Starting phenix.real_space_refine on Tue Jan 21 19:46:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bu6_44901/01_2025/9bu6_44901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bu6_44901/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bu6_44901/01_2025/9bu6_44901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bu6_44901/01_2025/9bu6_44901.map" model { file = "/net/cci-nas-00/data/ceres_data/9bu6_44901/01_2025/9bu6_44901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bu6_44901/01_2025/9bu6_44901.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.70, per 1000 atoms: 0.61 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: 4.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.67 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: 6.09 Time building geometry restraints manager: 5.38 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: 0.02 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: 1.350 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.640 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- 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 17802 Z= 0.233 Angle : 0.616 15.051 24102 Z= 0.358 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 : 5.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (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 TRP 0.019 0.001 TRP I 100B HIS 0.004 0.001 HIS C 247 PHE 0.012 0.001 PHE J 71 TYR 0.009 0.001 TYR B 32 ARG 0.008 0.000 ARG F 53 *********************** 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 : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8947 (p) REVERT: C 54 LYS cc_start: 0.8267 (tppt) cc_final: 0.7848 (tptp) REVERT: C 85 ASP cc_start: 0.8555 (t0) cc_final: 0.7811 (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: 0.8962 (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: 0.3085 time to fit residues: 169.4961 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 : 1.764 ------------------------------------------------------------------------------- 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 179 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 79 ASN D 125 GLN E 100AASN E 105 GLN G 145 ASN ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L 125 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148364 restraints weight = 23634.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149527 restraints weight = 22434.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150858 restraints weight = 19644.997| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 17802 Z= 0.615 Angle : 0.832 10.319 24102 Z= 0.449 Chirality : 0.054 0.409 2658 Planarity : 0.006 0.045 3123 Dihedral : 7.280 58.148 2929 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 4.13 % Allowed : 17.54 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2169 helix: -0.69 (0.29), residues: 309 sheet: -0.90 (0.23), residues: 543 loop : -1.01 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 100B HIS 0.014 0.003 HIS G 17 PHE 0.022 0.003 PHE K 161 TYR 0.026 0.003 TYR B 36 ARG 0.007 0.001 ARG G 90 *********************** 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: 76 poor density : 237 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.8524 (p90) REVERT: A 110 THR cc_start: 0.8825 (m) cc_final: 0.8380 (p) REVERT: C 54 LYS cc_start: 0.8462 (tppt) cc_final: 0.8010 (tptm) REVERT: C 85 ASP cc_start: 0.8797 (t0) cc_final: 0.8042 (t0) REVERT: D 17 MET cc_start: 0.8708 (mmt) cc_final: 0.8283 (tpt) REVERT: D 147 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7781 (t) REVERT: E 50 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.7435 (p90) REVERT: G 49 ASN cc_start: 0.8442 (m-40) cc_final: 0.8002 (t0) REVERT: G 54 LYS cc_start: 0.8521 (tppt) cc_final: 0.8132 (tttm) REVERT: G 85 ASP cc_start: 0.8671 (t0) cc_final: 0.8145 (t0) REVERT: H 67 GLU cc_start: 0.9015 (pp20) cc_final: 0.8299 (pt0) REVERT: H 150 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7353 (tm-30) REVERT: H 155 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (t0) REVERT: I 110 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8485 (p) REVERT: J 103 LYS cc_start: 0.7565 (tttt) cc_final: 0.7257 (tptm) REVERT: K 31 ASN cc_start: 0.7881 (t0) cc_final: 0.7558 (m-40) REVERT: K 54 LYS cc_start: 0.8501 (tppt) cc_final: 0.7997 (tttt) REVERT: K 85 ASP cc_start: 0.8848 (t0) cc_final: 0.8122 (t0) REVERT: K 175 GLU cc_start: 0.7812 (pm20) cc_final: 0.7605 (pt0) REVERT: L 38 TYR cc_start: 0.7416 (t80) cc_final: 0.7004 (m-80) REVERT: L 40 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8309 (m) REVERT: L 158 ASP cc_start: 0.8188 (t0) cc_final: 0.7794 (t0) outliers start: 76 outliers final: 48 residues processed: 302 average time/residue: 0.3044 time to fit residues: 140.9963 Evaluate side-chains 277 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TRP 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 231 ASP Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 81 ILE 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 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 33 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 25 ILE Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 279 SER 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 45 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** H 125 GLN ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132157 restraints weight = 23855.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135570 restraints weight = 19208.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136641 restraints weight = 14283.158| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17802 Z= 0.191 Angle : 0.577 7.603 24102 Z= 0.307 Chirality : 0.044 0.326 2658 Planarity : 0.004 0.040 3123 Dihedral : 6.706 59.900 2910 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.90 % Favored : 96.82 % Rotamer: Outliers : 3.75 % Allowed : 17.86 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2169 helix: -0.15 (0.30), residues: 303 sheet: -0.88 (0.22), residues: 609 loop : -0.79 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 83 HIS 0.005 0.001 HIS H 75 PHE 0.016 0.001 PHE D 9 TYR 0.018 0.001 TYR K 148 ARG 0.005 0.000 ARG A 100L *********************** 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 313 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 244 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 THR cc_start: 0.8697 (m) cc_final: 0.8231 (p) REVERT: C 54 LYS cc_start: 0.8442 (tppt) cc_final: 0.7902 (tptp) REVERT: C 85 ASP cc_start: 0.8750 (t0) cc_final: 0.8111 (t0) REVERT: G 49 ASN cc_start: 0.8330 (m-40) cc_final: 0.7959 (t0) REVERT: G 54 LYS cc_start: 0.8477 (tppt) cc_final: 0.8002 (tttm) REVERT: G 85 ASP cc_start: 0.8662 (t0) cc_final: 0.8108 (t0) REVERT: G 137 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7798 (tpp80) REVERT: H 67 GLU cc_start: 0.9025 (pp20) cc_final: 0.8308 (pt0) REVERT: H 168 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8602 (mt) REVERT: I 110 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8268 (p) REVERT: J 103 LYS cc_start: 0.7347 (tttt) cc_final: 0.7020 (tptm) REVERT: K 31 ASN cc_start: 0.7932 (t0) cc_final: 0.7466 (m-40) REVERT: K 54 LYS cc_start: 0.8486 (tppt) cc_final: 0.7939 (tttt) REVERT: K 85 ASP cc_start: 0.8807 (t0) cc_final: 0.8195 (t0) REVERT: K 172 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: K 175 GLU cc_start: 0.7868 (pm20) cc_final: 0.7646 (pt0) REVERT: L 19 ASP cc_start: 0.7179 (p0) cc_final: 0.6972 (p0) REVERT: L 54 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7545 (mtm180) REVERT: L 67 GLU cc_start: 0.8758 (pp20) cc_final: 0.8163 (pt0) REVERT: L 158 ASP cc_start: 0.8123 (t70) cc_final: 0.7656 (t70) outliers start: 69 outliers final: 38 residues processed: 296 average time/residue: 0.2961 time to fit residues: 131.7218 Evaluate side-chains 270 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 113 SER Chi-restraints excluded: chain E residue 51 ILE 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 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 J residue 93 SER 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 K residue 172 ASP Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 90 ASP 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 173 optimal weight: 0.3980 chunk 177 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** 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 = 0.3859 r_free = 0.3859 target = 0.165575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134475 restraints weight = 23782.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137701 restraints weight = 17988.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138877 restraints weight = 13772.162| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17802 Z= 0.158 Angle : 0.542 7.784 24102 Z= 0.285 Chirality : 0.043 0.339 2658 Planarity : 0.004 0.051 3123 Dihedral : 6.546 59.352 2904 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.64 % Favored : 96.08 % Rotamer: Outliers : 3.37 % Allowed : 18.78 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2169 helix: 0.10 (0.30), residues: 300 sheet: -0.79 (0.22), residues: 609 loop : -0.72 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100B HIS 0.003 0.001 HIS D 106 PHE 0.020 0.001 PHE D 9 TYR 0.013 0.001 TYR G 148 ARG 0.007 0.000 ARG A 100L *********************** 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 295 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8432 (tppt) cc_final: 0.7887 (tptp) REVERT: C 85 ASP cc_start: 0.8614 (t0) cc_final: 0.7994 (t0) REVERT: G 49 ASN cc_start: 0.8397 (m-40) cc_final: 0.7963 (t0) REVERT: G 54 LYS cc_start: 0.8502 (tppt) cc_final: 0.7993 (tttm) REVERT: G 85 ASP cc_start: 0.8705 (t0) cc_final: 0.8134 (t0) REVERT: G 148 TYR cc_start: 0.8713 (m-80) cc_final: 0.8376 (m-80) REVERT: H 67 GLU cc_start: 0.9066 (pp20) cc_final: 0.8370 (pt0) REVERT: I 12 LYS cc_start: 0.7971 (mptt) cc_final: 0.7703 (mmtm) REVERT: I 110 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8110 (p) REVERT: J 103 LYS cc_start: 0.7108 (tttt) cc_final: 0.6858 (tptm) REVERT: K 31 ASN cc_start: 0.7945 (t0) cc_final: 0.7485 (m-40) REVERT: K 54 LYS cc_start: 0.8440 (tppt) cc_final: 0.7875 (tttt) REVERT: K 85 ASP cc_start: 0.8822 (t0) cc_final: 0.8165 (t0) REVERT: K 175 GLU cc_start: 0.7968 (pm20) cc_final: 0.7540 (pm20) REVERT: L 19 ASP cc_start: 0.7201 (p0) cc_final: 0.6983 (p0) REVERT: L 54 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7444 (mtm180) REVERT: L 67 GLU cc_start: 0.8834 (pp20) cc_final: 0.8209 (pt0) outliers start: 62 outliers final: 33 residues processed: 286 average time/residue: 0.3023 time to fit residues: 130.2834 Evaluate side-chains 262 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 95 ASP 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 320 MET 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 G residue 18 HIS Chi-restraints excluded: chain G residue 81 THR 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 H residue 49 THR Chi-restraints excluded: chain H residue 113 SER 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 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 241 ASP Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 90 ASP 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 210 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 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 = 0.3800 r_free = 0.3800 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127220 restraints weight = 24265.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132466 restraints weight = 18713.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133511 restraints weight = 11942.881| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17802 Z= 0.318 Angle : 0.617 8.373 24102 Z= 0.326 Chirality : 0.047 0.433 2658 Planarity : 0.004 0.038 3123 Dihedral : 6.778 59.374 2903 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.79 % Favored : 94.93 % Rotamer: Outliers : 4.34 % Allowed : 19.44 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2169 helix: -0.01 (0.30), residues: 300 sheet: -0.94 (0.21), residues: 615 loop : -0.86 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 100B HIS 0.007 0.002 HIS K 17 PHE 0.017 0.002 PHE L 24 TYR 0.021 0.002 TYR L 94 ARG 0.005 0.000 ARG G 90 *********************** 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 308 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8529 (tppt) cc_final: 0.7984 (tttm) REVERT: C 85 ASP cc_start: 0.8760 (t0) cc_final: 0.8091 (t0) REVERT: C 137 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: C 212 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8149 (t0) REVERT: E 50 TRP cc_start: 0.8846 (OUTLIER) cc_final: 0.7842 (p90) REVERT: E 100 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8382 (tm-30) REVERT: G 49 ASN cc_start: 0.8368 (m-40) cc_final: 0.8101 (t0) REVERT: G 54 LYS cc_start: 0.8564 (tppt) cc_final: 0.8133 (tttm) REVERT: G 85 ASP cc_start: 0.8757 (t0) cc_final: 0.8252 (t0) REVERT: H 14 TRP cc_start: 0.9109 (m-10) cc_final: 0.7968 (m-10) REVERT: H 67 GLU cc_start: 0.9058 (pp20) cc_final: 0.8377 (pt0) REVERT: I 12 LYS cc_start: 0.8015 (mptt) cc_final: 0.7725 (mmtm) REVERT: I 110 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8321 (p) REVERT: K 31 ASN cc_start: 0.7940 (t0) cc_final: 0.7448 (m-40) REVERT: K 54 LYS cc_start: 0.8564 (tppt) cc_final: 0.8048 (tttt) REVERT: K 85 ASP cc_start: 0.8850 (t0) cc_final: 0.8085 (t0) REVERT: L 19 ASP cc_start: 0.7164 (p0) cc_final: 0.6907 (p0) REVERT: L 54 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7543 (mtm180) REVERT: L 67 GLU cc_start: 0.8894 (pp20) cc_final: 0.8268 (pt0) REVERT: L 158 ASP cc_start: 0.8068 (t0) cc_final: 0.7680 (t70) outliers start: 80 outliers final: 56 residues processed: 287 average time/residue: 0.2855 time to fit residues: 125.0476 Evaluate side-chains 283 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 65 HIS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 212 ASN 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 61 THR Chi-restraints excluded: chain D residue 113 SER 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 82 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 60 ASP 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 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 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 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 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 76 CYS 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 216 VAL Chi-restraints excluded: chain L residue 10 LEU 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 90 ASP Chi-restraints excluded: chain L residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 202 optimal weight: 0.8980 chunk 203 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.181829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152791 restraints weight = 23326.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156234 restraints weight = 15095.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158612 restraints weight = 11335.037| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17802 Z= 0.166 Angle : 0.533 8.042 24102 Z= 0.281 Chirality : 0.043 0.397 2658 Planarity : 0.004 0.038 3123 Dihedral : 6.560 58.896 2903 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.86 % Favored : 96.86 % Rotamer: Outliers : 3.69 % Allowed : 20.58 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2169 helix: 0.16 (0.29), residues: 303 sheet: -0.87 (0.22), residues: 615 loop : -0.70 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 98 HIS 0.004 0.001 HIS D 106 PHE 0.017 0.001 PHE D 9 TYR 0.014 0.001 TYR L 94 ARG 0.004 0.000 ARG K 137 *********************** 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 299 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8563 (tppt) cc_final: 0.8086 (tttm) REVERT: C 85 ASP cc_start: 0.8683 (t0) cc_final: 0.8033 (t0) REVERT: C 137 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7842 (ttm-80) REVERT: E 100 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8184 (tm-30) REVERT: G 54 LYS cc_start: 0.8491 (tppt) cc_final: 0.8094 (tttm) REVERT: G 85 ASP cc_start: 0.8693 (t0) cc_final: 0.8198 (t0) REVERT: H 14 TRP cc_start: 0.9076 (m-10) cc_final: 0.8128 (m-10) REVERT: H 67 GLU cc_start: 0.8979 (pp20) cc_final: 0.8363 (pt0) REVERT: I 12 LYS cc_start: 0.7956 (mptt) cc_final: 0.7702 (mmtm) REVERT: I 110 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8317 (p) REVERT: K 31 ASN cc_start: 0.7826 (t0) cc_final: 0.7491 (m-40) REVERT: K 54 LYS cc_start: 0.8546 (tppt) cc_final: 0.8128 (tttt) REVERT: K 65 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8260 (t-170) REVERT: K 76 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8031 (m) REVERT: K 85 ASP cc_start: 0.8759 (t0) cc_final: 0.8100 (t0) REVERT: L 19 ASP cc_start: 0.7159 (p0) cc_final: 0.6902 (p0) REVERT: L 54 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7426 (mtm180) REVERT: L 67 GLU cc_start: 0.8813 (pp20) cc_final: 0.8222 (pt0) REVERT: L 158 ASP cc_start: 0.8115 (t0) cc_final: 0.7681 (t70) REVERT: L 170 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7665 (ttt90) outliers start: 68 outliers final: 46 residues processed: 285 average time/residue: 0.2906 time to fit residues: 125.2012 Evaluate side-chains 274 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 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 302 VAL Chi-restraints excluded: chain C residue 320 MET 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 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 113 SER Chi-restraints excluded: chain I residue 18 VAL 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 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 65 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 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 10 LEU 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 90 ASP 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 15 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.188253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160186 restraints weight = 23248.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162997 restraints weight = 15976.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164062 restraints weight = 13181.219| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17802 Z= 0.360 Angle : 0.633 8.595 24102 Z= 0.335 Chirality : 0.047 0.458 2658 Planarity : 0.004 0.038 3123 Dihedral : 6.814 59.747 2903 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.30 % Favored : 94.47 % Rotamer: Outliers : 3.96 % Allowed : 20.68 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2169 helix: 0.07 (0.30), residues: 300 sheet: -0.95 (0.22), residues: 615 loop : -0.95 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 47 HIS 0.014 0.002 HIS K 65 PHE 0.018 0.002 PHE L 24 TYR 0.020 0.002 TYR L 94 ARG 0.004 0.000 ARG G 90 *********************** 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 299 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 226 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8659 (tppt) cc_final: 0.8168 (tttm) REVERT: C 85 ASP cc_start: 0.8698 (t0) cc_final: 0.8109 (t0) REVERT: C 137 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: C 212 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8150 (t0) REVERT: E 100 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8397 (tm-30) REVERT: G 54 LYS cc_start: 0.8553 (tppt) cc_final: 0.8236 (tttm) REVERT: G 85 ASP cc_start: 0.8768 (t0) cc_final: 0.8307 (t0) REVERT: H 14 TRP cc_start: 0.9074 (m-10) cc_final: 0.8013 (m-10) REVERT: H 67 GLU cc_start: 0.8989 (pp20) cc_final: 0.8388 (pt0) REVERT: I 100 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8239 (tm-30) REVERT: I 110 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8362 (p) REVERT: K 31 ASN cc_start: 0.7911 (t0) cc_final: 0.7466 (m-40) REVERT: K 54 LYS cc_start: 0.8561 (tppt) cc_final: 0.8197 (tttt) REVERT: K 85 ASP cc_start: 0.8759 (t0) cc_final: 0.8002 (t0) REVERT: L 19 ASP cc_start: 0.7134 (p0) cc_final: 0.6806 (p0) REVERT: L 54 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7533 (mtm180) REVERT: L 67 GLU cc_start: 0.8858 (pp20) cc_final: 0.8265 (pt0) REVERT: L 158 ASP cc_start: 0.8144 (t0) cc_final: 0.7754 (t70) REVERT: L 170 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7800 (ttt90) outliers start: 73 outliers final: 59 residues processed: 281 average time/residue: 0.2919 time to fit residues: 124.5737 Evaluate side-chains 282 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 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 212 ASN 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 113 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 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 I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR 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 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 71 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 10 LEU 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 90 ASP 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 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.191615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166145 restraints weight = 23011.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167922 restraints weight = 16172.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.168952 restraints weight = 12331.143| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17802 Z= 0.207 Angle : 0.562 8.816 24102 Z= 0.295 Chirality : 0.044 0.424 2658 Planarity : 0.004 0.038 3123 Dihedral : 6.657 59.685 2903 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 4.07 % Allowed : 21.39 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2169 helix: 0.25 (0.30), residues: 297 sheet: -0.82 (0.22), residues: 609 loop : -0.90 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.004 0.001 HIS D 106 PHE 0.015 0.001 PHE D 9 TYR 0.019 0.001 TYR G 148 ARG 0.003 0.000 ARG C 137 *********************** 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 301 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8609 (tppt) cc_final: 0.8146 (tttm) REVERT: C 85 ASP cc_start: 0.8670 (t0) cc_final: 0.8121 (t0) REVERT: E 100 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8156 (tm-30) REVERT: G 54 LYS cc_start: 0.8509 (tppt) cc_final: 0.8185 (tttm) REVERT: G 85 ASP cc_start: 0.8734 (t0) cc_final: 0.8263 (t0) REVERT: G 148 TYR cc_start: 0.8825 (m-80) cc_final: 0.8474 (m-80) REVERT: G 212 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (t0) REVERT: H 14 TRP cc_start: 0.9026 (m-10) cc_final: 0.8103 (m-10) REVERT: H 67 GLU cc_start: 0.8952 (pp20) cc_final: 0.8379 (pt0) REVERT: I 12 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7820 (mmtm) REVERT: I 100 ASN cc_start: 0.7975 (t0) cc_final: 0.7524 (t0) REVERT: I 100 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8300 (tm-30) REVERT: I 110 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8318 (p) REVERT: K 31 ASN cc_start: 0.7979 (t0) cc_final: 0.7625 (m-40) REVERT: K 54 LYS cc_start: 0.8576 (tppt) cc_final: 0.8210 (tttt) REVERT: K 85 ASP cc_start: 0.8740 (t0) cc_final: 0.7999 (t0) REVERT: L 19 ASP cc_start: 0.7178 (p0) cc_final: 0.6872 (p0) REVERT: L 54 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7483 (mtm180) REVERT: L 67 GLU cc_start: 0.8808 (pp20) cc_final: 0.8207 (pt0) REVERT: L 158 ASP cc_start: 0.8077 (t0) cc_final: 0.7654 (t70) REVERT: L 170 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7724 (ttt90) outliers start: 75 outliers final: 53 residues processed: 284 average time/residue: 0.2865 time to fit residues: 123.8561 Evaluate side-chains 280 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 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 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 61 THR 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 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 212 ASN 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 I residue 18 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR 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 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 71 ILE 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 182 ILE Chi-restraints excluded: chain L residue 10 LEU 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 90 ASP Chi-restraints excluded: chain L residue 144 CYS 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 211 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.180412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157471 restraints weight = 21752.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159413 restraints weight = 14866.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160873 restraints weight = 11282.045| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17802 Z= 0.245 Angle : 0.579 9.671 24102 Z= 0.303 Chirality : 0.045 0.434 2658 Planarity : 0.004 0.038 3123 Dihedral : 6.497 59.812 2900 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 3.85 % Allowed : 21.61 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2169 helix: 0.31 (0.30), residues: 294 sheet: -0.89 (0.22), residues: 615 loop : -0.95 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100B HIS 0.005 0.001 HIS K 17 PHE 0.013 0.001 PHE L 24 TYR 0.016 0.002 TYR L 94 ARG 0.003 0.000 ARG G 90 *********************** 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 299 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8599 (tppt) cc_final: 0.8220 (tttm) REVERT: C 85 ASP cc_start: 0.8706 (t0) cc_final: 0.8176 (t0) REVERT: E 100 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8133 (tm-30) REVERT: G 54 LYS cc_start: 0.8518 (tppt) cc_final: 0.8194 (tttm) REVERT: G 85 ASP cc_start: 0.8738 (t0) cc_final: 0.8290 (t0) REVERT: H 14 TRP cc_start: 0.9029 (m-10) cc_final: 0.8099 (m-10) REVERT: H 67 GLU cc_start: 0.8957 (pp20) cc_final: 0.8391 (pt0) REVERT: I 12 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7806 (mmtm) REVERT: I 100 ASN cc_start: 0.8045 (t0) cc_final: 0.7656 (t0) REVERT: I 100 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8315 (tm-30) REVERT: I 110 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8314 (p) REVERT: K 54 LYS cc_start: 0.8582 (tppt) cc_final: 0.8249 (tttt) REVERT: K 85 ASP cc_start: 0.8736 (t0) cc_final: 0.7970 (t0) REVERT: L 19 ASP cc_start: 0.7095 (p0) cc_final: 0.6750 (p0) REVERT: L 54 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7567 (mtm180) REVERT: L 67 GLU cc_start: 0.8812 (pp20) cc_final: 0.8235 (pt0) REVERT: L 158 ASP cc_start: 0.8106 (t0) cc_final: 0.7682 (t70) REVERT: L 170 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7728 (ttt90) outliers start: 71 outliers final: 54 residues processed: 282 average time/residue: 0.2904 time to fit residues: 124.2841 Evaluate side-chains 282 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 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 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 261 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 61 THR 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 58 ILE Chi-restraints excluded: chain G residue 18 HIS 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 I residue 18 VAL 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 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 K residue 182 ILE Chi-restraints excluded: chain L residue 10 LEU 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 90 ASP Chi-restraints excluded: chain L residue 144 CYS 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 197 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100AASN G 65 HIS ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132949 restraints weight = 21836.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135893 restraints weight = 14902.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137961 restraints weight = 11521.649| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17802 Z= 0.393 Angle : 0.655 9.840 24102 Z= 0.347 Chirality : 0.048 0.467 2658 Planarity : 0.004 0.042 3123 Dihedral : 6.799 59.497 2900 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.59 % Rotamer: Outliers : 3.53 % Allowed : 22.10 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2169 helix: 0.12 (0.30), residues: 300 sheet: -0.91 (0.22), residues: 609 loop : -1.13 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 47 HIS 0.009 0.002 HIS K 17 PHE 0.017 0.002 PHE L 24 TYR 0.019 0.002 TYR H 157 ARG 0.005 0.000 ARG C 137 ********************** 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 291 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 54 LYS cc_start: 0.8680 (tppt) cc_final: 0.8300 (tttm) REVERT: C 85 ASP cc_start: 0.8715 (t0) cc_final: 0.8131 (t0) REVERT: E 50 TRP cc_start: 0.8839 (OUTLIER) cc_final: 0.7877 (p90) REVERT: E 100 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8131 (tm-30) REVERT: G 54 LYS cc_start: 0.8575 (tppt) cc_final: 0.8242 (tttm) REVERT: G 85 ASP cc_start: 0.8823 (t0) cc_final: 0.8368 (t0) REVERT: H 14 TRP cc_start: 0.9067 (m-10) cc_final: 0.8054 (m-10) REVERT: H 67 GLU cc_start: 0.9003 (pp20) cc_final: 0.8415 (pt0) REVERT: I 12 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7810 (mmtm) REVERT: I 100 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8165 (tm-30) REVERT: I 110 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (p) REVERT: K 54 LYS cc_start: 0.8586 (tppt) cc_final: 0.8259 (tttt) REVERT: K 85 ASP cc_start: 0.8751 (t0) cc_final: 0.7992 (t0) REVERT: L 19 ASP cc_start: 0.7164 (p0) cc_final: 0.6804 (p0) REVERT: L 54 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7442 (mtm180) REVERT: L 67 GLU cc_start: 0.8861 (pp20) cc_final: 0.8269 (pt0) REVERT: L 158 ASP cc_start: 0.8147 (t0) cc_final: 0.7745 (t70) REVERT: L 170 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7789 (ttt90) outliers start: 65 outliers final: 58 residues processed: 274 average time/residue: 0.2921 time to fit residues: 120.5110 Evaluate side-chains 287 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 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 71 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 214 VAL 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 120 GLU 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 100 ASN Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain G residue 18 HIS 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 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 I residue 18 VAL 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 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 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 71 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 182 ILE Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 10 LEU 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 79 ASN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 144 CYS 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 105 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** 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 = 0.3996 r_free = 0.3996 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146685 restraints weight = 21772.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146530 restraints weight = 18747.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147660 restraints weight = 18644.272| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 17802 Z= 0.340 Angle : 0.866 59.200 24102 Z= 0.503 Chirality : 0.065 2.153 2658 Planarity : 0.005 0.158 3123 Dihedral : 6.809 59.606 2900 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.48 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2169 helix: 0.11 (0.30), residues: 300 sheet: -0.92 (0.22), residues: 609 loop : -1.12 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 100B HIS 0.009 0.002 HIS K 17 PHE 0.016 0.002 PHE L 24 TYR 0.018 0.002 TYR L 157 ARG 0.004 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.45 seconds wall clock time: 88 minutes 46.91 seconds (5326.91 seconds total)