Starting phenix.real_space_refine on Thu Sep 18 14:49:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8veb_43169/09_2025/8veb_43169.cif Found real_map, /net/cci-nas-00/data/ceres_data/8veb_43169/09_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_43169/09_2025/8veb_43169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8veb_43169/09_2025/8veb_43169.map" model { file = "/net/cci-nas-00/data/ceres_data/8veb_43169/09_2025/8veb_43169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8veb_43169/09_2025/8veb_43169.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.075 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.36, per 1000 atoms: 0.25 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: 1.72 Conformation dependent library (CDL) restraints added in 746.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.74 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: 3.09 Time building geometry restraints manager: 2.22 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: 0.02 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.220 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.017 0.001 ARG I 61 TYR 0.026 0.002 TYR H 50 PHE 0.021 0.003 PHE H 78 TRP 0.032 0.002 TRP A 86 HIS 0.010 0.002 HIS E1026 Details of bonding type rmsd covalent geometry : bond 0.00664 (17970) covalent geometry : angle 1.08462 (24378) SS BOND : bond 0.01615 ( 27) SS BOND : angle 2.11015 ( 54) hydrogen bonds : bond 0.20968 ( 630) hydrogen bonds : angle 9.02134 ( 1905) link_ALPHA1-3 : bond 0.00351 ( 3) link_ALPHA1-3 : angle 1.15947 ( 9) 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_NAG-ASN : bond 0.01677 ( 18) link_NAG-ASN : angle 4.00988 ( 54) *********************** 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 : 0.663 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: 0.6160 (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: 0.8371 (tp) REVERT: K 100 GLN cc_start: 0.7278 (mp10) cc_final: 0.6624 (mp10) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.5382 time to fit residues: 171.4700 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 : 0.585 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.5040 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.201985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171810 restraints weight = 17233.588| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.48 r_work: 0.3559 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18033 Z= 0.126 Angle : 0.589 10.910 24540 Z= 0.302 Chirality : 0.043 0.204 2730 Planarity : 0.005 0.076 3114 Dihedral : 9.561 81.711 3100 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 7.15 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2148 helix: 1.23 (0.25), residues: 360 sheet: 0.17 (0.21), residues: 546 loop : -1.32 (0.15), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 202 TYR 0.015 0.001 TYR H 50 PHE 0.014 0.001 PHE C 219 TRP 0.011 0.001 TRP H 35A HIS 0.009 0.001 HIS E1026 Details of bonding type rmsd covalent geometry : bond 0.00274 (17970) covalent geometry : angle 0.56307 (24378) SS BOND : bond 0.00774 ( 27) SS BOND : angle 1.25720 ( 54) hydrogen bonds : bond 0.03940 ( 630) hydrogen bonds : angle 5.76079 ( 1905) link_ALPHA1-3 : bond 0.01031 ( 3) link_ALPHA1-3 : angle 1.73596 ( 9) link_ALPHA1-6 : bond 0.00543 ( 6) link_ALPHA1-6 : angle 2.03933 ( 18) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.52521 ( 27) link_NAG-ASN : bond 0.00220 ( 18) link_NAG-ASN : angle 3.17554 ( 54) *********************** 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 287 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.801 Fit side-chains REVERT: A 45 ASP cc_start: 0.7915 (p0) cc_final: 0.7714 (p0) REVERT: A 64 ASN cc_start: 0.7290 (p0) cc_final: 0.6136 (t0) REVERT: A 199 THR cc_start: 0.8418 (m) cc_final: 0.8077 (p) REVERT: A 205 ASN cc_start: 0.7838 (m-40) cc_final: 0.7603 (m110) REVERT: A 1060 ASN cc_start: 0.7739 (t0) cc_final: 0.7174 (t0) REVERT: A 1150 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: A 1172 LYS cc_start: 0.7503 (mtmt) cc_final: 0.6904 (mttp) REVERT: C 50 LYS cc_start: 0.7015 (mtmm) cc_final: 0.6701 (pttp) REVERT: C 61 GLN cc_start: 0.8168 (tt0) cc_final: 0.7764 (tp-100) REVERT: C 252 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7171 (mt-10) REVERT: E 27 ASP cc_start: 0.8029 (m-30) cc_final: 0.7808 (m-30) REVERT: E 45 ASP cc_start: 0.7792 (p0) cc_final: 0.7536 (p0) REVERT: E 64 ASN cc_start: 0.7375 (p0) cc_final: 0.5989 (t0) REVERT: E 104 ASP cc_start: 0.8067 (m-30) cc_final: 0.7713 (t0) REVERT: E 225 LYS cc_start: 0.7498 (tttm) cc_final: 0.7195 (tttt) REVERT: E 252 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7434 (mt-10) REVERT: E 282 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6296 (p0) REVERT: E 1075 LYS cc_start: 0.8404 (tptt) cc_final: 0.8121 (tptp) REVERT: E 1082 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7534 (ptpp) REVERT: E 1172 LYS cc_start: 0.7434 (mtmt) cc_final: 0.6989 (tmtt) REVERT: G 66 ARG cc_start: 0.7022 (mtp180) cc_final: 0.6784 (mtp180) REVERT: H 31 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7383 (mtp180) REVERT: H 66 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7019 (mtp180) REVERT: H 105 GLN cc_start: 0.7876 (pm20) cc_final: 0.7538 (mt0) REVERT: I 100 GLN cc_start: 0.7503 (mp10) cc_final: 0.7048 (mp10) REVERT: J 31 ARG cc_start: 0.8194 (mpt180) cc_final: 0.7494 (mtp180) REVERT: K 100 GLN cc_start: 0.7472 (mp10) cc_final: 0.6901 (mp10) outliers start: 37 outliers final: 13 residues processed: 265 average time/residue: 0.6134 time to fit residues: 182.5776 Evaluate side-chains 224 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 282 ASP Chi-restraints excluded: chain E residue 1018 MET 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 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 30 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 256 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 ASN E 302 GLN E1026 HIS E1060 ASN ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180869 restraints weight = 16905.199| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.01 r_work: 0.3681 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18033 Z= 0.212 Angle : 0.650 11.711 24540 Z= 0.333 Chirality : 0.046 0.198 2730 Planarity : 0.005 0.052 3114 Dihedral : 8.714 72.560 3100 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.86 % Allowed : 9.75 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2148 helix: 1.52 (0.26), residues: 363 sheet: 0.08 (0.21), residues: 564 loop : -1.18 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 84 TYR 0.025 0.002 TYR J 50 PHE 0.019 0.003 PHE J 97 TRP 0.012 0.002 TRP G 35A HIS 0.009 0.002 HIS E1026 Details of bonding type rmsd covalent geometry : bond 0.00496 (17970) covalent geometry : angle 0.62360 (24378) SS BOND : bond 0.00960 ( 27) SS BOND : angle 1.69070 ( 54) hydrogen bonds : bond 0.04251 ( 630) hydrogen bonds : angle 5.55666 ( 1905) link_ALPHA1-3 : bond 0.01463 ( 3) link_ALPHA1-3 : angle 1.62106 ( 9) link_ALPHA1-6 : bond 0.00409 ( 6) link_ALPHA1-6 : angle 1.87832 ( 18) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 1.33956 ( 27) link_NAG-ASN : bond 0.00250 ( 18) link_NAG-ASN : angle 3.35610 ( 54) *********************** 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 282 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.754 Fit side-chains REVERT: A 115 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 252 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7388 (mp0) REVERT: A 1172 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7334 (mttp) REVERT: C 45 ASP cc_start: 0.8009 (p0) cc_final: 0.7759 (p0) REVERT: C 50 LYS cc_start: 0.7406 (mtmm) cc_final: 0.7148 (pttp) REVERT: C 61 GLN cc_start: 0.8373 (tt0) cc_final: 0.7969 (tp40) REVERT: C 115 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 139 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7153 (mpt180) REVERT: C 252 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 1017 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7354 (tpp) REVERT: E 27 ASP cc_start: 0.8177 (m-30) cc_final: 0.7893 (m-30) REVERT: E 45 ASP cc_start: 0.8002 (p0) cc_final: 0.7657 (p0) REVERT: E 64 ASN cc_start: 0.7634 (p0) cc_final: 0.6310 (t0) REVERT: E 104 ASP cc_start: 0.8131 (m-30) cc_final: 0.7777 (t0) REVERT: E 225 LYS cc_start: 0.7688 (tttm) cc_final: 0.7431 (tttt) REVERT: E 252 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7402 (mp0) REVERT: E 282 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6516 (p0) REVERT: E 1017 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.6400 (ttm) REVERT: E 1060 ASN cc_start: 0.7864 (t0) cc_final: 0.7481 (t0) REVERT: E 1075 LYS cc_start: 0.8464 (tptt) cc_final: 0.8221 (tptp) REVERT: E 1082 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7560 (ptpp) REVERT: E 1150 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: H 31 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: H 105 GLN cc_start: 0.7862 (pm20) cc_final: 0.7582 (mt0) REVERT: I 4 MET cc_start: 0.7917 (tpt) cc_final: 0.7670 (tpt) REVERT: I 100 GLN cc_start: 0.7634 (mp10) cc_final: 0.7078 (mp10) REVERT: J 31 ARG cc_start: 0.8123 (mpt180) cc_final: 0.7540 (mtp180) REVERT: K 100 GLN cc_start: 0.7733 (mp10) cc_final: 0.7160 (mp10) REVERT: L 100 GLN cc_start: 0.7167 (mp10) cc_final: 0.6967 (mp10) outliers start: 54 outliers final: 28 residues processed: 258 average time/residue: 0.6383 time to fit residues: 184.5366 Evaluate side-chains 238 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain E residue 29 VAL 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 1017 MET 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 68 THR 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 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 70 SER 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 110 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 32 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 278 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN E 302 GLN E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.204263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181298 restraints weight = 16973.393| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.10 r_work: 0.3631 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18033 Z= 0.155 Angle : 0.587 10.359 24540 Z= 0.298 Chirality : 0.044 0.211 2730 Planarity : 0.004 0.051 3114 Dihedral : 8.072 67.437 3100 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.81 % Allowed : 12.14 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2148 helix: 1.88 (0.26), residues: 363 sheet: 0.29 (0.21), residues: 561 loop : -1.08 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 61 TYR 0.017 0.002 TYR H 50 PHE 0.015 0.002 PHE A1110 TRP 0.009 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00362 (17970) covalent geometry : angle 0.55983 (24378) SS BOND : bond 0.00615 ( 27) SS BOND : angle 1.67873 ( 54) hydrogen bonds : bond 0.03702 ( 630) hydrogen bonds : angle 5.26105 ( 1905) link_ALPHA1-3 : bond 0.01315 ( 3) link_ALPHA1-3 : angle 1.82886 ( 9) link_ALPHA1-6 : bond 0.00421 ( 6) link_ALPHA1-6 : angle 1.87575 ( 18) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 1.35406 ( 27) link_NAG-ASN : bond 0.00156 ( 18) link_NAG-ASN : angle 3.09052 ( 54) *********************** 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 271 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.721 Fit side-chains REVERT: A 252 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7463 (mp0) REVERT: A 1150 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: A 1172 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7265 (mttp) REVERT: C 50 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7225 (pttp) REVERT: C 61 GLN cc_start: 0.8433 (tt0) cc_final: 0.8018 (tp40) REVERT: C 252 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 1150 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: E 27 ASP cc_start: 0.8119 (m-30) cc_final: 0.7876 (m-30) REVERT: E 45 ASP cc_start: 0.8042 (p0) cc_final: 0.7722 (p0) REVERT: E 53 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7252 (mtp-110) REVERT: E 64 ASN cc_start: 0.7561 (p0) cc_final: 0.6210 (t0) REVERT: E 104 ASP cc_start: 0.8074 (m-30) cc_final: 0.7713 (t0) REVERT: E 225 LYS cc_start: 0.7684 (tttm) cc_final: 0.7422 (tttt) REVERT: E 252 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7437 (mp0) REVERT: E 282 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6525 (p0) REVERT: E 1060 ASN cc_start: 0.7785 (t0) cc_final: 0.7399 (t0) REVERT: E 1075 LYS cc_start: 0.8508 (tptt) cc_final: 0.8251 (tptp) REVERT: E 1077 MET cc_start: 0.8064 (ttm) cc_final: 0.7743 (ttp) REVERT: E 1082 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7589 (ptpp) REVERT: E 1150 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: E 1169 ASN cc_start: 0.6455 (m-40) cc_final: 0.6202 (m110) REVERT: H 31 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7163 (mtp180) REVERT: H 105 GLN cc_start: 0.7830 (pm20) cc_final: 0.7528 (mt0) REVERT: I 100 GLN cc_start: 0.7676 (mp10) cc_final: 0.7069 (mp10) REVERT: J 31 ARG cc_start: 0.8207 (mpt180) cc_final: 0.7582 (mtp180) REVERT: J 105 GLN cc_start: 0.7665 (pm20) cc_final: 0.7380 (mp10) outliers start: 53 outliers final: 33 residues processed: 246 average time/residue: 0.6869 time to fit residues: 188.0705 Evaluate side-chains 241 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 287 LYS 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 161 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1150 GLU 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 292 GLN 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 23 THR 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 31 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 70 SER 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 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 14 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.202722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181293 restraints weight = 16813.625| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.00 r_work: 0.3696 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18033 Z= 0.176 Angle : 0.602 9.306 24540 Z= 0.306 Chirality : 0.044 0.217 2730 Planarity : 0.004 0.050 3114 Dihedral : 7.602 62.022 3100 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.44 % Allowed : 12.61 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2148 helix: 1.74 (0.26), residues: 363 sheet: 0.36 (0.22), residues: 561 loop : -1.06 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.019 0.002 TYR J 50 PHE 0.016 0.002 PHE J 97 TRP 0.010 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00415 (17970) covalent geometry : angle 0.57738 (24378) SS BOND : bond 0.00752 ( 27) SS BOND : angle 1.91943 ( 54) hydrogen bonds : bond 0.03723 ( 630) hydrogen bonds : angle 5.20234 ( 1905) link_ALPHA1-3 : bond 0.01365 ( 3) link_ALPHA1-3 : angle 1.77394 ( 9) link_ALPHA1-6 : bond 0.00450 ( 6) link_ALPHA1-6 : angle 1.78249 ( 18) link_BETA1-4 : bond 0.00385 ( 9) link_BETA1-4 : angle 1.37003 ( 27) link_NAG-ASN : bond 0.00202 ( 18) link_NAG-ASN : angle 2.87359 ( 54) *********************** 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 285 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 0.693 Fit side-chains REVERT: A 252 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7421 (mp0) REVERT: A 282 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.5098 (p0) REVERT: A 1150 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: A 1172 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7288 (mttp) REVERT: C 50 LYS cc_start: 0.7598 (mtmm) cc_final: 0.7324 (pttp) REVERT: C 61 GLN cc_start: 0.8436 (tt0) cc_final: 0.8053 (tp40) REVERT: C 139 ARG cc_start: 0.7536 (mmt180) cc_final: 0.7157 (mpt180) REVERT: C 252 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7383 (mp0) REVERT: C 1017 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7386 (tpp) REVERT: C 1150 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: E 27 ASP cc_start: 0.8022 (m-30) cc_final: 0.7762 (m-30) REVERT: E 45 ASP cc_start: 0.8028 (p0) cc_final: 0.7726 (p0) REVERT: E 64 ASN cc_start: 0.7576 (p0) cc_final: 0.6247 (t0) REVERT: E 104 ASP cc_start: 0.7952 (m-30) cc_final: 0.7599 (t0) REVERT: E 225 LYS cc_start: 0.7675 (tttm) cc_final: 0.7422 (tttt) REVERT: E 252 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7420 (mp0) REVERT: E 282 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6518 (p0) REVERT: E 1017 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6540 (ttm) REVERT: E 1060 ASN cc_start: 0.7839 (t0) cc_final: 0.7502 (t0) REVERT: E 1075 LYS cc_start: 0.8480 (tptt) cc_final: 0.8236 (tptp) REVERT: E 1077 MET cc_start: 0.7936 (ttm) cc_final: 0.7694 (ttp) REVERT: E 1082 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7576 (ptpp) REVERT: E 1150 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: G 31 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: H 31 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7105 (mtp180) REVERT: H 105 GLN cc_start: 0.7630 (pm20) cc_final: 0.7356 (mt0) REVERT: J 31 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7469 (mtp180) outliers start: 65 outliers final: 40 residues processed: 257 average time/residue: 0.6336 time to fit residues: 182.4619 Evaluate side-chains 252 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 282 ASP 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 118 VAL Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1017 MET 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 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 E residue 1017 MET 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 31 ARG 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 212 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 178 GLN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 292 GLN C1060 ASN E 292 GLN E 302 GLN ** E1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 ASN G 3 GLN I 100 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.204318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183711 restraints weight = 16606.484| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 0.94 r_work: 0.3697 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18033 Z= 0.148 Angle : 0.582 9.940 24540 Z= 0.295 Chirality : 0.043 0.230 2730 Planarity : 0.004 0.049 3114 Dihedral : 7.307 58.810 3100 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.02 % Allowed : 14.15 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.17), residues: 2148 helix: 1.87 (0.26), residues: 363 sheet: 0.42 (0.22), residues: 561 loop : -0.97 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.017 0.001 TYR J 50 PHE 0.015 0.002 PHE A1110 TRP 0.009 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00347 (17970) covalent geometry : angle 0.55647 (24378) SS BOND : bond 0.00725 ( 27) SS BOND : angle 2.00917 ( 54) hydrogen bonds : bond 0.03566 ( 630) hydrogen bonds : angle 5.07451 ( 1905) link_ALPHA1-3 : bond 0.01376 ( 3) link_ALPHA1-3 : angle 1.86548 ( 9) link_ALPHA1-6 : bond 0.00457 ( 6) link_ALPHA1-6 : angle 1.72892 ( 18) link_BETA1-4 : bond 0.00413 ( 9) link_BETA1-4 : angle 1.36762 ( 27) link_NAG-ASN : bond 0.00180 ( 18) link_NAG-ASN : angle 2.73877 ( 54) *********************** 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 267 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.726 Fit side-chains REVERT: A 252 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7449 (mp0) REVERT: A 1150 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: A 1172 LYS cc_start: 0.7666 (mtmt) cc_final: 0.7316 (mttp) REVERT: C 50 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7350 (pttp) REVERT: C 61 GLN cc_start: 0.8493 (tt0) cc_final: 0.8118 (tp40) REVERT: C 139 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7231 (mpt180) REVERT: C 252 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7416 (mp0) REVERT: C 292 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7534 (mm110) REVERT: E 27 ASP cc_start: 0.8036 (m-30) cc_final: 0.7786 (m-30) REVERT: E 45 ASP cc_start: 0.8054 (p0) cc_final: 0.7739 (p0) REVERT: E 64 ASN cc_start: 0.7546 (p0) cc_final: 0.6249 (t0) REVERT: E 104 ASP cc_start: 0.7985 (m-30) cc_final: 0.7629 (t0) REVERT: E 225 LYS cc_start: 0.7674 (tttm) cc_final: 0.7431 (tttt) REVERT: E 252 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7416 (mp0) REVERT: E 282 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6591 (p0) REVERT: E 1018 MET cc_start: 0.8186 (ptp) cc_final: 0.7922 (ptm) REVERT: E 1060 ASN cc_start: 0.7848 (t0) cc_final: 0.7484 (t0) REVERT: E 1075 LYS cc_start: 0.8482 (tptt) cc_final: 0.8244 (tptp) REVERT: E 1077 MET cc_start: 0.7886 (ttm) cc_final: 0.7686 (ttp) REVERT: E 1082 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7609 (ptpp) REVERT: E 1150 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: G 31 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7206 (mtp180) REVERT: H 31 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7140 (mtp180) REVERT: I 100 GLN cc_start: 0.7360 (mp10) cc_final: 0.7094 (mp-120) REVERT: J 31 ARG cc_start: 0.8111 (mpt180) cc_final: 0.7470 (mtp180) outliers start: 57 outliers final: 41 residues processed: 243 average time/residue: 0.6623 time to fit residues: 179.7649 Evaluate side-chains 243 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 275 ILE 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 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 31 ARG 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 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 19 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN C1125 GLN ** 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** G 3 GLN K 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.200005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.177559 restraints weight = 16798.028| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.04 r_work: 0.3602 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18033 Z= 0.252 Angle : 0.678 10.157 24540 Z= 0.346 Chirality : 0.047 0.249 2730 Planarity : 0.005 0.050 3114 Dihedral : 7.395 58.266 3100 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.87 % Allowed : 13.94 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2148 helix: 1.44 (0.26), residues: 363 sheet: 0.35 (0.22), residues: 552 loop : -0.96 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 317 TYR 0.021 0.002 TYR J 50 PHE 0.022 0.003 PHE J 97 TRP 0.009 0.002 TRP G 35A HIS 0.010 0.002 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00604 (17970) covalent geometry : angle 0.65397 (24378) SS BOND : bond 0.00995 ( 27) SS BOND : angle 2.27786 ( 54) hydrogen bonds : bond 0.04029 ( 630) hydrogen bonds : angle 5.35364 ( 1905) link_ALPHA1-3 : bond 0.01628 ( 3) link_ALPHA1-3 : angle 2.00481 ( 9) link_ALPHA1-6 : bond 0.00453 ( 6) link_ALPHA1-6 : angle 1.76014 ( 18) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 1.47727 ( 27) link_NAG-ASN : bond 0.00264 ( 18) link_NAG-ASN : angle 2.83679 ( 54) *********************** 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 289 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.689 Fit side-chains REVERT: A 61 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7413 (tp-100) REVERT: A 78 GLU cc_start: 0.7487 (tp30) cc_final: 0.7206 (tp30) REVERT: A 181 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: A 244 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 252 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7475 (mp0) REVERT: A 1017 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.6814 (tpp) REVERT: A 1150 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: A 1172 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7115 (mttp) REVERT: C 50 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7374 (pttp) REVERT: C 61 GLN cc_start: 0.8536 (tt0) cc_final: 0.8163 (tp40) REVERT: C 252 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7471 (mp0) REVERT: C 278 ASN cc_start: 0.8615 (m-40) cc_final: 0.8402 (m-40) REVERT: C 1150 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: E 27 ASP cc_start: 0.8128 (m-30) cc_final: 0.7834 (m-30) REVERT: E 45 ASP cc_start: 0.8094 (p0) cc_final: 0.7840 (p0) REVERT: E 64 ASN cc_start: 0.7557 (p0) cc_final: 0.6223 (t0) REVERT: E 104 ASP cc_start: 0.8108 (m-30) cc_final: 0.7752 (t0) REVERT: E 196 ASP cc_start: 0.7834 (m-30) cc_final: 0.7415 (m-30) REVERT: E 225 LYS cc_start: 0.7640 (tttm) cc_final: 0.7420 (tttt) REVERT: E 252 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 1017 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.6762 (ttm) REVERT: E 1018 MET cc_start: 0.8343 (ptp) cc_final: 0.8119 (ptm) REVERT: E 1060 ASN cc_start: 0.7811 (t0) cc_final: 0.7509 (t0) REVERT: E 1075 LYS cc_start: 0.8507 (tptt) cc_final: 0.8246 (tptp) REVERT: E 1082 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7569 (ptpp) REVERT: E 1121 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7478 (mttt) REVERT: E 1150 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: G 31 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7191 (mtp180) REVERT: H 31 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7100 (mtp180) REVERT: H 105 GLN cc_start: 0.7639 (pm20) cc_final: 0.7379 (mt0) REVERT: I 100 GLN cc_start: 0.7366 (mp10) cc_final: 0.6817 (mp10) REVERT: J 31 ARG cc_start: 0.8207 (mpt180) cc_final: 0.7480 (mtp180) REVERT: K 100 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7402 (mp-120) outliers start: 73 outliers final: 46 residues processed: 260 average time/residue: 0.6395 time to fit residues: 185.5984 Evaluate side-chains 254 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN 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 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 1066 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1150 GLU 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 275 ILE 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 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 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 30 SER Chi-restraints excluded: chain G residue 31 ARG 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 G residue 108 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 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 74 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 ASN G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.199037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168012 restraints weight = 17061.340| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.52 r_work: 0.3503 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18033 Z= 0.151 Angle : 0.601 11.315 24540 Z= 0.305 Chirality : 0.044 0.292 2730 Planarity : 0.004 0.050 3114 Dihedral : 7.023 57.227 3100 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.70 % Allowed : 15.63 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.17), residues: 2148 helix: 1.75 (0.26), residues: 363 sheet: 0.42 (0.22), residues: 555 loop : -0.90 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 61 TYR 0.016 0.001 TYR H 50 PHE 0.016 0.002 PHE A1110 TRP 0.009 0.001 TRP E1092 HIS 0.011 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00351 (17970) covalent geometry : angle 0.57447 (24378) SS BOND : bond 0.00919 ( 27) SS BOND : angle 2.37545 ( 54) hydrogen bonds : bond 0.03590 ( 630) hydrogen bonds : angle 5.08960 ( 1905) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 1.87195 ( 9) link_ALPHA1-6 : bond 0.00500 ( 6) link_ALPHA1-6 : angle 1.62047 ( 18) link_BETA1-4 : bond 0.00422 ( 9) link_BETA1-4 : angle 1.37806 ( 27) link_NAG-ASN : bond 0.00183 ( 18) link_NAG-ASN : angle 2.67833 ( 54) *********************** 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 260 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.732 Fit side-chains REVERT: A 244 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 252 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 1150 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: A 1172 LYS cc_start: 0.7427 (mtmt) cc_final: 0.6718 (mttp) REVERT: C 45 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7571 (p0) REVERT: C 50 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7202 (pttp) REVERT: C 61 GLN cc_start: 0.8584 (tt0) cc_final: 0.8186 (tp40) REVERT: C 139 ARG cc_start: 0.7501 (mmt180) cc_final: 0.7125 (mpt180) REVERT: C 252 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7520 (mp0) REVERT: C 278 ASN cc_start: 0.8710 (m-40) cc_final: 0.8457 (m-40) REVERT: C 1150 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: E 27 ASP cc_start: 0.8218 (m-30) cc_final: 0.7932 (m-30) REVERT: E 45 ASP cc_start: 0.8118 (p0) cc_final: 0.7813 (p0) REVERT: E 53 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7280 (mtp-110) REVERT: E 64 ASN cc_start: 0.7389 (p0) cc_final: 0.5974 (t0) REVERT: E 104 ASP cc_start: 0.8139 (m-30) cc_final: 0.7778 (t0) REVERT: E 196 ASP cc_start: 0.7708 (m-30) cc_final: 0.7241 (m-30) REVERT: E 225 LYS cc_start: 0.7517 (tttm) cc_final: 0.7150 (tttt) REVERT: E 252 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7683 (mt-10) REVERT: E 1018 MET cc_start: 0.8249 (ptp) cc_final: 0.7985 (ptm) REVERT: E 1060 ASN cc_start: 0.7901 (t0) cc_final: 0.7585 (t0) REVERT: E 1075 LYS cc_start: 0.8525 (tptt) cc_final: 0.8222 (tptp) REVERT: E 1082 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7525 (ptpp) REVERT: E 1131 LYS cc_start: 0.6589 (tttt) cc_final: 0.6191 (ptmm) REVERT: E 1150 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: E 1172 LYS cc_start: 0.7428 (mtmt) cc_final: 0.6993 (tmtt) REVERT: H 31 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7037 (mtp180) REVERT: I 100 GLN cc_start: 0.7349 (mp10) cc_final: 0.6816 (mp10) REVERT: J 31 ARG cc_start: 0.8243 (mpt180) cc_final: 0.7331 (mtp180) REVERT: K 100 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7207 (mp-120) outliers start: 51 outliers final: 38 residues processed: 241 average time/residue: 0.6967 time to fit residues: 186.3905 Evaluate side-chains 245 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 275 ILE Chi-restraints excluded: chain A residue 319 THR 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 A residue 1152 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 275 ILE 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 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 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 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 70 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 74 THR 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 K residue 45 GLN Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** A 302 GLN C 292 GLN C1060 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 = 0.4255 r_free = 0.4255 target = 0.201047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170312 restraints weight = 17116.450| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.53 r_work: 0.3552 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18033 Z= 0.116 Angle : 0.559 8.372 24540 Z= 0.283 Chirality : 0.042 0.282 2730 Planarity : 0.004 0.049 3114 Dihedral : 6.508 54.551 3100 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.17 % Allowed : 16.53 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2148 helix: 2.05 (0.26), residues: 363 sheet: 0.45 (0.22), residues: 531 loop : -0.80 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 131 TYR 0.014 0.001 TYR H 50 PHE 0.016 0.001 PHE A1110 TRP 0.011 0.001 TRP G 35A HIS 0.012 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00265 (17970) covalent geometry : angle 0.53669 (24378) SS BOND : bond 0.00799 ( 27) SS BOND : angle 2.02711 ( 54) hydrogen bonds : bond 0.03350 ( 630) hydrogen bonds : angle 4.83697 ( 1905) link_ALPHA1-3 : bond 0.01193 ( 3) link_ALPHA1-3 : angle 1.83554 ( 9) link_ALPHA1-6 : bond 0.00632 ( 6) link_ALPHA1-6 : angle 1.50600 ( 18) link_BETA1-4 : bond 0.00468 ( 9) link_BETA1-4 : angle 1.32841 ( 27) link_NAG-ASN : bond 0.00143 ( 18) link_NAG-ASN : angle 2.37878 ( 54) *********************** 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 262 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.831 Fit side-chains REVERT: A 50 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7403 (mtmm) REVERT: A 199 THR cc_start: 0.8494 (m) cc_final: 0.8126 (p) REVERT: A 244 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 252 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7485 (mp0) REVERT: A 282 ASP cc_start: 0.5518 (p0) cc_final: 0.4877 (p0) REVERT: A 1150 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: A 1172 LYS cc_start: 0.7357 (mtmt) cc_final: 0.6647 (mttp) REVERT: C 50 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7197 (pttp) REVERT: C 61 GLN cc_start: 0.8566 (tt0) cc_final: 0.8163 (tp40) REVERT: C 139 ARG cc_start: 0.7544 (mmt180) cc_final: 0.7131 (mpt180) REVERT: C 252 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7479 (mp0) REVERT: C 278 ASN cc_start: 0.8692 (m-40) cc_final: 0.8462 (m-40) REVERT: E 27 ASP cc_start: 0.8063 (m-30) cc_final: 0.7813 (m-30) REVERT: E 45 ASP cc_start: 0.8070 (p0) cc_final: 0.7771 (p0) REVERT: E 64 ASN cc_start: 0.7373 (p0) cc_final: 0.5950 (t0) REVERT: E 104 ASP cc_start: 0.8064 (m-30) cc_final: 0.7703 (t0) REVERT: E 196 ASP cc_start: 0.7832 (m-30) cc_final: 0.7378 (m-30) REVERT: E 225 LYS cc_start: 0.7506 (tttm) cc_final: 0.7166 (tttt) REVERT: E 252 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 1018 MET cc_start: 0.8233 (ptp) cc_final: 0.8003 (ptm) REVERT: E 1060 ASN cc_start: 0.7685 (t0) cc_final: 0.7370 (t0) REVERT: E 1075 LYS cc_start: 0.8501 (tptt) cc_final: 0.8182 (tptp) REVERT: E 1082 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7539 (ptpp) REVERT: E 1131 LYS cc_start: 0.6541 (tttt) cc_final: 0.6153 (ptmm) REVERT: E 1149 MET cc_start: 0.7624 (mmt) cc_final: 0.7358 (mmp) REVERT: E 1150 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.5766 (mp0) REVERT: E 1172 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7035 (tmtt) REVERT: H 31 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7034 (mtp180) REVERT: I 100 GLN cc_start: 0.7339 (mp10) cc_final: 0.6815 (mp10) REVERT: J 31 ARG cc_start: 0.8197 (mpt180) cc_final: 0.7199 (mtp180) REVERT: K 100 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7227 (mp-120) outliers start: 41 outliers final: 30 residues processed: 245 average time/residue: 0.6968 time to fit residues: 189.6842 Evaluate side-chains 233 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 275 ILE 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 A residue 1152 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain E residue 214 ASN 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 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 29 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 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 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 191 optimal weight: 0.0470 chunk 178 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 186 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- 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 ** A1026 HIS ** 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** J 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.195985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164756 restraints weight = 16954.292| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.55 r_work: 0.3489 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18033 Z= 0.239 Angle : 0.674 13.076 24540 Z= 0.342 Chirality : 0.047 0.317 2730 Planarity : 0.005 0.049 3114 Dihedral : 6.750 55.605 3100 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.33 % Allowed : 16.85 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2148 helix: 1.66 (0.26), residues: 363 sheet: 0.44 (0.22), residues: 567 loop : -0.88 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.021 0.002 TYR J 50 PHE 0.021 0.002 PHE J 97 TRP 0.008 0.002 TRP G 35A HIS 0.011 0.002 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00575 (17970) covalent geometry : angle 0.64947 (24378) SS BOND : bond 0.01068 ( 27) SS BOND : angle 2.67092 ( 54) hydrogen bonds : bond 0.03933 ( 630) hydrogen bonds : angle 5.19393 ( 1905) link_ALPHA1-3 : bond 0.01302 ( 3) link_ALPHA1-3 : angle 1.97106 ( 9) link_ALPHA1-6 : bond 0.00622 ( 6) link_ALPHA1-6 : angle 1.52412 ( 18) link_BETA1-4 : bond 0.00403 ( 9) link_BETA1-4 : angle 1.41877 ( 27) link_NAG-ASN : bond 0.00237 ( 18) link_NAG-ASN : angle 2.52517 ( 54) ********************** 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 243 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.617 Fit side-chains REVERT: A 50 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7474 (mtmm) REVERT: A 244 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 252 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 278 ASN cc_start: 0.8559 (m110) cc_final: 0.8354 (m-40) REVERT: A 282 ASP cc_start: 0.5657 (p0) cc_final: 0.5176 (p0) REVERT: A 1150 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: A 1172 LYS cc_start: 0.7363 (mtmt) cc_final: 0.6729 (mttp) REVERT: C 50 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7461 (ptpp) REVERT: C 61 GLN cc_start: 0.8627 (tt0) cc_final: 0.8219 (tp40) REVERT: C 139 ARG cc_start: 0.7521 (mmt180) cc_final: 0.7138 (mpt180) REVERT: C 181 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: C 252 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7494 (mp0) REVERT: C 278 ASN cc_start: 0.8698 (m-40) cc_final: 0.8466 (m-40) REVERT: E 27 ASP cc_start: 0.8207 (m-30) cc_final: 0.7920 (m-30) REVERT: E 45 ASP cc_start: 0.8085 (p0) cc_final: 0.7806 (p0) REVERT: E 64 ASN cc_start: 0.7420 (p0) cc_final: 0.6075 (t0) REVERT: E 104 ASP cc_start: 0.8158 (m-30) cc_final: 0.7801 (t0) REVERT: E 196 ASP cc_start: 0.7925 (m-30) cc_final: 0.7460 (m-30) REVERT: E 225 LYS cc_start: 0.7507 (tttm) cc_final: 0.7203 (tttt) REVERT: E 252 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7665 (mt-10) REVERT: E 1018 MET cc_start: 0.8368 (ptp) cc_final: 0.8093 (ptm) REVERT: E 1060 ASN cc_start: 0.7736 (t0) cc_final: 0.7465 (t0) REVERT: E 1075 LYS cc_start: 0.8561 (tptt) cc_final: 0.8244 (tptp) REVERT: E 1082 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7518 (ptpp) REVERT: E 1131 LYS cc_start: 0.6497 (tttt) cc_final: 0.6212 (ptmm) REVERT: E 1150 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: G 100 GLU cc_start: 0.8033 (mp0) cc_final: 0.7126 (tm-30) REVERT: H 31 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6997 (mtp180) REVERT: I 100 GLN cc_start: 0.7361 (mp10) cc_final: 0.6971 (mp-120) REVERT: J 31 ARG cc_start: 0.8228 (mpt180) cc_final: 0.7304 (mtp180) REVERT: K 100 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7127 (mp-120) outliers start: 44 outliers final: 38 residues processed: 231 average time/residue: 0.6628 time to fit residues: 170.6506 Evaluate side-chains 234 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 275 ILE 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 118 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain E residue 142 THR 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 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 70 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 74 THR 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 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 93 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 201 optimal weight: 0.3980 chunk 181 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** A 302 GLN A1060 ASN C 292 GLN C1060 ASN ** E 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1026 HIS ** E1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170687 restraints weight = 17089.462| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.49 r_work: 0.3550 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18033 Z= 0.124 Angle : 0.583 10.474 24540 Z= 0.295 Chirality : 0.043 0.281 2730 Planarity : 0.004 0.053 3114 Dihedral : 6.386 54.740 3100 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.38 % Allowed : 17.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.17), residues: 2148 helix: 2.00 (0.26), residues: 363 sheet: 0.47 (0.22), residues: 531 loop : -0.81 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.014 0.001 TYR H 50 PHE 0.016 0.001 PHE A1110 TRP 0.010 0.001 TRP C1092 HIS 0.012 0.001 HIS A1026 Details of bonding type rmsd covalent geometry : bond 0.00288 (17970) covalent geometry : angle 0.55838 (24378) SS BOND : bond 0.00789 ( 27) SS BOND : angle 2.36185 ( 54) hydrogen bonds : bond 0.03451 ( 630) hydrogen bonds : angle 4.89175 ( 1905) link_ALPHA1-3 : bond 0.01215 ( 3) link_ALPHA1-3 : angle 1.91410 ( 9) link_ALPHA1-6 : bond 0.00720 ( 6) link_ALPHA1-6 : angle 1.44573 ( 18) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.34438 ( 27) link_NAG-ASN : bond 0.00150 ( 18) link_NAG-ASN : angle 2.39968 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5471.05 seconds wall clock time: 94 minutes 30.24 seconds (5670.24 seconds total)