Starting phenix.real_space_refine on Sun Aug 24 06:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uaw_42073/08_2025/8uaw_42073.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 60 5.16 5 C 11300 2.51 5 N 3100 2.21 5 O 3370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17830 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "B" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "C" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "G" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "H" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "I" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain: "J" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Time building chain proxies: 4.82, per 1000 atoms: 0.27 Number of scatterers: 17830 At special positions: 0 Unit cell: (93.96, 89.64, 165.24, 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 60 16.00 O 3370 8.00 N 3100 7.00 C 11300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 58 " distance=2.03 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 58 " 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 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 881.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4260 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 43.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.775A pdb=" N LEU A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 116 removed outlier: 3.711A pdb=" N VAL A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.823A pdb=" N HIS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 182 Processing helix chain 'A' and resid 199 through 231 removed outlier: 3.562A pdb=" N HIS A 206 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.741A pdb=" N LEU B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 116 removed outlier: 3.660A pdb=" N VAL B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.736A pdb=" N HIS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 Processing helix chain 'B' and resid 199 through 231 removed outlier: 3.607A pdb=" N HIS B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.743A pdb=" N LEU C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 116 removed outlier: 3.708A pdb=" N VAL C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.666A pdb=" N HIS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 182 Processing helix chain 'C' and resid 199 through 231 removed outlier: 3.582A pdb=" N HIS C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.742A pdb=" N LEU D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.686A pdb=" N VAL D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 143 removed outlier: 3.696A pdb=" N HIS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 Processing helix chain 'D' and resid 199 through 231 removed outlier: 3.552A pdb=" N HIS D 206 " --> pdb=" O HIS D 202 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 3.736A pdb=" N LEU E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.711A pdb=" N VAL E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 132 through 143 removed outlier: 3.883A pdb=" N HIS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 182 Processing helix chain 'E' and resid 199 through 231 removed outlier: 3.595A pdb=" N HIS E 206 " --> pdb=" O HIS E 202 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.736A pdb=" N LEU F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 116 removed outlier: 3.687A pdb=" N VAL F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.700A pdb=" N HIS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 182 Processing helix chain 'F' and resid 199 through 231 removed outlier: 3.556A pdb=" N HIS F 206 " --> pdb=" O HIS F 202 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 removed outlier: 3.735A pdb=" N LEU G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 116 removed outlier: 3.710A pdb=" N VAL G 101 " --> pdb=" O HIS G 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 132 through 143 removed outlier: 3.665A pdb=" N HIS G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 182 Processing helix chain 'G' and resid 199 through 231 removed outlier: 3.584A pdb=" N HIS G 206 " --> pdb=" O HIS G 202 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 47 removed outlier: 3.782A pdb=" N LEU H 40 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 removed outlier: 3.659A pdb=" N VAL H 101 " --> pdb=" O HIS H 97 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'H' and resid 132 through 143 removed outlier: 3.740A pdb=" N HIS H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 182 Processing helix chain 'H' and resid 199 through 231 removed outlier: 3.607A pdb=" N HIS H 206 " --> pdb=" O HIS H 202 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 47 removed outlier: 3.774A pdb=" N LEU I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 116 removed outlier: 3.701A pdb=" N VAL I 101 " --> pdb=" O HIS I 97 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'I' and resid 132 through 143 removed outlier: 3.824A pdb=" N HIS I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 182 Processing helix chain 'I' and resid 199 through 231 removed outlier: 3.553A pdb=" N HIS I 206 " --> pdb=" O HIS I 202 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL I 214 " --> pdb=" O LYS I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 47 removed outlier: 3.743A pdb=" N LEU J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 116 removed outlier: 3.710A pdb=" N VAL J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 131 No H-bonds generated for 'chain 'J' and resid 129 through 131' Processing helix chain 'J' and resid 132 through 143 removed outlier: 3.884A pdb=" N HIS J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 182 Processing helix chain 'J' and resid 199 through 231 removed outlier: 3.598A pdb=" N HIS J 206 " --> pdb=" O HIS J 202 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA J 207 " --> pdb=" O ASP J 203 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 214 " --> pdb=" O LYS J 210 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA J 231 " --> pdb=" O ARG J 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 16 removed outlier: 4.055A pdb=" N PHE A 12 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 31 current: chain 'B' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 32 current: chain 'C' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 32 current: chain 'D' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 28 through 32 current: chain 'E' and resid 20 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 127 removed outlier: 3.998A pdb=" N ALA A 148 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 154 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 149 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 151 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 190 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 153 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 127 removed outlier: 6.897A pdb=" N LYS B 88 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL B 150 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA B 90 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA B 152 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 92 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N PHE B 154 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA B 94 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 149 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 188 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY B 151 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 190 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA B 153 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 127 removed outlier: 6.798A pdb=" N LYS C 88 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL C 150 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA C 90 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA C 152 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 92 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE C 154 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA C 94 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 149 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL C 188 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY C 151 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C 190 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 153 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 120 through 127 removed outlier: 6.844A pdb=" N LYS D 88 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL D 150 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA D 90 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 152 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 92 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N PHE D 154 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ALA D 94 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 149 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL D 188 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY D 151 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 190 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 153 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 120 through 127 removed outlier: 6.840A pdb=" N LYS E 88 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL E 150 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA E 90 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA E 152 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 92 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE E 154 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ALA E 94 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 149 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL E 188 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY E 151 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 190 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA E 153 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 16 removed outlier: 4.035A pdb=" N PHE F 12 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 28 through 32 current: chain 'G' and resid 6 through 16 removed outlier: 4.039A pdb=" N PHE G 12 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR G 20 " --> pdb=" O ASN G 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 28 through 32 current: chain 'H' and resid 4 through 16 removed outlier: 4.072A pdb=" N PHE H 12 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 28 through 32 current: chain 'I' and resid 6 through 16 removed outlier: 4.019A pdb=" N PHE I 12 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 28 through 31 current: chain 'J' and resid 6 through 16 removed outlier: 4.034A pdb=" N PHE J 12 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 120 through 127 removed outlier: 6.844A pdb=" N LYS F 88 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL F 150 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA F 90 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA F 152 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE F 92 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N PHE F 154 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ALA F 94 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE F 149 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL F 188 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY F 151 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU F 190 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA F 153 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 120 through 127 removed outlier: 3.578A pdb=" N GLU G 121 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS G 88 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL G 150 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA G 90 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA G 152 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE G 92 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N PHE G 154 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ALA G 94 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE G 149 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL G 188 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY G 151 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU G 190 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 153 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 127 removed outlier: 6.904A pdb=" N LYS H 88 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL H 150 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA H 90 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA H 152 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE H 92 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N PHE H 154 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ALA H 94 " --> pdb=" O PHE H 154 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE H 149 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL H 188 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY H 151 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU H 190 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA H 153 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 120 through 127 removed outlier: 3.994A pdb=" N ALA I 148 " --> pdb=" O LYS I 88 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE I 154 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE I 149 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL I 188 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY I 151 " --> pdb=" O VAL I 188 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU I 190 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA I 153 " --> pdb=" O LEU I 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 120 through 127 removed outlier: 6.843A pdb=" N LYS J 88 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL J 150 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA J 90 " --> pdb=" O VAL J 150 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA J 152 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE J 92 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N PHE J 154 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ALA J 94 " --> pdb=" O PHE J 154 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE J 149 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL J 188 " --> pdb=" O ILE J 149 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY J 151 " --> pdb=" O VAL J 188 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU J 190 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA J 153 " --> pdb=" O LEU J 190 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2541 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5905 1.34 - 1.46: 4217 1.46 - 1.58: 8018 1.58 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 18240 Sorted by residual: bond pdb=" N THR G 85 " pdb=" CA THR G 85 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.15e-02 7.56e+03 7.21e+00 bond pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.46e+00 bond pdb=" N ASN I 16 " pdb=" CA ASN I 16 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.44e+00 bond pdb=" N ASN A 16 " pdb=" CA ASN A 16 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.41e+00 bond pdb=" N THR I 20 " pdb=" CA THR I 20 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.19e-02 7.06e+03 6.14e+00 ... (remaining 18235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 24195 1.43 - 2.87: 335 2.87 - 4.30: 99 4.30 - 5.74: 36 5.74 - 7.17: 5 Bond angle restraints: 24670 Sorted by residual: angle pdb=" C SER D 198 " pdb=" N LYS D 199 " pdb=" CA LYS D 199 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C SER H 198 " pdb=" N LYS H 199 " pdb=" CA LYS H 199 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C SER B 198 " pdb=" N LYS B 199 " pdb=" CA LYS B 199 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N THR G 85 " pdb=" CA THR G 85 " pdb=" C THR G 85 " ideal model delta sigma weight residual 113.38 109.44 3.94 1.17e+00 7.31e-01 1.13e+01 angle pdb=" CA ASN I 16 " pdb=" C ASN I 16 " pdb=" O ASN I 16 " ideal model delta sigma weight residual 121.81 118.05 3.76 1.18e+00 7.18e-01 1.01e+01 ... (remaining 24665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9255 17.88 - 35.75: 1009 35.75 - 53.63: 302 53.63 - 71.51: 68 71.51 - 89.38: 26 Dihedral angle restraints: 10660 sinusoidal: 4040 harmonic: 6620 Sorted by residual: dihedral pdb=" CA ASP I 126 " pdb=" CB ASP I 126 " pdb=" CG ASP I 126 " pdb=" OD1 ASP I 126 " ideal model delta sinusoidal sigma weight residual -30.00 -83.06 53.06 1 2.00e+01 2.50e-03 9.58e+00 dihedral pdb=" CA ASP A 126 " pdb=" CB ASP A 126 " pdb=" CG ASP A 126 " pdb=" OD1 ASP A 126 " ideal model delta sinusoidal sigma weight residual -30.00 -83.06 53.06 1 2.00e+01 2.50e-03 9.58e+00 dihedral pdb=" N ASN F 71 " pdb=" CA ASN F 71 " pdb=" CB ASN F 71 " pdb=" CG ASN F 71 " ideal model delta sinusoidal sigma weight residual -60.00 -119.96 59.96 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 10657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1878 0.035 - 0.070: 519 0.070 - 0.105: 242 0.105 - 0.141: 85 0.141 - 0.176: 6 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA LEU B 112 " pdb=" N LEU B 112 " pdb=" C LEU B 112 " pdb=" CB LEU B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA LEU E 112 " pdb=" N LEU E 112 " pdb=" C LEU E 112 " pdb=" CB LEU E 112 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA LEU H 112 " pdb=" N LEU H 112 " pdb=" C LEU H 112 " pdb=" CB LEU H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 2727 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 199 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.81e+00 pdb=" C LYS E 199 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS E 199 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU E 200 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 199 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C LYS J 199 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS J 199 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU J 200 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 199 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C LYS G 199 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS G 199 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU G 200 " -0.015 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3074 2.77 - 3.30: 16432 3.30 - 3.84: 29976 3.84 - 4.37: 33937 4.37 - 4.90: 62366 Nonbonded interactions: 145785 Sorted by model distance: nonbonded pdb=" OD1 ASP G 102 " pdb=" NH2 ARG G 105 " model vdw 2.238 3.120 nonbonded pdb=" OD1 ASP C 102 " pdb=" NH2 ARG C 105 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP E 18 " pdb=" OG1 THR E 20 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASP F 18 " pdb=" OG1 THR F 20 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP J 18 " pdb=" OG1 THR J 20 " model vdw 2.309 3.040 ... (remaining 145780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.020 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.003 0.036 18250 Z= 0.155 Angle : 0.505 7.171 24690 Z= 0.294 Chirality : 0.044 0.176 2730 Planarity : 0.003 0.030 3180 Dihedral : 17.185 89.385 6370 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.67 % Allowed : 23.01 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2300 helix: 1.54 (0.17), residues: 930 sheet: -0.15 (0.28), residues: 310 loop : -1.34 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 142 TYR 0.004 0.001 TYR H 146 PHE 0.012 0.001 PHE G 108 TRP 0.003 0.000 TRP H 96 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00298 (18240) covalent geometry : angle 0.50554 (24670) SS BOND : bond 0.00042 ( 10) SS BOND : angle 0.24789 ( 20) hydrogen bonds : bond 0.14562 ( 857) hydrogen bonds : angle 5.88488 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 MET cc_start: -0.2985 (ptm) cc_final: -0.4362 (ttp) outliers start: 31 outliers final: 8 residues processed: 163 average time/residue: 0.7817 time to fit residues: 140.2319 Evaluate side-chains 143 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 178 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 208 HIS B 178 GLN B 208 HIS B 222 GLN C 45 GLN C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 208 HIS G 222 GLN ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 178 GLN H 208 HIS H 222 GLN I 16 ASN I 208 HIS J 208 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.210670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109329 restraints weight = 20850.980| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.24 r_work: 0.3000 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18250 Z= 0.138 Angle : 0.490 7.719 24690 Z= 0.265 Chirality : 0.045 0.143 2730 Planarity : 0.003 0.030 3180 Dihedral : 4.459 49.337 2458 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.92 % Allowed : 20.65 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2300 helix: 1.71 (0.17), residues: 930 sheet: 0.39 (0.30), residues: 290 loop : -1.32 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 142 TYR 0.007 0.001 TYR A 15 PHE 0.023 0.001 PHE A 21 TRP 0.004 0.001 TRP I 35 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00324 (18240) covalent geometry : angle 0.49063 (24670) SS BOND : bond 0.00027 ( 10) SS BOND : angle 0.22971 ( 20) hydrogen bonds : bond 0.06167 ( 857) hydrogen bonds : angle 4.36342 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 128 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8385 (t70) REVERT: D 121 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: F 121 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: F 187 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9193 (t) REVERT: G 136 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8353 (t70) REVERT: H 132 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8438 (mm-30) outliers start: 73 outliers final: 22 residues processed: 191 average time/residue: 0.7155 time to fit residues: 151.4222 Evaluate side-chains 160 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 160 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 156 optimal weight: 0.0060 chunk 170 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 199 optimal weight: 5.9990 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 208 HIS H 45 GLN H 178 GLN H 208 HIS I 208 HIS J 208 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.214129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112841 restraints weight = 21066.642| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.30 r_work: 0.3068 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18250 Z= 0.098 Angle : 0.443 6.425 24690 Z= 0.239 Chirality : 0.043 0.143 2730 Planarity : 0.003 0.029 3180 Dihedral : 4.078 50.316 2452 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.44 % Allowed : 21.40 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2300 helix: 1.82 (0.17), residues: 950 sheet: 0.55 (0.30), residues: 290 loop : -1.41 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 142 TYR 0.005 0.001 TYR I 15 PHE 0.011 0.001 PHE E 108 TRP 0.004 0.001 TRP H 31 HIS 0.002 0.000 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00195 (18240) covalent geometry : angle 0.44351 (24670) SS BOND : bond 0.00014 ( 10) SS BOND : angle 0.14279 ( 20) hydrogen bonds : bond 0.04658 ( 857) hydrogen bonds : angle 3.98193 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6917 (mmm) cc_final: 0.6487 (tmm) REVERT: A 85 THR cc_start: 0.4582 (OUTLIER) cc_final: 0.4274 (p) REVERT: A 126 ASP cc_start: 0.8833 (m-30) cc_final: 0.8481 (m-30) REVERT: A 143 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 85 THR cc_start: 0.4490 (OUTLIER) cc_final: 0.4208 (p) REVERT: C 1 MET cc_start: 0.7172 (mmm) cc_final: 0.6834 (tmm) REVERT: C 85 THR cc_start: 0.4451 (OUTLIER) cc_final: 0.4120 (p) REVERT: C 136 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8320 (t70) REVERT: C 199 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6973 (pptt) REVERT: C 200 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: D 1 MET cc_start: 0.6851 (mmm) cc_final: 0.6643 (tmm) REVERT: D 121 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: E 1 MET cc_start: 0.6859 (mmm) cc_final: 0.6559 (tmm) REVERT: E 126 ASP cc_start: 0.9031 (m-30) cc_final: 0.8821 (m-30) REVERT: F 121 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: F 199 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7172 (pptt) REVERT: F 222 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: G 1 MET cc_start: 0.7144 (mmm) cc_final: 0.6802 (tmm) REVERT: G 136 HIS cc_start: 0.8955 (OUTLIER) cc_final: 0.8366 (t70) REVERT: G 199 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6966 (pptt) REVERT: G 200 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: H 85 THR cc_start: 0.4369 (OUTLIER) cc_final: 0.4105 (p) REVERT: I 1 MET cc_start: 0.6941 (mmm) cc_final: 0.6493 (tmm) REVERT: I 85 THR cc_start: 0.4532 (OUTLIER) cc_final: 0.4190 (p) REVERT: I 126 ASP cc_start: 0.8836 (m-30) cc_final: 0.8524 (m-30) REVERT: I 143 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (t) REVERT: J 1 MET cc_start: 0.7015 (mmm) cc_final: 0.6704 (tmm) REVERT: J 126 ASP cc_start: 0.9032 (m-30) cc_final: 0.8822 (m-30) outliers start: 64 outliers final: 18 residues processed: 187 average time/residue: 0.7040 time to fit residues: 145.7366 Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 136 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 146 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 40.0000 chunk 156 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 46 optimal weight: 0.3980 chunk 6 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 166 optimal weight: 50.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 208 HIS B 45 GLN B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 16 ASN G 208 HIS G 222 GLN H 16 ASN H 178 GLN H 208 HIS H 222 GLN I 38 GLN I 208 HIS J 208 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.213186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111577 restraints weight = 20911.029| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.32 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18250 Z= 0.105 Angle : 0.441 6.274 24690 Z= 0.239 Chirality : 0.044 0.144 2730 Planarity : 0.003 0.028 3180 Dihedral : 4.069 50.391 2452 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.03 % Allowed : 21.13 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2300 helix: 2.11 (0.17), residues: 930 sheet: 0.55 (0.30), residues: 290 loop : -1.24 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 142 TYR 0.005 0.001 TYR I 15 PHE 0.010 0.001 PHE C 108 TRP 0.004 0.000 TRP H 31 HIS 0.002 0.001 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00228 (18240) covalent geometry : angle 0.44130 (24670) SS BOND : bond 0.00013 ( 10) SS BOND : angle 0.12244 ( 20) hydrogen bonds : bond 0.04931 ( 857) hydrogen bonds : angle 3.91877 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 140 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6931 (mmm) cc_final: 0.6500 (tmm) REVERT: A 85 THR cc_start: 0.4460 (OUTLIER) cc_final: 0.4141 (p) REVERT: B 85 THR cc_start: 0.4290 (OUTLIER) cc_final: 0.3972 (p) REVERT: B 132 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: C 1 MET cc_start: 0.7153 (mmm) cc_final: 0.6798 (tmm) REVERT: C 136 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8345 (t70) REVERT: C 199 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7003 (pptt) REVERT: C 200 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: C 210 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8699 (tttp) REVERT: D 1 MET cc_start: 0.6783 (mmm) cc_final: 0.6547 (tmm) REVERT: D 121 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: E 1 MET cc_start: 0.7001 (mmm) cc_final: 0.6667 (tmm) REVERT: E 126 ASP cc_start: 0.8985 (m-30) cc_final: 0.8739 (m-30) REVERT: F 1 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.5789 (tmm) REVERT: F 121 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: F 199 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7128 (pptt) REVERT: F 222 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: G 1 MET cc_start: 0.7093 (mmm) cc_final: 0.6717 (tmm) REVERT: G 85 THR cc_start: 0.3829 (OUTLIER) cc_final: 0.3563 (p) REVERT: G 136 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8304 (t70) REVERT: G 199 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6982 (pptt) REVERT: G 200 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: H 85 THR cc_start: 0.4279 (OUTLIER) cc_final: 0.3972 (p) REVERT: H 222 GLN cc_start: 0.8471 (tt0) cc_final: 0.8218 (tm-30) REVERT: I 1 MET cc_start: 0.7008 (mmm) cc_final: 0.6560 (tmm) REVERT: I 85 THR cc_start: 0.4485 (OUTLIER) cc_final: 0.4114 (p) REVERT: J 1 MET cc_start: 0.6921 (mmm) cc_final: 0.6630 (tmm) REVERT: J 126 ASP cc_start: 0.8979 (m-30) cc_final: 0.8732 (m-30) outliers start: 75 outliers final: 24 residues processed: 192 average time/residue: 0.7482 time to fit residues: 158.5009 Evaluate side-chains 181 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 136 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 82 optimal weight: 3.9990 chunk 210 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS B 222 GLN C 208 HIS D 208 HIS E 45 GLN E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 208 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.207181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106124 restraints weight = 21029.184| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.25 r_work: 0.2950 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18250 Z= 0.224 Angle : 0.522 5.776 24690 Z= 0.290 Chirality : 0.047 0.154 2730 Planarity : 0.004 0.032 3180 Dihedral : 4.543 49.416 2452 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.46 % Allowed : 21.13 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2300 helix: 1.89 (0.17), residues: 920 sheet: 0.32 (0.29), residues: 290 loop : -1.42 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 227 TYR 0.008 0.001 TYR J 131 PHE 0.015 0.002 PHE H 87 TRP 0.004 0.001 TRP C 96 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00570 (18240) covalent geometry : angle 0.52257 (24670) SS BOND : bond 0.00028 ( 10) SS BOND : angle 0.16007 ( 20) hydrogen bonds : bond 0.07646 ( 857) hydrogen bonds : angle 4.39117 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 134 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6801 (mmm) cc_final: 0.6367 (tmm) REVERT: B 132 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: C 1 MET cc_start: 0.7008 (mmm) cc_final: 0.6677 (tmm) REVERT: C 136 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8164 (t70) REVERT: C 199 LYS cc_start: 0.7574 (tptt) cc_final: 0.7338 (tptt) REVERT: C 210 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8607 (tttp) REVERT: D 1 MET cc_start: 0.6600 (mmm) cc_final: 0.6349 (tmm) REVERT: D 121 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: D 132 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: E 1 MET cc_start: 0.6813 (mmm) cc_final: 0.6475 (tmm) REVERT: F 1 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5524 (tmm) REVERT: F 121 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: F 132 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: G 1 MET cc_start: 0.6912 (mmm) cc_final: 0.6595 (tmm) REVERT: G 136 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8156 (t70) REVERT: G 210 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8607 (tttp) REVERT: I 1 MET cc_start: 0.6846 (mmm) cc_final: 0.6409 (tmm) REVERT: J 1 MET cc_start: 0.6870 (mmm) cc_final: 0.6622 (tmm) outliers start: 83 outliers final: 25 residues processed: 210 average time/residue: 0.7073 time to fit residues: 164.6763 Evaluate side-chains 171 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 210 LYS Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 222 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 213 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 45 GLN C 208 HIS D 208 HIS E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 208 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.207873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108339 restraints weight = 20982.012| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.16 r_work: 0.2926 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 18250 Z= 0.284 Angle : 0.565 5.737 24690 Z= 0.315 Chirality : 0.049 0.156 2730 Planarity : 0.004 0.034 3180 Dihedral : 4.720 49.163 2452 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.19 % Allowed : 22.04 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2300 helix: 1.62 (0.17), residues: 920 sheet: 0.10 (0.29), residues: 290 loop : -1.51 (0.15), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 227 TYR 0.009 0.001 TYR G 131 PHE 0.017 0.002 PHE H 87 TRP 0.005 0.001 TRP J 96 HIS 0.006 0.001 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00731 (18240) covalent geometry : angle 0.56532 (24670) SS BOND : bond 0.00030 ( 10) SS BOND : angle 0.21486 ( 20) hydrogen bonds : bond 0.08339 ( 857) hydrogen bonds : angle 4.56726 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6864 (mmm) cc_final: 0.6418 (tmm) REVERT: C 1 MET cc_start: 0.7053 (mmm) cc_final: 0.6713 (tmm) REVERT: C 136 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8185 (t70) REVERT: C 210 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8635 (tttp) REVERT: D 1 MET cc_start: 0.6587 (mmm) cc_final: 0.6360 (tmm) REVERT: D 121 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: D 132 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: E 1 MET cc_start: 0.6865 (mmm) cc_final: 0.6504 (tmm) REVERT: F 1 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.5574 (tmm) REVERT: F 121 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: F 132 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8634 (mm-30) REVERT: F 222 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: G 1 MET cc_start: 0.6965 (mmm) cc_final: 0.6637 (tmm) REVERT: G 136 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8176 (t70) REVERT: I 1 MET cc_start: 0.6883 (mmm) cc_final: 0.6427 (tmm) REVERT: J 1 MET cc_start: 0.6917 (mmm) cc_final: 0.6663 (tmm) outliers start: 78 outliers final: 39 residues processed: 206 average time/residue: 0.6915 time to fit residues: 158.3987 Evaluate side-chains 186 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 174 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 45 GLN C 208 HIS D 208 HIS E 136 HIS E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 136 HIS J 208 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.211588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108506 restraints weight = 21000.089| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.31 r_work: 0.3010 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18250 Z= 0.118 Angle : 0.462 6.423 24690 Z= 0.251 Chirality : 0.044 0.150 2730 Planarity : 0.003 0.032 3180 Dihedral : 4.487 51.294 2452 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.28 % Allowed : 23.17 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2300 helix: 1.76 (0.17), residues: 940 sheet: 0.12 (0.24), residues: 440 loop : -1.43 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 142 TYR 0.005 0.001 TYR I 15 PHE 0.011 0.001 PHE F 108 TRP 0.005 0.001 TRP C 96 HIS 0.003 0.001 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00260 (18240) covalent geometry : angle 0.46186 (24670) SS BOND : bond 0.00018 ( 10) SS BOND : angle 0.12963 ( 20) hydrogen bonds : bond 0.05573 ( 857) hydrogen bonds : angle 4.06196 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7102 (mmm) cc_final: 0.6625 (tmm) REVERT: B 132 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8081 (mm-30) REVERT: C 1 MET cc_start: 0.7243 (mmm) cc_final: 0.6883 (tmm) REVERT: C 136 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8353 (t70) REVERT: C 210 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8733 (tttp) REVERT: D 1 MET cc_start: 0.6791 (mmm) cc_final: 0.6532 (tmm) REVERT: D 121 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: E 1 MET cc_start: 0.7039 (mmm) cc_final: 0.6711 (tmm) REVERT: F 1 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5798 (tmm) REVERT: F 121 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: F 222 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: G 1 MET cc_start: 0.7117 (mmm) cc_final: 0.6759 (tmm) REVERT: G 136 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8327 (t70) REVERT: H 132 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: I 1 MET cc_start: 0.7090 (mmm) cc_final: 0.6615 (tmm) REVERT: J 1 MET cc_start: 0.7062 (mmm) cc_final: 0.6800 (tmm) outliers start: 61 outliers final: 23 residues processed: 186 average time/residue: 0.7198 time to fit residues: 148.2986 Evaluate side-chains 165 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 169 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS B 222 GLN C 45 GLN C 208 HIS D 208 HIS E 208 HIS F 16 ASN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 208 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.315351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.4947 r_free = 0.4947 target = 0.256126 restraints weight = 24158.736| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 0.92 r_work: 0.3162 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 18250 Z= 0.327 Angle : 0.590 5.681 24690 Z= 0.329 Chirality : 0.050 0.161 2730 Planarity : 0.004 0.035 3180 Dihedral : 4.589 48.843 2448 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.28 % Allowed : 23.01 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2300 helix: 1.62 (0.17), residues: 920 sheet: -0.06 (0.23), residues: 440 loop : -1.46 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 227 TYR 0.010 0.002 TYR E 131 PHE 0.019 0.002 PHE H 87 TRP 0.007 0.001 TRP E 96 HIS 0.006 0.001 HIS F 136 Details of bonding type rmsd covalent geometry : bond 0.00844 (18240) covalent geometry : angle 0.59066 (24670) SS BOND : bond 0.00037 ( 10) SS BOND : angle 0.24659 ( 20) hydrogen bonds : bond 0.08728 ( 857) hydrogen bonds : angle 4.59664 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5351 (mmm) cc_final: 0.5052 (tmm) REVERT: C 136 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.8408 (t70) REVERT: C 210 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8720 (tttp) REVERT: D 121 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: F 1 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.3938 (tmm) REVERT: F 121 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: G 136 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8404 (t70) REVERT: I 1 MET cc_start: 0.5422 (mmm) cc_final: 0.5154 (tmm) outliers start: 61 outliers final: 28 residues processed: 190 average time/residue: 0.6915 time to fit residues: 146.1520 Evaluate side-chains 171 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 175 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 chunk 134 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 136 HIS E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 136 HIS J 208 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.210468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107787 restraints weight = 20746.798| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.25 r_work: 0.2999 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18250 Z= 0.131 Angle : 0.481 6.367 24690 Z= 0.261 Chirality : 0.045 0.149 2730 Planarity : 0.003 0.034 3180 Dihedral : 4.199 51.096 2448 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.74 % Allowed : 23.82 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.17), residues: 2300 helix: 1.72 (0.17), residues: 940 sheet: 0.10 (0.24), residues: 440 loop : -1.47 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 142 TYR 0.005 0.001 TYR I 15 PHE 0.012 0.001 PHE E 108 TRP 0.006 0.001 TRP B 96 HIS 0.004 0.001 HIS H 218 Details of bonding type rmsd covalent geometry : bond 0.00306 (18240) covalent geometry : angle 0.48125 (24670) SS BOND : bond 0.00023 ( 10) SS BOND : angle 0.17786 ( 20) hydrogen bonds : bond 0.05924 ( 857) hydrogen bonds : angle 4.10725 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7102 (mmm) cc_final: 0.6607 (tmm) REVERT: B 132 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: C 136 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8360 (t70) REVERT: C 210 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8700 (tttp) REVERT: D 1 MET cc_start: 0.6931 (tmm) cc_final: 0.5861 (tmm) REVERT: D 121 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: E 1 MET cc_start: 0.7278 (tmm) cc_final: 0.6278 (tmm) REVERT: F 1 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.5951 (tmm) REVERT: F 121 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: G 1 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6163 (tmm) REVERT: G 136 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.8248 (t70) REVERT: H 132 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: I 1 MET cc_start: 0.7134 (mmm) cc_final: 0.6663 (tmm) REVERT: J 1 MET cc_start: 0.7263 (tmm) cc_final: 0.6390 (tmm) outliers start: 51 outliers final: 26 residues processed: 176 average time/residue: 0.7529 time to fit residues: 146.1748 Evaluate side-chains 168 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 178 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 49 optimal weight: 40.0000 chunk 114 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS H 222 GLN I 208 HIS J 208 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.318058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.4558 r_free = 0.4558 target = 0.241163 restraints weight = 24061.288| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.13 r_work: 0.2999 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18250 Z= 0.192 Angle : 0.517 7.733 24690 Z= 0.283 Chirality : 0.046 0.152 2730 Planarity : 0.003 0.034 3180 Dihedral : 4.354 49.976 2448 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.12 % Allowed : 23.49 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2300 helix: 1.80 (0.17), residues: 920 sheet: 0.08 (0.24), residues: 440 loop : -1.38 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 142 TYR 0.007 0.001 TYR G 131 PHE 0.012 0.002 PHE H 87 TRP 0.003 0.001 TRP I 96 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd covalent geometry : bond 0.00484 (18240) covalent geometry : angle 0.51750 (24670) SS BOND : bond 0.00027 ( 10) SS BOND : angle 0.19954 ( 20) hydrogen bonds : bond 0.07079 ( 857) hydrogen bonds : angle 4.28451 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6953 (mmm) cc_final: 0.6450 (tmm) REVERT: B 132 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: C 1 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6271 (tmm) REVERT: C 136 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8361 (t70) REVERT: C 210 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8759 (tttp) REVERT: D 1 MET cc_start: 0.6925 (tmm) cc_final: 0.5901 (tmm) REVERT: D 121 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: D 222 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 1 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6505 (tmm) REVERT: F 1 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.5968 (tmm) REVERT: F 121 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: F 222 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: G 1 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6157 (tmm) REVERT: G 136 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8376 (t70) REVERT: H 132 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: I 1 MET cc_start: 0.6933 (mmm) cc_final: 0.6448 (tmm) REVERT: J 1 MET cc_start: 0.7095 (tmm) cc_final: 0.6207 (tmm) outliers start: 58 outliers final: 30 residues processed: 183 average time/residue: 0.6622 time to fit residues: 134.2101 Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 178 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 84 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 35 optimal weight: 0.6980 chunk 163 optimal weight: 40.0000 chunk 214 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 94 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 208 HIS C 222 GLN D 208 HIS E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS G 222 GLN H 178 GLN H 208 HIS H 222 GLN I 208 HIS J 208 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.319155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.259809 restraints weight = 24279.707| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.21 r_work: 0.3188 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18250 Z= 0.153 Angle : 0.495 7.853 24690 Z= 0.270 Chirality : 0.045 0.150 2730 Planarity : 0.003 0.033 3180 Dihedral : 4.243 50.548 2448 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.01 % Allowed : 23.66 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2300 helix: 1.78 (0.17), residues: 930 sheet: 0.14 (0.24), residues: 440 loop : -1.46 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 142 TYR 0.006 0.001 TYR I 15 PHE 0.011 0.001 PHE D 108 TRP 0.003 0.001 TRP I 96 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd covalent geometry : bond 0.00374 (18240) covalent geometry : angle 0.49510 (24670) SS BOND : bond 0.00024 ( 10) SS BOND : angle 0.17501 ( 20) hydrogen bonds : bond 0.06393 ( 857) hydrogen bonds : angle 4.16872 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8762.68 seconds wall clock time: 149 minutes 50.80 seconds (8990.80 seconds total)