Starting phenix.real_space_refine on Thu Sep 18 14:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu6_44901/09_2025/9bu6_44901.map" } resolution = 3.65 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= 0.044 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 93 5.16 5 C 10842 2.51 5 N 3069 2.21 5 O 3435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s 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: 17439 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "B" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2465 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 14, 'TRANS': 307} Chain: "D" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1390 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2465 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 14, 'TRANS': 307} Chain: "H" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1390 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "I" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "J" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "K" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2465 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 14, 'TRANS': 307} Chain: "L" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1390 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.39, per 1000 atoms: 0.25 Number of scatterers: 17439 At special positions: 0 Unit cell: (137.541, 146.205, 153.786, 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 93 16.00 O 3435 8.00 N 3069 7.00 C 10842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS H 137 " distance=2.04 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.04 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS L 137 " distance=2.04 Simple disulfide: pdb=" SG CYS K 52 " - pdb=" SG CYS K 277 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 76 " distance=2.03 Simple disulfide: pdb=" SG CYS K 97 " - pdb=" SG CYS K 139 " distance=2.03 Simple disulfide: pdb=" SG CYS K 281 " - pdb=" SG CYS K 305 " distance=2.03 Simple disulfide: pdb=" SG CYS L 144 " - pdb=" SG CYS L 148 " distance=2.03 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG D 301 " - " ASN D 154 " " NAG H 301 " - " ASN H 154 " " NAG L 301 " - " ASN L 154 " " NAG M 1 " - " ASN C 38 " " NAG N 1 " - " ASN C 242 " " NAG O 1 " - " ASN D 82 " " NAG P 1 " - " ASN G 38 " " NAG Q 1 " - " ASN G 242 " " NAG R 1 " - " ASN H 82 " " NAG S 1 " - " ASN K 38 " " NAG T 1 " - " ASN K 242 " " NAG U 1 " - " ASN L 82 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 749.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 49 sheets defined 19.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 100C through 100G Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.722A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.715A pdb=" N MET C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 70 " --> pdb=" O PRO C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 115 removed outlier: 3.569A pdb=" N LYS C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 115 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 37 through 50 removed outlier: 4.138A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.918A pdb=" N VAL D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.615A pdb=" N SER D 151 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.674A pdb=" N GLN D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.784A pdb=" N LEU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 100C through 100G Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.606A pdb=" N ASP F 82 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'G' and resid 65 through 72 removed outlier: 3.827A pdb=" N MET G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 71 " --> pdb=" O ILE G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 104 through 115 removed outlier: 3.655A pdb=" N LYS G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.678A pdb=" N ASP G 193 " --> pdb=" O GLN G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.518A pdb=" N GLN H 42 " --> pdb=" O TYR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 51 No H-bonds generated for 'chain 'H' and resid 50 through 51' Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.514A pdb=" N VAL H 56 " --> pdb=" O ASN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 127 removed outlier: 3.891A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP H 86 " --> pdb=" O ASN H 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS H 106 " --> pdb=" O MET H 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 116 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.568A pdb=" N SER H 151 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 161 removed outlier: 3.789A pdb=" N GLN H 161 " --> pdb=" O ASP H 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 158 through 161' Processing helix chain 'H' and resid 162 through 171 removed outlier: 3.844A pdb=" N LEU H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN H 169 " --> pdb=" O GLU H 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100G Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.678A pdb=" N ASP J 82 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'K' and resid 65 through 70 removed outlier: 3.772A pdb=" N MET K 69 " --> pdb=" O HIS K 65 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU K 70 " --> pdb=" O PRO K 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 65 through 70' Processing helix chain 'K' and resid 73 through 77 Processing helix chain 'K' and resid 104 through 115 removed outlier: 3.680A pdb=" N LYS K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 195 removed outlier: 3.524A pdb=" N LYS K 191 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP K 193 " --> pdb=" O GLN K 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 50 removed outlier: 4.037A pdb=" N GLY L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 56 Processing helix chain 'L' and resid 74 through 127 removed outlier: 3.941A pdb=" N VAL L 80 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 92 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR L 94 " --> pdb=" O ASP L 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS L 106 " --> pdb=" O MET L 102 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 116 " --> pdb=" O ASP L 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 155 Processing helix chain 'L' and resid 158 through 161 removed outlier: 3.857A pdb=" N GLN L 161 " --> pdb=" O ASP L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 162 through 171 removed outlier: 3.833A pdb=" N LEU L 168 " --> pdb=" O GLU L 164 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN L 169 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.644A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.345A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.597A pdb=" N ILE B 75 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.512A pdb=" N ARG B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.835A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 35 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 27 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.752A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.615A pdb=" N LYS C 59 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.537A pdb=" N GLY C 82 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.748A pdb=" N ALA C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N TRP C 234 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N MET C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.915A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.587A pdb=" N ASN C 211 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.605A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.533A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.331A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.508A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 75 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.510A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 36 removed outlier: 3.696A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS H 26 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 35 " --> pdb=" O PHE H 24 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY G 16 " --> pdb=" O GLY H 23 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 27 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU H 131 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 24 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 52 removed outlier: 5.708A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.553A pdb=" N LYS G 59 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 82 through 83 removed outlier: 3.771A pdb=" N GLY G 82 " --> pdb=" O ILE G 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.708A pdb=" N ALA G 101 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N TRP G 234 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG G 229 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N MET G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY G 181 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'G' and resid 136 through 141 removed outlier: 4.588A pdb=" N CYS G 139 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER G 146 " --> pdb=" O CYS G 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.595A pdb=" N ASN G 211 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 286 through 288 removed outlier: 3.557A pdb=" N ILE G 288 " --> pdb=" O CYS G 281 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.932A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.533A pdb=" N ALA J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE J 75 " --> pdb=" O ALA J 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.568A pdb=" N ARG J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 32 through 36 removed outlier: 3.695A pdb=" N GLY L 33 " --> pdb=" O HIS L 26 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS L 26 " --> pdb=" O GLY L 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY K 16 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN L 27 " --> pdb=" O LYS K 12 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 24 through 26 Processing sheet with id=AE4, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AE5, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AE6, first strand: chain 'K' and resid 51 through 52 removed outlier: 5.815A pdb=" N LEU K 51 " --> pdb=" O ASP K 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.603A pdb=" N LYS K 59 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU K 87 " --> pdb=" O ILE K 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'K' and resid 82 through 83 removed outlier: 3.552A pdb=" N GLY K 82 " --> pdb=" O ILE K 118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.796A pdb=" N ALA K 101 " --> pdb=" O PHE K 232 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N TRP K 234 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG K 229 " --> pdb=" O HIS K 184 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N MET K 179 " --> pdb=" O PRO K 254 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 181 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 130 through 131 Processing sheet with id=AF2, first strand: chain 'K' and resid 136 through 141 removed outlier: 3.558A pdb=" N SER K 146 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA K 138 " --> pdb=" O GLY K 144 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N GLY K 144 " --> pdb=" O ALA K 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 164 through 169 removed outlier: 3.551A pdb=" N ILE K 243 " --> pdb=" O TYR K 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN K 211 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 286 through 288 removed outlier: 3.696A pdb=" N ILE K 288 " --> pdb=" O CYS K 281 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS K 281 " --> pdb=" O ILE K 288 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1365 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: 3.37 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5826 1.35 - 1.48: 4520 1.48 - 1.61: 7318 1.61 - 1.74: 0 1.74 - 1.87: 138 Bond restraints: 17802 Sorted by residual: bond pdb=" N TRP I 100B" pdb=" CA TRP I 100B" ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.43e+00 bond pdb=" N GLY L 31 " pdb=" CA GLY L 31 " ideal model delta sigma weight residual 1.448 1.478 -0.030 1.05e-02 9.07e+03 8.38e+00 bond pdb=" N ILE I 97 " pdb=" CA ILE I 97 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.15e-02 7.56e+03 8.26e+00 bond pdb=" CA THR L 32 " pdb=" C THR L 32 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.35e-02 5.49e+03 7.82e+00 bond pdb=" N GLY L 33 " pdb=" CA GLY L 33 " ideal model delta sigma weight residual 1.448 1.476 -0.028 1.05e-02 9.07e+03 7.22e+00 ... (remaining 17797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 23961 3.01 - 6.02: 128 6.02 - 9.03: 9 9.03 - 12.04: 2 12.04 - 15.05: 2 Bond angle restraints: 24102 Sorted by residual: angle pdb=" N THR H 32 " pdb=" CA THR H 32 " pdb=" CB THR H 32 " ideal model delta sigma weight residual 111.56 126.61 -15.05 1.55e+00 4.16e-01 9.43e+01 angle pdb=" N THR H 32 " pdb=" CA THR H 32 " pdb=" C THR H 32 " ideal model delta sigma weight residual 108.79 94.88 13.91 1.53e+00 4.27e-01 8.26e+01 angle pdb=" N ASN E 100A" pdb=" CA ASN E 100A" pdb=" C ASN E 100A" ideal model delta sigma weight residual 110.88 119.93 -9.05 1.28e+00 6.10e-01 5.00e+01 angle pdb=" CA ASN E 100A" pdb=" C ASN E 100A" pdb=" O ASN E 100A" ideal model delta sigma weight residual 121.32 114.24 7.08 1.16e+00 7.43e-01 3.72e+01 angle pdb=" CA GLY L 33 " pdb=" C GLY L 33 " pdb=" O GLY L 33 " ideal model delta sigma weight residual 121.75 116.43 5.32 1.02e+00 9.61e-01 2.73e+01 ... (remaining 24097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9548 18.01 - 36.01: 998 36.01 - 54.02: 243 54.02 - 72.02: 55 72.02 - 90.03: 31 Dihedral angle restraints: 10875 sinusoidal: 4668 harmonic: 6207 Sorted by residual: dihedral pdb=" CB CYS G 64 " pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " pdb=" CB CYS G 76 " ideal model delta sinusoidal sigma weight residual 93.00 24.94 68.06 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual 93.00 31.61 61.39 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS K 64 " pdb=" SG CYS K 64 " pdb=" SG CYS K 76 " pdb=" CB CYS K 76 " ideal model delta sinusoidal sigma weight residual 93.00 33.12 59.88 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 10872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2416 0.071 - 0.142: 233 0.142 - 0.213: 7 0.213 - 0.284: 0 0.284 - 0.355: 2 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN D 82 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN H 82 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN H 82 " pdb=" N ASN H 82 " pdb=" C ASN H 82 " pdb=" CB ASN H 82 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2655 not shown) Planarity restraints: 3135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 53 " -0.569 9.50e-02 1.11e+02 2.55e-01 4.00e+01 pdb=" NE ARG F 53 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 53 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 53 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 53 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 54 " -0.344 9.50e-02 1.11e+02 1.54e-01 1.47e+01 pdb=" NE ARG F 54 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG F 54 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 54 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 54 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 100 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLY E 100 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY E 100 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN E 100A" 0.018 2.00e-02 2.50e+03 ... (remaining 3132 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 94 2.50 - 3.10: 12309 3.10 - 3.70: 23670 3.70 - 4.30: 34705 4.30 - 4.90: 61216 Nonbonded interactions: 131994 Sorted by model distance: nonbonded pdb=" OH TYR L 119 " pdb=" OE1 GLU L 132 " model vdw 1.900 3.040 nonbonded pdb=" O3 NAG O 1 " pdb=" O7 NAG O 1 " model vdw 1.992 3.040 nonbonded pdb=" O3 NAG R 1 " pdb=" O7 NAG R 1 " model vdw 2.022 3.040 nonbonded pdb=" N GLN A 1 " pdb=" OE1 GLN A 1 " model vdw 2.073 3.120 nonbonded pdb=" OD2 ASP L 37 " pdb=" OG SER L 40 " model vdw 2.087 3.040 ... (remaining 131989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.400 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.004 0.064 17850 Z= 0.178 Angle : 0.659 15.682 24222 Z= 0.367 Chirality : 0.043 0.355 2658 Planarity : 0.007 0.255 3123 Dihedral : 15.967 90.030 6861 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.96 % Favored : 95.76 % Rotamer: Outliers : 2.88 % Allowed : 14.12 % Favored : 83.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.50 (0.17), residues: 2169 helix: -1.46 (0.29), residues: 306 sheet: -1.07 (0.22), residues: 555 loop : -0.77 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 53 TYR 0.009 0.001 TYR B 32 PHE 0.012 0.001 PHE J 71 TRP 0.019 0.001 TRP I 100B HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00355 (17802) covalent geometry : angle 0.61629 (24102) SS BOND : bond 0.00452 ( 24) SS BOND : angle 1.67991 ( 48) hydrogen bonds : bond 0.28406 ( 531) hydrogen bonds : angle 8.97450 ( 1365) link_BETA1-4 : bond 0.00773 ( 12) link_BETA1-4 : angle 2.13277 ( 36) link_NAG-ASN : bond 0.00653 ( 12) link_NAG-ASN : angle 5.47732 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 337 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 54 LYS cc_start: 0.8267 (tppt) cc_final: 0.7847 (tptp) REVERT: C 85 ASP cc_start: 0.8555 (t0) cc_final: 0.7810 (t0) REVERT: D 17 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8254 (tpt) REVERT: D 102 MET cc_start: 0.8555 (mtm) cc_final: 0.8326 (mtt) REVERT: E 77 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8961 (p) REVERT: G 49 ASN cc_start: 0.7871 (m-40) cc_final: 0.7650 (t0) REVERT: G 54 LYS cc_start: 0.8109 (tppt) cc_final: 0.7736 (tttm) REVERT: G 85 ASP cc_start: 0.8395 (t0) cc_final: 0.7899 (t0) REVERT: H 67 GLU cc_start: 0.8750 (pp20) cc_final: 0.8080 (pt0) REVERT: I 77 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8805 (p) REVERT: K 54 LYS cc_start: 0.8334 (tppt) cc_final: 0.7801 (tptp) REVERT: K 85 ASP cc_start: 0.8676 (t0) cc_final: 0.8008 (t0) outliers start: 53 outliers final: 23 residues processed: 370 average time/residue: 0.1444 time to fit residues: 79.9858 Evaluate side-chains 272 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 231 ASP Chi-restraints excluded: chain K residue 301 THR 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: 0.3980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 overall best weight: 2.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN C 184 HIS C 247 HIS D 26 HIS D 125 GLN E 100AASN E 105 GLN G 145 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN G 247 HIS G 304 GLN H 26 HIS H 125 GLN I 61 GLN ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 HIS K 247 HIS K 276AASN K 304 GLN L 26 HIS L 79 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147612 restraints weight = 23444.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.150977 restraints weight = 15519.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153265 restraints weight = 11794.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154865 restraints weight = 9807.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155971 restraints weight = 8573.563| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17850 Z= 0.285 Angle : 0.782 19.839 24222 Z= 0.410 Chirality : 0.051 0.378 2658 Planarity : 0.005 0.043 3123 Dihedral : 7.217 58.260 2929 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.03 % Favored : 94.70 % Rotamer: Outliers : 4.07 % Allowed : 17.32 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.18), residues: 2169 helix: -0.70 (0.29), residues: 294 sheet: -0.84 (0.23), residues: 543 loop : -0.90 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 90 TYR 0.024 0.003 TYR B 36 PHE 0.019 0.002 PHE K 161 TRP 0.023 0.002 TRP E 100B HIS 0.010 0.002 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00691 (17802) covalent geometry : angle 0.74076 (24102) SS BOND : bond 0.00709 ( 24) SS BOND : angle 1.91715 ( 48) hydrogen bonds : bond 0.07804 ( 531) hydrogen bonds : angle 5.92261 ( 1365) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.58929 ( 36) link_NAG-ASN : bond 0.00394 ( 12) link_NAG-ASN : angle 6.01752 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 238 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 THR cc_start: 0.8777 (m) cc_final: 0.8346 (p) REVERT: C 54 LYS cc_start: 0.8468 (tppt) cc_final: 0.8046 (tptm) REVERT: C 85 ASP cc_start: 0.8864 (t0) cc_final: 0.8152 (t0) REVERT: D 147 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7855 (t) REVERT: E 50 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.7823 (p90) REVERT: G 49 ASN cc_start: 0.8385 (m-40) cc_final: 0.7999 (t0) REVERT: G 54 LYS cc_start: 0.8497 (tppt) cc_final: 0.8126 (tttm) REVERT: G 85 ASP cc_start: 0.8652 (t0) cc_final: 0.8125 (t0) REVERT: H 67 GLU cc_start: 0.9007 (pp20) cc_final: 0.8314 (pt0) REVERT: H 150 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7628 (tm-30) REVERT: H 155 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8773 (t0) REVERT: I 110 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8379 (p) REVERT: J 103 LYS cc_start: 0.7464 (tttt) cc_final: 0.7224 (tptm) REVERT: K 31 ASN cc_start: 0.7816 (t0) cc_final: 0.7501 (m-40) REVERT: K 54 LYS cc_start: 0.8494 (tppt) cc_final: 0.8029 (tttm) REVERT: K 85 ASP cc_start: 0.8837 (t0) cc_final: 0.8117 (t0) REVERT: L 38 TYR cc_start: 0.7217 (t80) cc_final: 0.6699 (m-80) REVERT: L 158 ASP cc_start: 0.8117 (t0) cc_final: 0.7701 (t0) outliers start: 75 outliers final: 45 residues processed: 301 average time/residue: 0.1366 time to fit residues: 62.9566 Evaluate side-chains 274 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 155 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 123 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131984 restraints weight = 24021.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136943 restraints weight = 19018.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138117 restraints weight = 12984.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138345 restraints weight = 10780.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138671 restraints weight = 10973.076| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17850 Z= 0.132 Angle : 0.609 18.866 24222 Z= 0.310 Chirality : 0.044 0.327 2658 Planarity : 0.004 0.039 3123 Dihedral : 6.664 59.110 2905 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.81 % Favored : 96.91 % Rotamer: Outliers : 3.91 % Allowed : 17.48 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.12 (0.18), residues: 2169 helix: -0.19 (0.29), residues: 303 sheet: -0.86 (0.22), residues: 609 loop : -0.75 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100L TYR 0.015 0.001 TYR L 94 PHE 0.017 0.001 PHE D 9 TRP 0.014 0.001 TRP I 100B HIS 0.005 0.001 HIS G 17 Details of bonding type rmsd covalent geometry : bond 0.00294 (17802) covalent geometry : angle 0.56398 (24102) SS BOND : bond 0.00509 ( 24) SS BOND : angle 1.22775 ( 48) hydrogen bonds : bond 0.06220 ( 531) hydrogen bonds : angle 5.31007 ( 1365) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 1.30908 ( 36) link_NAG-ASN : bond 0.00497 ( 12) link_NAG-ASN : angle 5.72812 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 THR cc_start: 0.8663 (m) cc_final: 0.8175 (p) REVERT: C 54 LYS cc_start: 0.8424 (tppt) cc_final: 0.7888 (tptp) REVERT: C 85 ASP cc_start: 0.8758 (t0) cc_final: 0.8124 (t0) REVERT: E 12 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8123 (mmtm) REVERT: G 49 ASN cc_start: 0.8349 (m-40) cc_final: 0.8115 (t0) REVERT: G 54 LYS cc_start: 0.8477 (tppt) cc_final: 0.7977 (tttm) REVERT: G 85 ASP cc_start: 0.8693 (t0) cc_final: 0.8136 (t0) REVERT: G 148 TYR cc_start: 0.8823 (m-80) cc_final: 0.8511 (m-80) REVERT: H 67 GLU cc_start: 0.9074 (pp20) cc_final: 0.8348 (pt0) REVERT: H 168 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8593 (mt) REVERT: I 110 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8185 (p) REVERT: J 103 LYS cc_start: 0.7232 (tttt) cc_final: 0.6897 (tptm) REVERT: K 31 ASN cc_start: 0.7944 (t0) cc_final: 0.7434 (m-40) REVERT: K 54 LYS cc_start: 0.8457 (tppt) cc_final: 0.7866 (tttt) REVERT: K 85 ASP cc_start: 0.8829 (t0) cc_final: 0.8182 (t0) REVERT: K 172 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8306 (t70) REVERT: L 19 ASP cc_start: 0.7219 (p0) cc_final: 0.7007 (p0) REVERT: L 54 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8001 (mtt90) REVERT: L 67 GLU cc_start: 0.8804 (pp20) cc_final: 0.8213 (pt0) REVERT: L 158 ASP cc_start: 0.8184 (t70) cc_final: 0.7775 (t70) outliers start: 72 outliers final: 36 residues processed: 295 average time/residue: 0.1270 time to fit residues: 57.3192 Evaluate side-chains 260 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 148 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 30 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 170 optimal weight: 0.0870 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 HIS H 125 GLN ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.163167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131869 restraints weight = 24077.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134462 restraints weight = 20575.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136202 restraints weight = 15314.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136835 restraints weight = 12971.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137192 restraints weight = 12398.455| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17850 Z= 0.150 Angle : 0.616 19.037 24222 Z= 0.311 Chirality : 0.045 0.369 2658 Planarity : 0.004 0.050 3123 Dihedral : 6.673 59.717 2905 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.15 % Favored : 95.57 % Rotamer: Outliers : 4.02 % Allowed : 18.46 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.11 (0.18), residues: 2169 helix: -0.10 (0.29), residues: 303 sheet: -0.84 (0.22), residues: 609 loop : -0.78 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 100L TYR 0.016 0.002 TYR L 94 PHE 0.020 0.001 PHE D 9 TRP 0.014 0.001 TRP E 100B HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00353 (17802) covalent geometry : angle 0.57257 (24102) SS BOND : bond 0.00506 ( 24) SS BOND : angle 1.28076 ( 48) hydrogen bonds : bond 0.05994 ( 531) hydrogen bonds : angle 5.08351 ( 1365) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 1.31827 ( 36) link_NAG-ASN : bond 0.00447 ( 12) link_NAG-ASN : angle 5.66492 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 226 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8471 (tppt) cc_final: 0.7935 (tttm) REVERT: C 85 ASP cc_start: 0.8679 (t0) cc_final: 0.8051 (t0) REVERT: C 137 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: E 100 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8165 (tm-30) REVERT: E 105 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: G 49 ASN cc_start: 0.8308 (m-40) cc_final: 0.8076 (t0) REVERT: G 54 LYS cc_start: 0.8512 (tppt) cc_final: 0.8053 (tttm) REVERT: G 85 ASP cc_start: 0.8686 (t0) cc_final: 0.8147 (t0) REVERT: H 67 GLU cc_start: 0.9017 (pp20) cc_final: 0.8351 (pt0) REVERT: I 12 LYS cc_start: 0.7982 (mptt) cc_final: 0.7781 (mmtm) REVERT: I 110 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8320 (p) REVERT: J 103 LYS cc_start: 0.7457 (tttt) cc_final: 0.7190 (tptm) REVERT: K 31 ASN cc_start: 0.7967 (t0) cc_final: 0.7472 (m-40) REVERT: K 54 LYS cc_start: 0.8511 (tppt) cc_final: 0.7991 (tttt) REVERT: K 85 ASP cc_start: 0.8820 (t0) cc_final: 0.8083 (t0) REVERT: L 19 ASP cc_start: 0.7151 (p0) cc_final: 0.6911 (p0) REVERT: L 54 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7627 (mtm180) REVERT: L 67 GLU cc_start: 0.8793 (pp20) cc_final: 0.8248 (pt0) REVERT: L 158 ASP cc_start: 0.8148 (t70) cc_final: 0.7734 (t70) outliers start: 74 outliers final: 52 residues processed: 284 average time/residue: 0.1210 time to fit residues: 52.5554 Evaluate side-chains 276 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132816 restraints weight = 23894.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135938 restraints weight = 20428.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137617 restraints weight = 14993.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138516 restraints weight = 12746.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138968 restraints weight = 12053.551| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17850 Z= 0.125 Angle : 0.583 18.661 24222 Z= 0.293 Chirality : 0.044 0.382 2658 Planarity : 0.004 0.037 3123 Dihedral : 6.540 58.646 2904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.14 % Favored : 96.59 % Rotamer: Outliers : 4.07 % Allowed : 18.95 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.00 (0.18), residues: 2169 helix: 0.10 (0.29), residues: 303 sheet: -0.81 (0.21), residues: 609 loop : -0.71 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 137 TYR 0.015 0.001 TYR L 94 PHE 0.016 0.001 PHE D 9 TRP 0.014 0.001 TRP A 98 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00284 (17802) covalent geometry : angle 0.53923 (24102) SS BOND : bond 0.00525 ( 24) SS BOND : angle 1.20778 ( 48) hydrogen bonds : bond 0.05580 ( 531) hydrogen bonds : angle 4.91999 ( 1365) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.28423 ( 36) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 5.53215 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 225 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8514 (tppt) cc_final: 0.7919 (tttm) REVERT: C 85 ASP cc_start: 0.8657 (t0) cc_final: 0.8133 (t0) REVERT: E 100 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8154 (tm-30) REVERT: E 105 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: G 49 ASN cc_start: 0.8346 (m-40) cc_final: 0.8093 (t0) REVERT: G 54 LYS cc_start: 0.8488 (tppt) cc_final: 0.8013 (tttm) REVERT: G 85 ASP cc_start: 0.8734 (t0) cc_final: 0.8209 (t0) REVERT: G 148 TYR cc_start: 0.8781 (m-80) cc_final: 0.8499 (m-80) REVERT: H 67 GLU cc_start: 0.9066 (pp20) cc_final: 0.8399 (pt0) REVERT: I 12 LYS cc_start: 0.7981 (mptt) cc_final: 0.7725 (mmtm) REVERT: I 110 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8209 (p) REVERT: J 103 LYS cc_start: 0.7258 (tttt) cc_final: 0.6991 (tptm) REVERT: K 31 ASN cc_start: 0.7874 (t0) cc_final: 0.7443 (m-40) REVERT: K 54 LYS cc_start: 0.8437 (tppt) cc_final: 0.7908 (tttt) REVERT: K 76 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8021 (m) REVERT: K 85 ASP cc_start: 0.8816 (t0) cc_final: 0.8111 (t0) REVERT: L 19 ASP cc_start: 0.7187 (p0) cc_final: 0.6915 (p0) REVERT: L 54 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7335 (mtm180) REVERT: L 67 GLU cc_start: 0.8865 (pp20) cc_final: 0.8282 (pt0) REVERT: L 158 ASP cc_start: 0.8256 (t70) cc_final: 0.7875 (t70) outliers start: 75 outliers final: 50 residues processed: 286 average time/residue: 0.1274 time to fit residues: 55.5280 Evaluate side-chains 275 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 79 ASN Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 160 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 HIS ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151005 restraints weight = 23160.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154514 restraints weight = 15166.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156919 restraints weight = 11397.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158528 restraints weight = 9386.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159441 restraints weight = 8182.898| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17850 Z= 0.144 Angle : 0.597 18.730 24222 Z= 0.301 Chirality : 0.044 0.412 2658 Planarity : 0.004 0.037 3123 Dihedral : 6.535 59.159 2903 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.33 % Favored : 95.44 % Rotamer: Outliers : 4.51 % Allowed : 19.60 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.03 (0.18), residues: 2169 helix: 0.15 (0.29), residues: 303 sheet: -0.85 (0.21), residues: 615 loop : -0.74 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 137 TYR 0.016 0.002 TYR L 94 PHE 0.019 0.001 PHE D 9 TRP 0.015 0.001 TRP A 98 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00337 (17802) covalent geometry : angle 0.55454 (24102) SS BOND : bond 0.00509 ( 24) SS BOND : angle 1.29938 ( 48) hydrogen bonds : bond 0.05705 ( 531) hydrogen bonds : angle 4.84629 ( 1365) link_BETA1-4 : bond 0.00446 ( 12) link_BETA1-4 : angle 1.28777 ( 36) link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 5.49693 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8582 (tppt) cc_final: 0.8135 (tttm) REVERT: C 85 ASP cc_start: 0.8691 (t0) cc_final: 0.8038 (t0) REVERT: E 100 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 105 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: G 54 LYS cc_start: 0.8461 (tppt) cc_final: 0.8131 (tttm) REVERT: G 85 ASP cc_start: 0.8692 (t0) cc_final: 0.8212 (t0) REVERT: H 14 TRP cc_start: 0.9112 (m-10) cc_final: 0.8093 (m-10) REVERT: H 67 GLU cc_start: 0.8988 (pp20) cc_final: 0.8391 (pt0) REVERT: I 12 LYS cc_start: 0.7963 (mptt) cc_final: 0.7742 (mmtm) REVERT: I 110 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8317 (p) REVERT: J 103 LYS cc_start: 0.7452 (tttt) cc_final: 0.7180 (tptm) REVERT: K 31 ASN cc_start: 0.7813 (t0) cc_final: 0.7476 (m-40) REVERT: K 54 LYS cc_start: 0.8462 (tppt) cc_final: 0.8112 (tttt) REVERT: K 65 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8297 (t-170) REVERT: K 76 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8082 (m) REVERT: K 85 ASP cc_start: 0.8731 (t0) cc_final: 0.8039 (t0) REVERT: L 19 ASP cc_start: 0.7114 (p0) cc_final: 0.6839 (p0) REVERT: L 54 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7446 (mtm180) REVERT: L 67 GLU cc_start: 0.8822 (pp20) cc_final: 0.8260 (pt0) REVERT: L 158 ASP cc_start: 0.8194 (t70) cc_final: 0.7616 (t0) REVERT: L 170 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7713 (ttt90) outliers start: 83 outliers final: 59 residues processed: 292 average time/residue: 0.1154 time to fit residues: 51.8720 Evaluate side-chains 288 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 64 CYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 65 HIS Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 170 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 161 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 159 optimal weight: 0.0030 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 overall best weight: 0.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN G 49 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152483 restraints weight = 23326.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156006 restraints weight = 15213.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158389 restraints weight = 11402.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159755 restraints weight = 9373.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.161025 restraints weight = 8209.813| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17850 Z= 0.123 Angle : 0.580 18.457 24222 Z= 0.292 Chirality : 0.044 0.400 2658 Planarity : 0.004 0.037 3123 Dihedral : 6.447 58.197 2903 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.18 % Favored : 96.63 % Rotamer: Outliers : 3.80 % Allowed : 21.06 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.95 (0.18), residues: 2169 helix: 0.26 (0.29), residues: 303 sheet: -0.80 (0.22), residues: 615 loop : -0.69 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.014 0.001 TYR L 94 PHE 0.013 0.001 PHE D 9 TRP 0.016 0.001 TRP A 98 HIS 0.020 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00279 (17802) covalent geometry : angle 0.53729 (24102) SS BOND : bond 0.00450 ( 24) SS BOND : angle 1.26659 ( 48) hydrogen bonds : bond 0.05425 ( 531) hydrogen bonds : angle 4.77571 ( 1365) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.29006 ( 36) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 5.42312 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8608 (tppt) cc_final: 0.8102 (tttm) REVERT: C 85 ASP cc_start: 0.8656 (t0) cc_final: 0.8066 (t0) REVERT: E 100 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8187 (tm-30) REVERT: E 105 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7205 (pt0) REVERT: G 54 LYS cc_start: 0.8508 (tppt) cc_final: 0.8159 (tttm) REVERT: G 85 ASP cc_start: 0.8682 (t0) cc_final: 0.8212 (t0) REVERT: H 14 TRP cc_start: 0.9067 (m-10) cc_final: 0.8076 (m-10) REVERT: H 67 GLU cc_start: 0.8981 (pp20) cc_final: 0.8402 (pt0) REVERT: I 110 THR cc_start: 0.8580 (m) cc_final: 0.8293 (p) REVERT: J 103 LYS cc_start: 0.7455 (tttt) cc_final: 0.7191 (tptm) REVERT: K 31 ASN cc_start: 0.7808 (t0) cc_final: 0.7468 (m-40) REVERT: K 54 LYS cc_start: 0.8481 (tppt) cc_final: 0.8134 (tttt) REVERT: K 76 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (m) REVERT: K 85 ASP cc_start: 0.8727 (t0) cc_final: 0.8027 (t0) REVERT: L 19 ASP cc_start: 0.7141 (p0) cc_final: 0.6822 (p0) REVERT: L 54 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7424 (mtm180) REVERT: L 67 GLU cc_start: 0.8835 (pp20) cc_final: 0.8278 (pt0) REVERT: L 158 ASP cc_start: 0.8148 (t70) cc_final: 0.7774 (t70) REVERT: L 170 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7685 (ttt90) outliers start: 70 outliers final: 56 residues processed: 278 average time/residue: 0.1282 time to fit residues: 54.8804 Evaluate side-chains 284 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 64 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 170 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.193328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166642 restraints weight = 23093.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.169283 restraints weight = 16299.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171144 restraints weight = 12894.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172471 restraints weight = 10922.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173125 restraints weight = 9728.095| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17850 Z= 0.131 Angle : 0.585 18.409 24222 Z= 0.294 Chirality : 0.044 0.407 2658 Planarity : 0.004 0.035 3123 Dihedral : 6.390 58.193 2903 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 4.07 % Allowed : 20.85 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.92 (0.18), residues: 2169 helix: 0.33 (0.29), residues: 303 sheet: -0.77 (0.22), residues: 615 loop : -0.70 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.015 0.001 TYR G 148 PHE 0.016 0.001 PHE D 9 TRP 0.013 0.001 TRP A 98 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00302 (17802) covalent geometry : angle 0.54288 (24102) SS BOND : bond 0.00475 ( 24) SS BOND : angle 1.29051 ( 48) hydrogen bonds : bond 0.05451 ( 531) hydrogen bonds : angle 4.71442 ( 1365) link_BETA1-4 : bond 0.00469 ( 12) link_BETA1-4 : angle 1.28500 ( 36) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 5.38966 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8589 (tppt) cc_final: 0.8143 (tttm) REVERT: C 85 ASP cc_start: 0.8666 (t0) cc_final: 0.8084 (t0) REVERT: E 100 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8181 (tm-30) REVERT: E 105 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: G 54 LYS cc_start: 0.8511 (tppt) cc_final: 0.8154 (tttm) REVERT: G 85 ASP cc_start: 0.8747 (t0) cc_final: 0.8278 (t0) REVERT: G 148 TYR cc_start: 0.8817 (m-80) cc_final: 0.8240 (m-80) REVERT: G 194 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7990 (mt) REVERT: H 67 GLU cc_start: 0.9019 (pp20) cc_final: 0.8436 (pt0) REVERT: I 110 THR cc_start: 0.8574 (m) cc_final: 0.8267 (p) REVERT: J 103 LYS cc_start: 0.7436 (tttt) cc_final: 0.7149 (tptm) REVERT: K 31 ASN cc_start: 0.7789 (t0) cc_final: 0.7457 (m-40) REVERT: K 54 LYS cc_start: 0.8503 (tppt) cc_final: 0.8144 (tttt) REVERT: K 85 ASP cc_start: 0.8746 (t0) cc_final: 0.8057 (t0) REVERT: L 19 ASP cc_start: 0.7123 (p0) cc_final: 0.6764 (p0) REVERT: L 54 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7398 (mtm180) REVERT: L 67 GLU cc_start: 0.8892 (pp20) cc_final: 0.8322 (pt0) REVERT: L 158 ASP cc_start: 0.8264 (t70) cc_final: 0.7937 (t70) REVERT: L 170 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7636 (ttt90) outliers start: 75 outliers final: 59 residues processed: 283 average time/residue: 0.1252 time to fit residues: 54.3357 Evaluate side-chains 287 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 64 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 170 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 0.0870 chunk 17 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.195101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167866 restraints weight = 22986.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170156 restraints weight = 17662.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170849 restraints weight = 14880.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.171535 restraints weight = 12986.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171908 restraints weight = 11654.356| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17850 Z= 0.228 Angle : 0.677 19.296 24222 Z= 0.345 Chirality : 0.047 0.452 2658 Planarity : 0.004 0.039 3123 Dihedral : 6.716 59.239 2902 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.81 % Favored : 94.01 % Rotamer: Outliers : 4.34 % Allowed : 21.06 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.19 (0.18), residues: 2169 helix: 0.18 (0.30), residues: 300 sheet: -0.89 (0.22), residues: 615 loop : -0.94 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.019 0.002 TYR G 148 PHE 0.015 0.002 PHE L 24 TRP 0.017 0.002 TRP I 47 HIS 0.008 0.002 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00553 (17802) covalent geometry : angle 0.63681 (24102) SS BOND : bond 0.00594 ( 24) SS BOND : angle 1.59584 ( 48) hydrogen bonds : bond 0.06483 ( 531) hydrogen bonds : angle 4.98907 ( 1365) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.26483 ( 36) link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 5.62615 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 231 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 54 LYS cc_start: 0.8682 (tppt) cc_final: 0.8237 (tttm) REVERT: C 85 ASP cc_start: 0.8686 (t0) cc_final: 0.8121 (t0) REVERT: E 50 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.7877 (p90) REVERT: E 100 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 105 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: G 54 LYS cc_start: 0.8598 (tppt) cc_final: 0.8281 (tttm) REVERT: G 85 ASP cc_start: 0.8763 (t0) cc_final: 0.8315 (t0) REVERT: G 194 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8120 (mt) REVERT: H 14 TRP cc_start: 0.9015 (m-10) cc_final: 0.7936 (m-10) REVERT: H 67 GLU cc_start: 0.9028 (pp20) cc_final: 0.8441 (pt0) REVERT: I 100 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8159 (tm-30) REVERT: I 110 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8339 (p) REVERT: K 54 LYS cc_start: 0.8591 (tppt) cc_final: 0.8196 (tttt) REVERT: K 85 ASP cc_start: 0.8809 (t0) cc_final: 0.8085 (t0) REVERT: L 19 ASP cc_start: 0.7119 (p0) cc_final: 0.6772 (p0) REVERT: L 54 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7438 (mtm180) REVERT: L 67 GLU cc_start: 0.8906 (pp20) cc_final: 0.8274 (pt0) REVERT: L 158 ASP cc_start: 0.8131 (t70) cc_final: 0.7850 (t70) REVERT: L 170 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7762 (ttt90) outliers start: 80 outliers final: 60 residues processed: 291 average time/residue: 0.1250 time to fit residues: 55.0606 Evaluate side-chains 294 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 64 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 79 ASN Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 146 optimal weight: 0.0770 chunk 83 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154149 restraints weight = 21530.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153877 restraints weight = 23669.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155754 restraints weight = 21984.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156339 restraints weight = 16048.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156414 restraints weight = 15819.505| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17850 Z= 0.115 Angle : 0.588 18.378 24222 Z= 0.296 Chirality : 0.044 0.411 2658 Planarity : 0.004 0.039 3123 Dihedral : 6.405 58.997 2902 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 2.99 % Allowed : 22.80 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.98 (0.18), residues: 2169 helix: 0.42 (0.30), residues: 297 sheet: -0.79 (0.22), residues: 615 loop : -0.79 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.016 0.001 TYR G 148 PHE 0.015 0.001 PHE D 9 TRP 0.013 0.001 TRP H 83 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00252 (17802) covalent geometry : angle 0.54604 (24102) SS BOND : bond 0.00489 ( 24) SS BOND : angle 1.23511 ( 48) hydrogen bonds : bond 0.05400 ( 531) hydrogen bonds : angle 4.75166 ( 1365) link_BETA1-4 : bond 0.00483 ( 12) link_BETA1-4 : angle 1.27654 ( 36) link_NAG-ASN : bond 0.00473 ( 12) link_NAG-ASN : angle 5.41555 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4338 Ramachandran restraints generated. 2169 Oldfield, 0 Emsley, 2169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8636 (tppt) cc_final: 0.8324 (tttm) REVERT: C 85 ASP cc_start: 0.8580 (t0) cc_final: 0.8069 (t0) REVERT: C 172 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: E 100 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8137 (tm-30) REVERT: G 54 LYS cc_start: 0.8466 (tppt) cc_final: 0.8161 (tttm) REVERT: G 85 ASP cc_start: 0.8666 (t0) cc_final: 0.8259 (t0) REVERT: G 148 TYR cc_start: 0.8808 (m-80) cc_final: 0.8158 (m-80) REVERT: G 194 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8139 (mt) REVERT: H 67 GLU cc_start: 0.8868 (pp20) cc_final: 0.8369 (pt0) REVERT: I 100 ASN cc_start: 0.7880 (t0) cc_final: 0.7436 (t0) REVERT: I 100 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8268 (tm-30) REVERT: K 54 LYS cc_start: 0.8576 (tppt) cc_final: 0.8283 (tttt) REVERT: K 85 ASP cc_start: 0.8660 (t0) cc_final: 0.8029 (t0) REVERT: L 19 ASP cc_start: 0.6986 (p0) cc_final: 0.6679 (p0) REVERT: L 54 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7430 (mtm180) REVERT: L 67 GLU cc_start: 0.8718 (pp20) cc_final: 0.8108 (pt0) REVERT: L 158 ASP cc_start: 0.8086 (t70) cc_final: 0.7723 (t70) REVERT: L 170 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7674 (ttt90) outliers start: 55 outliers final: 46 residues processed: 275 average time/residue: 0.1351 time to fit residues: 56.6904 Evaluate side-chains 278 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 CYS Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 58 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.193113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166552 restraints weight = 23233.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.169197 restraints weight = 16375.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171077 restraints weight = 12933.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172366 restraints weight = 10949.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173044 restraints weight = 9749.725| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17850 Z= 0.126 Angle : 0.582 18.220 24222 Z= 0.293 Chirality : 0.044 0.411 2658 Planarity : 0.004 0.037 3123 Dihedral : 6.314 58.393 2902 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 3.04 % Allowed : 22.91 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.92 (0.18), residues: 2169 helix: 0.54 (0.30), residues: 297 sheet: -0.71 (0.22), residues: 609 loop : -0.79 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.013 0.001 TYR L 94 PHE 0.013 0.001 PHE D 9 TRP 0.012 0.001 TRP A 98 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00287 (17802) covalent geometry : angle 0.54079 (24102) SS BOND : bond 0.00471 ( 24) SS BOND : angle 1.33234 ( 48) hydrogen bonds : bond 0.05392 ( 531) hydrogen bonds : angle 4.67455 ( 1365) link_BETA1-4 : bond 0.00471 ( 12) link_BETA1-4 : angle 1.27647 ( 36) link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 5.32425 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.04 seconds wall clock time: 47 minutes 28.66 seconds (2848.66 seconds total)