e+03 ... (remaining 3129 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4716 2.81 - 3.33: 13924 3.33 - 3.86: 30098 3.86 - 4.38: 35148 4.38 - 4.90: 62558 Nonbonded interactions: 146444 Sorted by model distance: nonbonded pdb=" O CYS E 52 " pdb=" OH TYR E 88 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR C 137 " pdb=" OG1 THR C 161 " model vdw 2.327 3.040 nonbonded pdb=" O CYS C 52 " pdb=" OH TYR C 88 " model vdw 2.333 3.040 nonbonded pdb=" O CYS A 52 " pdb=" OH TYR A 88 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU J 101 " pdb=" OH TYR K 36 " model vdw 2.351 3.040 ... (remaining 146439 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.570 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.007 0.170 18033 Z= 0.394 Angle : 1.104 15.498 24540 Z= 0.668 Chirality : 0.063 0.465 2730 Planarity : 0.009 0.083 3114 Dihedral : 15.055 106.563 7086 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 3.33 % 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: -1.60 (0.16), residues: 2148 helix: -1.01 (0.21), residues: 360 sheet: 0.24 (0.23), residues: 501 loop : -1.68 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 86 HIS 0.010 0.002 HIS E1026 PHE 0.021 0.003 PHE H 78 TYR 0.026 0.002 TYR H 50 ARG 0.017 0.001 ARG I 61 Details of bonding type rmsd link_NAG-ASN : bond 0.01677 ( 18) link_NAG-ASN : angle 4.00988 ( 54) link_ALPHA1-6 : bond 0.00271 ( 6) link_ALPHA1-6 : angle 1.36933 ( 18) link_BETA1-4 : bond 0.00999 ( 9) link_BETA1-4 : angle 1.38965 ( 27) link_ALPHA1-3 : bond 0.00351 ( 3) link_ALPHA1-3 : angle 1.15947 ( 9) hydrogen bonds : bond 0.20968 ( 630) hydrogen bonds : angle 9.02134 ( 1905) SS BOND : bond 0.01615 ( 27) SS BOND : angle 2.11015 ( 54) covalent geometry : bond 0.00664 (17970) covalent geometry : angle 1.08462 (24378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 1.796 Fit side-chains REVERT: A 64 ASN cc_start: 0.7190 (p0) cc_final: 0.6089 (t0) REVERT: A 205 ASN cc_start: 0.7669 (m-40) cc_final: 0.7381 (m110) REVERT: A 1058 LYS cc_start: 0.7565 (mmtm) cc_final: 0.6692 (mmmm) REVERT: A 1060 ASN cc_start: 0.7684 (t0) cc_final: 0.7306 (t0) REVERT: C 50 LYS cc_start: 0.6732 (mtmm) cc_final: 0.6305 (pttp) REVERT: C 61 GLN cc_start: 0.7384 (tt0) cc_final: 0.7132 (tp-100) REVERT: C 66 ASN cc_start: 0.7622 (m-40) cc_final: 0.7341 (m-40) REVERT: C 155 LYS cc_start: 0.8306 (mmpt) cc_final: 0.8089 (mmtm) REVERT: C 1077 MET cc_start: 0.7403 (ttm) cc_final: 0.7074 (ttt) REVERT: E 27 ASP cc_start: 0.7939 (m-30) cc_final: 0.7689 (m-30) REVERT: E 45 ASP cc_start: 0.7467 (p0) cc_final: 0.7201 (p0) REVERT: E 50 LYS cc_start: 0.6464 (mtmm) cc_final: 0.6161 (pttp) REVERT: E 53 ARG cc_start: 0.6872 (mtp85) cc_final: 0.6537 (mtp-110) REVERT: E 64 ASN cc_start: 0.7330 (p0) cc_final: 0.6092 (t0) REVERT: E 104 ASP cc_start: 0.7615 (m-30) cc_final: 0.7233 (t0) REVERT: E 204 ASP cc_start: 0.7900 (m-30) cc_final: 0.7643 (m-30) REVERT: E 225 LYS cc_start: 0.7538 (tttm) cc_final: 0.7158 (tttt) REVERT: E 1082 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7038 (ptpt) REVERT: G 30 SER cc_start: 0.8937 (p) cc_final: 0.8351 (m) REVERT: G 57 THR cc_start: 0.8796 (p) cc_final: 0.8569 (p) REVERT: G 79 SER cc_start: 0.8137 (m) cc_final: 0.7788 (p) REVERT: H 30 SER cc_start: 0.8591 (p) cc_final: 0.8287 (m) REVERT: H 31 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6886 (mtp180) REVERT: I 33 LEU cc_start: 0.8445 (tp) cc_final: 0.8207 (tp) REVERT: I 50 SER cc_start: 0.7832 (m) cc_final: 0.7473 (t) REVERT: J 31 ARG cc_start: 0.7702 (mpt180) cc_final: 0.7106 (mtp180) REVERT: K 33 LEU cc_start: 0.8597 (tp) cc_final: 0.8368 (tp) REVERT: K 100 GLN cc_start: 0.7278 (mp10) cc_final: 0.6622 (mp10) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 1.2092 time to fit residues: 387.4746 Evaluate side-chains 225 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 48 ASN C1125 GLN E 66 ASN E1026 HIS E1060 ASN ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN I 100 GLN K 95 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.191673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158423 restraints weight = 17171.288| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.64 r_work: 0.3419 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18033 Z= 0.235 Angle : 0.688 10.982 24540 Z= 0.353 Chirality : 0.047 0.205 2730 Planarity : 0.006 0.062 3114 Dihedral : 9.769 81.612 3100 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.38 % Allowed : 8.27 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.89 (0.16), residues: 2148 helix: 0.88 (0.25), residues: 360 sheet: -0.03 (0.21), residues: 567 loop : -1.35 (0.15), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 35A HIS 0.007 0.002 HIS E1026 PHE 0.022 0.003 PHE J 97 TYR 0.022 0.002 TYR J 50 ARG 0.006 0.001 ARG C 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 18) link_NAG-ASN : angle 3.34320 ( 54) link_ALPHA1-6 : bond 0.00602 ( 6) link_ALPHA1-6 : angle 2.26202 ( 18) link_BETA1-4 : bond 0.00468 ( 9) link_BETA1-4 : angle 1.65056 ( 27) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 1.90418 ( 9) hydrogen bonds : bond 0.04588 ( 630) hydrogen bonds : angle 6.00435 ( 1905) SS BOND : bond 0.00623 ( 27) SS BOND : angle 1.42070 ( 54) covalent geometry : bond 0.00556 (17970) covalent geometry : angle 0.66242 (24378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 2.089 Fit side-chains REVERT: A 29 VAL cc_start: 0.7981 (p) cc_final: 0.7585 (t) REVERT: A 45 ASP cc_start: 0.8057 (p0) cc_final: 0.7830 (p0) REVERT: A 252 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 1060 ASN cc_start: 0.7819 (t0) cc_final: 0.7342 (t0) REVERT: A 1150 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: A 1172 LYS cc_start: 0.7557 (mtmt) cc_final: 0.7001 (mttp) REVERT: C 45 ASP cc_start: 0.7991 (p0) cc_final: 0.7724 (p0) REVERT: C 50 LYS cc_start: 0.7239 (mtmm) cc_final: 0.6751 (pttp) REVERT: C 61 GLN cc_start: 0.8298 (tt0) cc_final: 0.7900 (tp40) REVERT: C 115 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8275 (mt) REVERT: C 202 ARG cc_start: 0.8227 (mmp80) cc_final: 0.7997 (mmt180) REVERT: C 204 ASP cc_start: 0.8439 (m-30) cc_final: 0.8186 (m-30) REVERT: C 252 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7290 (mt-10) REVERT: C 1169 ASN cc_start: 0.6320 (m-40) cc_final: 0.5761 (m110) REVERT: E 27 ASP cc_start: 0.8284 (m-30) cc_final: 0.7969 (m-30) REVERT: E 45 ASP cc_start: 0.7943 (p0) cc_final: 0.7609 (p0) REVERT: E 64 ASN cc_start: 0.7522 (p0) cc_final: 0.6026 (t0) REVERT: E 104 ASP cc_start: 0.8208 (m-30) cc_final: 0.7857 (t0) REVERT: E 202 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8100 (mmt180) REVERT: E 225 LYS cc_start: 0.7680 (tttm) cc_final: 0.7308 (tttt) REVERT: E 252 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7576 (mt-10) REVERT: E 282 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6453 (p0) REVERT: E 1060 ASN cc_start: 0.7930 (t0) cc_final: 0.7536 (t0) REVERT: E 1075 LYS cc_start: 0.8489 (tptt) cc_final: 0.8179 (tptp) REVERT: E 1082 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7495 (ptpp) REVERT: E 1150 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: G 66 ARG cc_start: 0.7104 (mtp180) cc_final: 0.6760 (mtp180) REVERT: H 31 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7260 (mtp180) REVERT: H 105 GLN cc_start: 0.7891 (pm20) cc_final: 0.7556 (mt0) REVERT: I 100 GLN cc_start: 0.7418 (mp10) cc_final: 0.6966 (mp10) REVERT: J 31 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7371 (mtp180) REVERT: K 100 GLN cc_start: 0.7578 (mp10) cc_final: 0.6945 (mp10) REVERT: L 52 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7463 (t) outliers start: 45 outliers final: 19 residues processed: 268 average time/residue: 1.1398 time to fit residues: 345.9339 Evaluate side-chains 237 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 278 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 135 ASN E 205 ASN ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.200689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177219 restraints weight = 16815.580| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.13 r_work: 0.3589 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18033 Z= 0.223 Angle : 0.657 11.721 24540 Z= 0.336 Chirality : 0.046 0.197 2730 Planarity : 0.005 0.057 3114 Dihedral : 8.968 74.457 3100 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.39 % Allowed : 10.65 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.56 (0.17), residues: 2148 helix: 1.25 (0.26), residues: 363 sheet: 0.19 (0.21), residues: 561 loop : -1.18 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 35A HIS 0.007 0.001 HIS E1026 PHE 0.019 0.002 PHE J 97 TYR 0.021 0.002 TYR A1034 ARG 0.005 0.001 ARG C 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 18) link_NAG-ASN : angle 3.43920 ( 54) link_ALPHA1-6 : bond 0.00426 ( 6) link_ALPHA1-6 : angle 1.90137 ( 18) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 1.37565 ( 27) link_ALPHA1-3 : bond 0.01308 ( 3) link_ALPHA1-3 : angle 1.61793 ( 9) hydrogen bonds : bond 0.04276 ( 630) hydrogen bonds : angle 5.67732 ( 1905) SS BOND : bond 0.00693 ( 27) SS BOND : angle 1.66255 ( 54) covalent geometry : bond 0.00526 (17970) covalent geometry : angle 0.62990 (24378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 1.956 Fit side-chains REVERT: A 45 ASP cc_start: 0.8213 (p0) cc_final: 0.7985 (p0) REVERT: A 115 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8425 (mt) REVERT: A 252 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 1017 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7103 (ttm) REVERT: A 1060 ASN cc_start: 0.7784 (t0) cc_final: 0.7195 (t0) REVERT: A 1172 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7214 (mttp) REVERT: C 50 LYS cc_start: 0.7521 (mtmm) cc_final: 0.7247 (pttp) REVERT: C 61 GLN cc_start: 0.8482 (tt0) cc_final: 0.8089 (tp40) REVERT: C 139 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7208 (mpt180) REVERT: C 204 ASP cc_start: 0.8376 (m-30) cc_final: 0.8169 (m-30) REVERT: C 252 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7382 (mt-10) REVERT: C 287 LYS cc_start: 0.8367 (mttp) cc_final: 0.8119 (mttt) REVERT: E 27 ASP cc_start: 0.8244 (m-30) cc_final: 0.7937 (m-30) REVERT: E 45 ASP cc_start: 0.8092 (p0) cc_final: 0.7776 (p0) REVERT: E 64 ASN cc_start: 0.7631 (p0) cc_final: 0.6235 (t0) REVERT: E 104 ASP cc_start: 0.8185 (m-30) cc_final: 0.7810 (t0) REVERT: E 252 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7475 (mp0) REVERT: E 282 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6642 (p0) REVERT: E 1060 ASN cc_start: 0.7933 (t0) cc_final: 0.7563 (t0) REVERT: E 1075 LYS cc_start: 0.8530 (tptt) cc_final: 0.8290 (tptp) REVERT: E 1082 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7544 (ptpp) REVERT: G 66 ARG cc_start: 0.7275 (mtp180) cc_final: 0.7008 (mtp180) REVERT: H 31 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: H 105 GLN cc_start: 0.7885 (pm20) cc_final: 0.7613 (mt0) REVERT: I 4 MET cc_start: 0.7975 (tpt) cc_final: 0.7679 (tpt) REVERT: I 100 GLN cc_start: 0.7634 (mp10) cc_final: 0.7027 (mp10) REVERT: J 31 ARG cc_start: 0.8221 (mpt180) cc_final: 0.7561 (mtp180) REVERT: K 100 GLN cc_start: 0.7718 (mp10) cc_final: 0.7090 (mp10) outliers start: 64 outliers final: 40 residues processed: 262 average time/residue: 1.1374 time to fit residues: 337.0138 Evaluate side-chains 255 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 292 GLN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 135 ASN A 178 GLN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 135 ASN ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.180492 restraints weight = 16808.358| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.02 r_work: 0.3633 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18033 Z= 0.169 Angle : 0.600 10.551 24540 Z= 0.305 Chirality : 0.044 0.207 2730 Planarity : 0.004 0.054 3114 Dihedral : 8.273 69.087 3100 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.13 % Allowed : 12.40 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.35 (0.17), residues: 2148 helix: 1.63 (0.26), residues: 363 sheet: 0.23 (0.22), residues: 570 loop : -1.08 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 35A HIS 0.013 0.001 HIS A1026 PHE 0.016 0.002 PHE A1110 TYR 0.018 0.002 TYR H 50 ARG 0.003 0.000 ARG C 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 18) link_NAG-ASN : angle 3.18261 ( 54) link_ALPHA1-6 : bond 0.00423 ( 6) link_ALPHA1-6 : angle 1.87076 ( 18) link_BETA1-4 : bond 0.00400 ( 9) link_BETA1-4 : angle 1.40636 ( 27) link_ALPHA1-3 : bond 0.01432 ( 3) link_ALPHA1-3 : angle 1.85989 ( 9) hydrogen bonds : bond 0.03773 ( 630) hydrogen bonds : angle 5.33365 ( 1905) SS BOND : bond 0.00863 ( 27) SS BOND : angle 1.61839 ( 54) covalent geometry : bond 0.00391 (17970) covalent geometry : angle 0.57246 (24378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 2.029 Fit side-chains REVERT: A 252 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7460 (mp0) REVERT: A 1017 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.6970 (ttm) REVERT: A 1060 ASN cc_start: 0.7774 (t0) cc_final: 0.7191 (t0) REVERT: A 1150 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: A 1172 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7188 (mttp) REVERT: C 50 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7303 (pttp) REVERT: C 61 GLN cc_start: 0.8451 (tt0) cc_final: 0.8062 (tp40) REVERT: C 139 ARG cc_start: 0.7454 (mmt180) cc_final: 0.7145 (mpt180) REVERT: C 204 ASP cc_start: 0.8369 (m-30) cc_final: 0.8157 (m-30) REVERT: C 252 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7427 (mp0) REVERT: C 287 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8084 (mttt) REVERT: E 27 ASP cc_start: 0.8244 (m-30) cc_final: 0.7929 (m-30) REVERT: E 45 ASP cc_start: 0.8090 (p0) cc_final: 0.7794 (p0) REVERT: E 64 ASN cc_start: 0.7603 (p0) cc_final: 0.6233 (t0) REVERT: E 104 ASP cc_start: 0.8018 (m-30) cc_final: 0.7658 (t0) REVERT: E 252 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7442 (mp0) REVERT: E 282 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6567 (p0) REVERT: E 309 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7761 (mt) REVERT: E 1060 ASN cc_start: 0.7961 (t0) cc_final: 0.7599 (t0) REVERT: E 1075 LYS cc_start: 0.8505 (tptt) cc_final: 0.8262 (tptp) REVERT: E 1077 MET cc_start: 0.8048 (ttm) cc_final: 0.7731 (ttp) REVERT: E 1082 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7592 (ptpp) REVERT: E 1121 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7429 (mttt) REVERT: E 1150 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: H 31 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7188 (mtp180) REVERT: H 105 GLN cc_start: 0.7730 (pm20) cc_final: 0.7429 (mt0) REVERT: I 100 GLN cc_start: 0.7624 (mp10) cc_final: 0.7076 (mp10) REVERT: J 31 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7502 (mtp180) outliers start: 59 outliers final: 39 residues processed: 259 average time/residue: 1.1985 time to fit residues: 349.6383 Evaluate side-chains 258 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 292 GLN Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1121 LYS Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 27 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 chunk 203 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 129 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 178 GLN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 135 ASN E 292 GLN E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.203480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180309 restraints weight = 16883.772| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.12 r_work: 0.3607 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18033 Z= 0.139 Angle : 0.566 9.681 24540 Z= 0.287 Chirality : 0.043 0.205 2730 Planarity : 0.004 0.052 3114 Dihedral : 7.704 64.310 3100 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 13.35 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2148 helix: 1.85 (0.26), residues: 363 sheet: 0.33 (0.22), residues: 570 loop : -0.97 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 PHE 0.016 0.002 PHE A1110 TYR 0.016 0.001 TYR H 50 ARG 0.002 0.000 ARG E 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 18) link_NAG-ASN : angle 2.92556 ( 54) link_ALPHA1-6 : bond 0.00443 ( 6) link_ALPHA1-6 : angle 1.78088 ( 18) link_BETA1-4 : bond 0.00428 ( 9) link_BETA1-4 : angle 1.36709 ( 27) link_ALPHA1-3 : bond 0.01326 ( 3) link_ALPHA1-3 : angle 1.81483 ( 9) hydrogen bonds : bond 0.03574 ( 630) hydrogen bonds : angle 5.11751 ( 1905) SS BOND : bond 0.00581 ( 27) SS BOND : angle 1.62957 ( 54) covalent geometry : bond 0.00321 (17970) covalent geometry : angle 0.54088 (24378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 1.931 Fit side-chains REVERT: A 252 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 1017 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6910 (ttm) REVERT: A 1150 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6041 (mp0) REVERT: A 1172 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7161 (mttp) REVERT: C 50 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7299 (pttp) REVERT: C 61 GLN cc_start: 0.8527 (tt0) cc_final: 0.8124 (tp40) REVERT: C 139 ARG cc_start: 0.7471 (mmt180) cc_final: 0.7132 (mpt180) REVERT: C 252 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7481 (mp0) REVERT: C 287 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: C 1150 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: E 27 ASP cc_start: 0.8182 (m-30) cc_final: 0.7912 (m-30) REVERT: E 45 ASP cc_start: 0.8099 (p0) cc_final: 0.7775 (p0) REVERT: E 53 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7270 (mtp-110) REVERT: E 64 ASN cc_start: 0.7479 (p0) cc_final: 0.6082 (t0) REVERT: E 104 ASP cc_start: 0.8051 (m-30) cc_final: 0.7669 (t0) REVERT: E 252 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7476 (mp0) REVERT: E 282 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6550 (p0) REVERT: E 308 THR cc_start: 0.7871 (p) cc_final: 0.7661 (p) REVERT: E 1060 ASN cc_start: 0.7966 (t0) cc_final: 0.7601 (t0) REVERT: E 1075 LYS cc_start: 0.8535 (tptt) cc_final: 0.8258 (tptp) REVERT: E 1082 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7594 (ptpp) REVERT: E 1112 ASP cc_start: 0.8212 (m-30) cc_final: 0.8009 (m-30) REVERT: E 1169 ASN cc_start: 0.6331 (m-40) cc_final: 0.6112 (m110) REVERT: E 1172 LYS cc_start: 0.7601 (mtmt) cc_final: 0.7144 (tmtt) REVERT: H 31 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: H 105 GLN cc_start: 0.7705 (pm20) cc_final: 0.7396 (mt0) REVERT: I 100 GLN cc_start: 0.7542 (mp10) cc_final: 0.6948 (mp10) REVERT: J 31 ARG cc_start: 0.8166 (mpt180) cc_final: 0.7435 (mtp180) outliers start: 65 outliers final: 42 residues processed: 256 average time/residue: 1.2371 time to fit residues: 356.4996 Evaluate side-chains 253 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 172 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 278 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.202667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179434 restraints weight = 16851.478| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.12 r_work: 0.3603 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18033 Z= 0.157 Angle : 0.583 10.172 24540 Z= 0.295 Chirality : 0.043 0.210 2730 Planarity : 0.004 0.051 3114 Dihedral : 7.414 60.968 3100 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.55 % Allowed : 14.04 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.11 (0.17), residues: 2148 helix: 1.91 (0.26), residues: 363 sheet: 0.33 (0.22), residues: 564 loop : -0.90 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 35A HIS 0.011 0.001 HIS A1026 PHE 0.016 0.002 PHE A1110 TYR 0.017 0.002 TYR J 50 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 18) link_NAG-ASN : angle 2.81249 ( 54) link_ALPHA1-6 : bond 0.00465 ( 6) link_ALPHA1-6 : angle 1.76691 ( 18) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 1.38892 ( 27) link_ALPHA1-3 : bond 0.01326 ( 3) link_ALPHA1-3 : angle 1.82570 ( 9) hydrogen bonds : bond 0.03546 ( 630) hydrogen bonds : angle 5.08400 ( 1905) SS BOND : bond 0.00707 ( 27) SS BOND : angle 1.72850 ( 54) covalent geometry : bond 0.00369 (17970) covalent geometry : angle 0.55881 (24378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 2.032 Fit side-chains REVERT: A 244 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 252 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7419 (mp0) REVERT: A 1017 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.6924 (ttm) REVERT: A 1150 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.5941 (mp0) REVERT: A 1172 LYS cc_start: 0.7567 (mtmt) cc_final: 0.6954 (mttp) REVERT: C 50 LYS cc_start: 0.7628 (mtmm) cc_final: 0.7303 (pttp) REVERT: C 61 GLN cc_start: 0.8438 (tt0) cc_final: 0.8053 (tp40) REVERT: C 139 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7147 (mpt180) REVERT: C 252 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7406 (mp0) REVERT: C 287 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8097 (mttt) REVERT: C 1017 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.6922 (tpp) REVERT: C 1150 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: E 27 ASP cc_start: 0.8106 (m-30) cc_final: 0.7819 (m-30) REVERT: E 45 ASP cc_start: 0.8021 (p0) cc_final: 0.7710 (p0) REVERT: E 64 ASN cc_start: 0.7466 (p0) cc_final: 0.6134 (t0) REVERT: E 104 ASP cc_start: 0.7949 (m-30) cc_final: 0.7604 (t0) REVERT: E 252 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7396 (mp0) REVERT: E 282 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6596 (p0) REVERT: E 308 THR cc_start: 0.7853 (p) cc_final: 0.7639 (p) REVERT: E 317 ARG cc_start: 0.7715 (mtt90) cc_final: 0.7513 (mtt90) REVERT: E 1018 MET cc_start: 0.8171 (ptp) cc_final: 0.7929 (ptm) REVERT: E 1060 ASN cc_start: 0.7766 (t0) cc_final: 0.7452 (t0) REVERT: E 1075 LYS cc_start: 0.8477 (tptt) cc_final: 0.8223 (tptp) REVERT: E 1082 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7581 (ptpp) REVERT: E 1112 ASP cc_start: 0.8089 (m-30) cc_final: 0.7878 (m-30) REVERT: E 1150 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: E 1172 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7112 (tmtt) REVERT: H 31 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: I 100 GLN cc_start: 0.7530 (mp10) cc_final: 0.6964 (mp10) REVERT: J 31 ARG cc_start: 0.8135 (mpt180) cc_final: 0.7396 (mtp180) outliers start: 67 outliers final: 49 residues processed: 253 average time/residue: 1.2400 time to fit residues: 351.8138 Evaluate side-chains 262 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 170 optimal weight: 0.0470 chunk 45 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.205182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.183054 restraints weight = 16753.411| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.05 r_work: 0.3670 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18033 Z= 0.116 Angle : 0.556 9.767 24540 Z= 0.282 Chirality : 0.042 0.267 2730 Planarity : 0.004 0.049 3114 Dihedral : 6.997 56.738 3100 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.39 % Allowed : 15.05 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2148 helix: 2.17 (0.26), residues: 363 sheet: 0.48 (0.22), residues: 558 loop : -0.83 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 PHE 0.015 0.001 PHE A1110 TYR 0.015 0.001 TYR H 50 ARG 0.004 0.000 ARG E 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 18) link_NAG-ASN : angle 2.62676 ( 54) link_ALPHA1-6 : bond 0.00512 ( 6) link_ALPHA1-6 : angle 1.65565 ( 18) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.35233 ( 27) link_ALPHA1-3 : bond 0.01280 ( 3) link_ALPHA1-3 : angle 1.79837 ( 9) hydrogen bonds : bond 0.03403 ( 630) hydrogen bonds : angle 4.88181 ( 1905) SS BOND : bond 0.00796 ( 27) SS BOND : angle 2.03038 ( 54) covalent geometry : bond 0.00263 (17970) covalent geometry : angle 0.53084 (24378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 1.963 Fit side-chains REVERT: A 244 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 252 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7518 (mp0) REVERT: A 1150 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: A 1172 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7073 (mttp) REVERT: C 50 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7450 (ptpp) REVERT: C 61 GLN cc_start: 0.8585 (tt0) cc_final: 0.8187 (tp40) REVERT: C 218 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8043 (ttm110) REVERT: C 252 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7523 (mp0) REVERT: C 287 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8140 (mttt) REVERT: C 292 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7489 (mm110) REVERT: E 27 ASP cc_start: 0.8057 (m-30) cc_final: 0.7778 (m-30) REVERT: E 45 ASP cc_start: 0.8101 (p0) cc_final: 0.7787 (p0) REVERT: E 53 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7327 (mtp-110) REVERT: E 64 ASN cc_start: 0.7480 (p0) cc_final: 0.6168 (t0) REVERT: E 104 ASP cc_start: 0.8069 (m-30) cc_final: 0.7731 (t0) REVERT: E 252 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7459 (mp0) REVERT: E 287 LYS cc_start: 0.8551 (mttp) cc_final: 0.8308 (ptpt) REVERT: E 1018 MET cc_start: 0.8240 (ptp) cc_final: 0.7995 (ptm) REVERT: E 1060 ASN cc_start: 0.7715 (t0) cc_final: 0.7389 (t0) REVERT: E 1075 LYS cc_start: 0.8513 (tptt) cc_final: 0.8236 (tptp) REVERT: E 1082 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7601 (ptpp) REVERT: E 1133 LEU cc_start: 0.7146 (mp) cc_final: 0.6887 (mt) REVERT: E 1150 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: E 1172 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7223 (tmtt) REVERT: H 31 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7162 (mtp180) REVERT: J 31 ARG cc_start: 0.8186 (mpt180) cc_final: 0.7424 (mtp180) REVERT: K 100 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7427 (mp-120) outliers start: 64 outliers final: 40 residues processed: 254 average time/residue: 1.2667 time to fit residues: 361.5331 Evaluate side-chains 253 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 302 GLN C 292 GLN C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.178024 restraints weight = 16793.292| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.12 r_work: 0.3578 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18033 Z= 0.201 Angle : 0.623 13.171 24540 Z= 0.316 Chirality : 0.045 0.230 2730 Planarity : 0.004 0.049 3114 Dihedral : 6.996 56.223 3100 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.55 % Allowed : 15.32 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.04 (0.17), residues: 2148 helix: 1.92 (0.26), residues: 363 sheet: 0.43 (0.22), residues: 558 loop : -0.86 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 35A HIS 0.010 0.001 HIS A1026 PHE 0.017 0.002 PHE J 97 TYR 0.019 0.002 TYR J 50 ARG 0.007 0.001 ARG C 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 18) link_NAG-ASN : angle 2.62152 ( 54) link_ALPHA1-6 : bond 0.00501 ( 6) link_ALPHA1-6 : angle 1.68684 ( 18) link_BETA1-4 : bond 0.00413 ( 9) link_BETA1-4 : angle 1.40795 ( 27) link_ALPHA1-3 : bond 0.01278 ( 3) link_ALPHA1-3 : angle 1.82314 ( 9) hydrogen bonds : bond 0.03717 ( 630) hydrogen bonds : angle 5.09530 ( 1905) SS BOND : bond 0.01022 ( 27) SS BOND : angle 2.04980 ( 54) covalent geometry : bond 0.00479 (17970) covalent geometry : angle 0.60005 (24378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 1.874 Fit side-chains REVERT: A 244 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 252 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7522 (mp0) REVERT: A 1017 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7018 (ttm) REVERT: A 1150 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: A 1172 LYS cc_start: 0.7592 (mtmt) cc_final: 0.6921 (mttp) REVERT: C 50 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7351 (pttp) REVERT: C 61 GLN cc_start: 0.8582 (tt0) cc_final: 0.8196 (tp40) REVERT: C 139 ARG cc_start: 0.7598 (mmt180) cc_final: 0.7195 (mpt180) REVERT: C 252 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7531 (mp0) REVERT: C 278 ASN cc_start: 0.8656 (m-40) cc_final: 0.8422 (m-40) REVERT: C 1017 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7070 (tpp) REVERT: C 1150 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: E 27 ASP cc_start: 0.8184 (m-30) cc_final: 0.7902 (m-30) REVERT: E 45 ASP cc_start: 0.8117 (p0) cc_final: 0.7836 (p0) REVERT: E 53 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7339 (mtp-110) REVERT: E 64 ASN cc_start: 0.7477 (p0) cc_final: 0.6166 (t0) REVERT: E 104 ASP cc_start: 0.8123 (m-30) cc_final: 0.7775 (t0) REVERT: E 252 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7481 (mp0) REVERT: E 287 LYS cc_start: 0.8606 (mttp) cc_final: 0.8379 (ptpt) REVERT: E 1018 MET cc_start: 0.8317 (ptp) cc_final: 0.8058 (ptm) REVERT: E 1060 ASN cc_start: 0.7839 (t0) cc_final: 0.7551 (t0) REVERT: E 1075 LYS cc_start: 0.8509 (tptt) cc_final: 0.8240 (tptp) REVERT: E 1082 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7576 (ptpp) REVERT: E 1150 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: H 31 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7125 (mtp180) REVERT: I 100 GLN cc_start: 0.7424 (mp10) cc_final: 0.6909 (mp10) REVERT: J 31 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7415 (mtp180) REVERT: K 100 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7371 (mp-120) outliers start: 67 outliers final: 51 residues processed: 255 average time/residue: 1.2815 time to fit residues: 367.7631 Evaluate side-chains 260 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 189 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A1169 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.199779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176997 restraints weight = 16786.405| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.06 r_work: 0.3571 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18033 Z= 0.242 Angle : 0.674 15.805 24540 Z= 0.342 Chirality : 0.047 0.341 2730 Planarity : 0.005 0.049 3114 Dihedral : 7.108 57.896 3100 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.71 % Allowed : 15.42 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2148 helix: 1.55 (0.26), residues: 363 sheet: 0.33 (0.21), residues: 576 loop : -0.91 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 70 HIS 0.010 0.002 HIS A1026 PHE 0.019 0.002 PHE J 97 TYR 0.021 0.002 TYR J 50 ARG 0.006 0.001 ARG E 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 18) link_NAG-ASN : angle 2.75962 ( 54) link_ALPHA1-6 : bond 0.00498 ( 6) link_ALPHA1-6 : angle 1.63038 ( 18) link_BETA1-4 : bond 0.00388 ( 9) link_BETA1-4 : angle 1.45320 ( 27) link_ALPHA1-3 : bond 0.01210 ( 3) link_ALPHA1-3 : angle 1.88625 ( 9) hydrogen bonds : bond 0.03984 ( 630) hydrogen bonds : angle 5.30499 ( 1905) SS BOND : bond 0.00937 ( 27) SS BOND : angle 2.43489 ( 54) covalent geometry : bond 0.00580 (17970) covalent geometry : angle 0.64957 (24378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 1.888 Fit side-chains REVERT: A 50 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7673 (mtmm) REVERT: A 181 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: A 244 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 252 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7533 (mp0) REVERT: A 282 ASP cc_start: 0.5753 (OUTLIER) cc_final: 0.5092 (p0) REVERT: A 1017 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7060 (ttm) REVERT: A 1150 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: C 50 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7377 (pttp) REVERT: C 61 GLN cc_start: 0.8608 (tt0) cc_final: 0.8233 (tp40) REVERT: C 139 ARG cc_start: 0.7505 (mmt180) cc_final: 0.7127 (mpt180) REVERT: C 252 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7533 (mp0) REVERT: C 278 ASN cc_start: 0.8640 (m-40) cc_final: 0.8426 (m-40) REVERT: C 1017 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7141 (tpp) REVERT: C 1150 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: E 27 ASP cc_start: 0.8199 (m-30) cc_final: 0.7881 (m-30) REVERT: E 45 ASP cc_start: 0.8131 (p0) cc_final: 0.7847 (p0) REVERT: E 53 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7386 (mtp-110) REVERT: E 64 ASN cc_start: 0.7549 (p0) cc_final: 0.6302 (t0) REVERT: E 104 ASP cc_start: 0.8142 (m-30) cc_final: 0.7782 (t0) REVERT: E 196 ASP cc_start: 0.7931 (m-30) cc_final: 0.7498 (m-30) REVERT: E 252 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7690 (mt-10) REVERT: E 1017 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.6854 (ttm) REVERT: E 1018 MET cc_start: 0.8385 (ptp) cc_final: 0.8140 (ptm) REVERT: E 1060 ASN cc_start: 0.7768 (t0) cc_final: 0.7513 (t0) REVERT: E 1075 LYS cc_start: 0.8507 (tptt) cc_final: 0.8249 (tptp) REVERT: E 1082 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7569 (ptpp) REVERT: E 1172 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7234 (tmtt) REVERT: H 31 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7153 (mtp180) REVERT: I 100 GLN cc_start: 0.7463 (mp10) cc_final: 0.6945 (mp10) REVERT: J 31 ARG cc_start: 0.8245 (mpt180) cc_final: 0.7460 (mtp180) REVERT: K 100 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7372 (mp-120) outliers start: 70 outliers final: 51 residues processed: 261 average time/residue: 1.2219 time to fit residues: 357.8379 Evaluate side-chains 253 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1017 MET Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 1017 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 104 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 66 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.199207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169817 restraints weight = 17046.824| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.38 r_work: 0.3564 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18033 Z= 0.122 Angle : 0.607 13.619 24540 Z= 0.308 Chirality : 0.043 0.326 2730 Planarity : 0.004 0.050 3114 Dihedral : 6.660 56.169 3100 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.76 % Allowed : 16.85 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2148 helix: 2.00 (0.26), residues: 363 sheet: 0.45 (0.22), residues: 558 loop : -0.83 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 86 HIS 0.012 0.001 HIS A1026 PHE 0.016 0.001 PHE A1110 TYR 0.014 0.001 TYR H 50 ARG 0.006 0.000 ARG E 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 2.55126 ( 54) link_ALPHA1-6 : bond 0.00613 ( 6) link_ALPHA1-6 : angle 1.51032 ( 18) link_BETA1-4 : bond 0.00468 ( 9) link_BETA1-4 : angle 1.36975 ( 27) link_ALPHA1-3 : bond 0.01188 ( 3) link_ALPHA1-3 : angle 1.86295 ( 9) hydrogen bonds : bond 0.03569 ( 630) hydrogen bonds : angle 4.96829 ( 1905) SS BOND : bond 0.00905 ( 27) SS BOND : angle 2.75881 ( 54) covalent geometry : bond 0.00280 (17970) covalent geometry : angle 0.57812 (24378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.808 Fit side-chains REVERT: A 244 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 252 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7467 (mp0) REVERT: A 1150 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: C 50 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7554 (ptpp) REVERT: C 61 GLN cc_start: 0.8545 (tt0) cc_final: 0.8145 (tp40) REVERT: C 139 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7136 (mpt180) REVERT: C 218 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7924 (ttm110) REVERT: C 252 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7474 (mt-10) REVERT: C 278 ASN cc_start: 0.8677 (m-40) cc_final: 0.8433 (m-40) REVERT: C 1150 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: E 27 ASP cc_start: 0.8103 (m-30) cc_final: 0.7826 (m-30) REVERT: E 45 ASP cc_start: 0.8035 (p0) cc_final: 0.7756 (p0) REVERT: E 64 ASN cc_start: 0.7392 (p0) cc_final: 0.6069 (t0) REVERT: E 104 ASP cc_start: 0.8043 (m-30) cc_final: 0.7697 (t0) REVERT: E 196 ASP cc_start: 0.7674 (m-30) cc_final: 0.7210 (m-30) REVERT: E 252 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7442 (mp0) REVERT: E 1018 MET cc_start: 0.8226 (ptp) cc_final: 0.7967 (ptm) REVERT: E 1060 ASN cc_start: 0.7642 (t0) cc_final: 0.7339 (t0) REVERT: E 1075 LYS cc_start: 0.8458 (tptt) cc_final: 0.8159 (tptp) REVERT: E 1082 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7542 (ptpp) REVERT: E 1112 ASP cc_start: 0.8139 (m-30) cc_final: 0.7881 (m-30) REVERT: E 1172 LYS cc_start: 0.7460 (mtmt) cc_final: 0.6894 (tmtt) REVERT: H 31 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6960 (mtp180) REVERT: H 68 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8032 (m) REVERT: I 100 GLN cc_start: 0.7437 (mp10) cc_final: 0.7036 (mp-120) REVERT: J 31 ARG cc_start: 0.8200 (mpt180) cc_final: 0.7288 (mtp180) REVERT: K 100 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7229 (mp-120) outliers start: 52 outliers final: 40 residues processed: 239 average time/residue: 1.3061 time to fit residues: 349.0497 Evaluate side-chains 244 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 165 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 66 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169365 restraints weight = 17062.870| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.50 r_work: 0.3535 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18033 Z= 0.129 Angle : 0.592 11.567 24540 Z= 0.300 Chirality : 0.043 0.309 2730 Planarity : 0.004 0.049 3114 Dihedral : 6.413 54.489 3100 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.65 % Allowed : 17.06 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.08 (0.17), residues: 2148 helix: 2.12 (0.26), residues: 363 sheet: 0.47 (0.22), residues: 558 loop : -0.80 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 PHE 0.016 0.001 PHE A1110 TYR 0.015 0.001 TYR J 50 ARG 0.007 0.000 ARG K 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 18) link_NAG-ASN : angle 2.39143 ( 54) link_ALPHA1-6 : bond 0.00681 ( 6) link_ALPHA1-6 : angle 1.47203 ( 18) link_BETA1-4 : bond 0.00479 ( 9) link_BETA1-4 : angle 1.34295 ( 27) link_ALPHA1-3 : bond 0.01162 ( 3) link_ALPHA1-3 : angle 1.85595 ( 9) hydrogen bonds : bond 0.03504 ( 630) hydrogen bonds : angle 4.87914 ( 1905) SS BOND : bond 0.00811 ( 27) SS BOND : angle 2.65432 ( 54) covalent geometry : bond 0.00302 (17970) covalent geometry : angle 0.56561 (24378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10377.62 seconds wall clock time: 180 minutes 49.51 seconds (10849.51 seconds total)