Starting phenix.real_space_refine on Mon May 19 00:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uaw_42073/05_2025/8uaw_42073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uaw_42073/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uaw_42073/05_2025/8uaw_42073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uaw_42073/05_2025/8uaw_42073.map" model { file = "/net/cci-nas-00/data/ceres_data/8uaw_42073/05_2025/8uaw_42073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uaw_42073/05_2025/8uaw_42073.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.84, per 1000 atoms: 0.55 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: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.65 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: 4.70 Time building geometry restraints manager: 4.80 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: 0.02 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 36.700 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 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 TRP 0.003 0.000 TRP H 96 HIS 0.005 0.001 HIS B 218 PHE 0.012 0.001 PHE G 108 TYR 0.004 0.001 TYR H 146 ARG 0.006 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.14562 ( 857) hydrogen bonds : angle 5.88488 ( 2541) SS BOND : bond 0.00042 ( 10) SS BOND : angle 0.24789 ( 20) covalent geometry : bond 0.00298 (18240) covalent geometry : angle 0.50554 (24670) *********************** 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 : 1.741 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: 1.5040 time to fit residues: 271.1135 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 : 1.997 ------------------------------------------------------------------------------- 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 194 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 180 optimal weight: 0.6980 chunk 69 optimal weight: 0.0570 chunk 109 optimal weight: 0.8980 chunk 134 optimal weight: 0.0020 chunk 208 optimal weight: 50.0000 overall best weight: 0.7308 ------------------------------------------------------------------------------- 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 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.213021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112446 restraints weight = 20958.216| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.26 r_work: 0.3041 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18250 Z= 0.110 Angle : 0.471 7.583 24690 Z= 0.252 Chirality : 0.044 0.150 2730 Planarity : 0.003 0.029 3180 Dihedral : 4.308 49.779 2458 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.25 % Allowed : 20.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2300 helix: 1.65 (0.17), residues: 950 sheet: 0.49 (0.30), residues: 290 loop : -1.42 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 35 HIS 0.002 0.001 HIS G 136 PHE 0.019 0.001 PHE A 21 TYR 0.007 0.001 TYR I 15 ARG 0.005 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 857) hydrogen bonds : angle 4.19536 ( 2541) SS BOND : bond 0.00023 ( 10) SS BOND : angle 0.22124 ( 20) covalent geometry : bond 0.00233 (18240) covalent geometry : angle 0.47127 (24670) *********************** 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 217 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 1.764 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: 0.8962 (OUTLIER) cc_final: 0.8374 (t70) REVERT: C 200 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: E 126 ASP cc_start: 0.8966 (m-30) cc_final: 0.8746 (m-30) REVERT: F 187 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9176 (t) REVERT: F 199 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7185 (pptt) REVERT: G 136 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8340 (t70) REVERT: G 199 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6973 (pptt) REVERT: G 200 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7412 (mt-10) outliers start: 79 outliers final: 18 residues processed: 200 average time/residue: 1.3133 time to fit residues: 292.9403 Evaluate side-chains 165 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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 132 GLU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 LYS 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 112 LEU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 198 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 71 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 181 optimal weight: 4.9990 chunk 164 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 chunk 143 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 208 HIS H 16 ASN 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 = 0.4356 r_free = 0.4356 target = 0.208481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108459 restraints weight = 21012.835| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.18 r_work: 0.2949 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18250 Z= 0.231 Angle : 0.531 5.767 24690 Z= 0.295 Chirality : 0.047 0.151 2730 Planarity : 0.004 0.034 3180 Dihedral : 4.513 49.336 2452 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.39 % Allowed : 22.42 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2300 helix: 1.74 (0.17), residues: 920 sheet: 0.28 (0.29), residues: 290 loop : -1.41 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 31 HIS 0.005 0.001 HIS D 97 PHE 0.015 0.002 PHE H 87 TYR 0.007 0.001 TYR C 131 ARG 0.004 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.07644 ( 857) hydrogen bonds : angle 4.49746 ( 2541) SS BOND : bond 0.00025 ( 10) SS BOND : angle 0.19416 ( 20) covalent geometry : bond 0.00585 (18240) covalent geometry : angle 0.53166 (24670) *********************** 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 200 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 137 time to evaluate : 1.776 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: 0.6828 (mmm) cc_final: 0.6408 (tmm) REVERT: A 85 THR cc_start: 0.4432 (OUTLIER) cc_final: 0.4095 (p) REVERT: B 85 THR cc_start: 0.4420 (OUTLIER) cc_final: 0.4109 (p) REVERT: B 132 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 1 MET cc_start: 0.7085 (mmm) cc_final: 0.6749 (tmm) REVERT: C 136 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.8224 (t70) REVERT: D 121 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: E 1 MET cc_start: 0.6873 (mmm) cc_final: 0.6566 (tmm) REVERT: F 121 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: G 1 MET cc_start: 0.6996 (mmm) cc_final: 0.6640 (tmm) REVERT: G 136 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8225 (t70) REVERT: H 85 THR cc_start: 0.4420 (OUTLIER) cc_final: 0.4118 (p) REVERT: I 1 MET cc_start: 0.6829 (mmm) cc_final: 0.6397 (tmm) REVERT: J 1 MET cc_start: 0.7003 (mmm) cc_final: 0.6722 (tmm) outliers start: 63 outliers final: 23 residues processed: 196 average time/residue: 1.5414 time to fit residues: 335.4912 Evaluate side-chains 168 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 B residue 230 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain D residue 121 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 198 SER Chi-restraints excluded: chain G residue 136 HIS 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 H residue 230 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 71 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 121 optimal weight: 50.0000 chunk 171 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 38 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 = 0.4361 r_free = 0.4361 target = 0.209030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109294 restraints weight = 20971.572| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.17 r_work: 0.2958 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18250 Z= 0.197 Angle : 0.507 6.028 24690 Z= 0.281 Chirality : 0.046 0.150 2730 Planarity : 0.004 0.033 3180 Dihedral : 4.503 49.572 2452 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.09 % Allowed : 21.83 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2300 helix: 1.73 (0.17), residues: 920 sheet: 0.19 (0.29), residues: 290 loop : -1.43 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 31 HIS 0.004 0.001 HIS D 136 PHE 0.012 0.002 PHE F 87 TYR 0.007 0.001 TYR C 131 ARG 0.004 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.07152 ( 857) hydrogen bonds : angle 4.38828 ( 2541) SS BOND : bond 0.00026 ( 10) SS BOND : angle 0.18588 ( 20) covalent geometry : bond 0.00493 (18240) covalent geometry : angle 0.50752 (24670) *********************** 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 208 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 132 time to evaluate : 1.851 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: 0.6846 (mmm) cc_final: 0.6405 (tmm) REVERT: B 132 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: C 1 MET cc_start: 0.7096 (mmm) cc_final: 0.6753 (tmm) REVERT: C 136 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8229 (t70) REVERT: C 199 LYS cc_start: 0.7618 (tptt) cc_final: 0.7388 (tptt) REVERT: C 210 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8687 (tttp) REVERT: D 1 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.5813 (tmm) REVERT: D 121 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: D 222 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: E 1 MET cc_start: 0.6881 (mmm) cc_final: 0.6562 (tmm) REVERT: F 1 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.5664 (tmm) REVERT: F 121 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: F 222 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: G 1 MET cc_start: 0.6979 (mmm) cc_final: 0.6664 (tmm) REVERT: G 136 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.8216 (t70) REVERT: G 199 LYS cc_start: 0.7639 (tptt) cc_final: 0.7434 (tptt) REVERT: H 132 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: I 1 MET cc_start: 0.6832 (mmm) cc_final: 0.6392 (tmm) REVERT: I 199 LYS cc_start: 0.7635 (tptt) cc_final: 0.7407 (tptt) REVERT: J 1 MET cc_start: 0.6925 (mmm) cc_final: 0.6694 (tmm) REVERT: J 199 LYS cc_start: 0.7846 (tptt) cc_final: 0.7645 (tptt) outliers start: 76 outliers final: 30 residues processed: 195 average time/residue: 1.3503 time to fit residues: 293.7069 Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 1 MET 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 D residue 230 ILE 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 198 SER Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain F residue 230 ILE 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 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 85 THR Chi-restraints excluded: chain I residue 115 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 173 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 40.0000 chunk 183 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.209883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106978 restraints weight = 20945.833| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.27 r_work: 0.2986 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1275 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= 0.144 Angle : 0.473 6.289 24690 Z= 0.259 Chirality : 0.045 0.150 2730 Planarity : 0.003 0.032 3180 Dihedral : 4.384 49.733 2452 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.03 % Allowed : 21.88 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2300 helix: 1.81 (0.17), residues: 930 sheet: 0.29 (0.30), residues: 290 loop : -1.41 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 31 HIS 0.004 0.001 HIS D 136 PHE 0.011 0.001 PHE D 108 TYR 0.005 0.001 TYR D 30 ARG 0.005 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.06209 ( 857) hydrogen bonds : angle 4.19486 ( 2541) SS BOND : bond 0.00022 ( 10) SS BOND : angle 0.14558 ( 20) covalent geometry : bond 0.00345 (18240) covalent geometry : angle 0.47328 (24670) *********************** 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 209 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 1.725 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: 0.6843 (mmm) cc_final: 0.6404 (tmm) REVERT: B 132 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: C 1 MET cc_start: 0.7033 (mmm) cc_final: 0.6690 (tmm) REVERT: C 136 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8269 (t70) REVERT: C 210 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8708 (tttp) REVERT: D 1 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.5554 (tmm) REVERT: D 121 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: D 222 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: E 1 MET cc_start: 0.6872 (mmm) cc_final: 0.6531 (tmm) REVERT: E 142 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8663 (mtm-85) REVERT: E 199 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7575 (tptt) REVERT: F 1 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5591 (tmm) REVERT: F 121 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: F 222 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: G 1 MET cc_start: 0.6904 (mmm) cc_final: 0.6594 (tmm) REVERT: G 136 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8260 (t70) REVERT: G 210 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8736 (tttp) REVERT: H 132 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: I 1 MET cc_start: 0.6804 (mmm) cc_final: 0.6348 (tmm) REVERT: I 199 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7248 (tptt) REVERT: J 1 MET cc_start: 0.6907 (mmm) cc_final: 0.6681 (tmm) REVERT: J 142 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8660 (mtm-85) REVERT: J 199 LYS cc_start: 0.7804 (tptt) cc_final: 0.7598 (tptt) outliers start: 75 outliers final: 27 residues processed: 193 average time/residue: 1.3485 time to fit residues: 290.4567 Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1 MET 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 D residue 222 GLN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 136 HIS 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 198 SER Chi-restraints excluded: chain F residue 222 GLN 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 127 VAL 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 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 199 LYS 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 201 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 207 optimal weight: 0.0060 chunk 221 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 0.0370 chunk 195 optimal weight: 2.9990 chunk 1 optimal weight: 40.0000 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.212402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110320 restraints weight = 20954.072| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.33 r_work: 0.3036 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18250 Z= 0.105 Angle : 0.445 6.481 24690 Z= 0.241 Chirality : 0.044 0.147 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.201 50.347 2452 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.87 % Allowed : 22.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2300 helix: 2.02 (0.17), residues: 930 sheet: 0.16 (0.24), residues: 440 loop : -1.23 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 31 HIS 0.002 0.000 HIS G 136 PHE 0.010 0.001 PHE D 108 TYR 0.005 0.001 TYR I 15 ARG 0.005 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 857) hydrogen bonds : angle 3.96859 ( 2541) SS BOND : bond 0.00014 ( 10) SS BOND : angle 0.10618 ( 20) covalent geometry : bond 0.00223 (18240) covalent geometry : angle 0.44513 (24670) *********************** 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 208 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 1.814 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: 0.6897 (mmm) cc_final: 0.6444 (tmm) REVERT: B 132 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: C 1 MET cc_start: 0.7087 (mmm) cc_final: 0.6733 (tmm) REVERT: C 136 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8384 (t70) REVERT: C 199 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6994 (pptt) REVERT: D 1 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.5852 (tmm) REVERT: D 121 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: D 222 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 1 MET cc_start: 0.6982 (mmm) cc_final: 0.6618 (tmm) REVERT: E 199 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7456 (tptt) REVERT: F 1 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.5584 (tmm) REVERT: F 121 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: F 222 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: G 1 MET cc_start: 0.6960 (mmm) cc_final: 0.6636 (tmm) REVERT: G 136 HIS cc_start: 0.8985 (OUTLIER) cc_final: 0.8332 (t70) REVERT: G 199 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7050 (pptt) REVERT: H 132 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: I 1 MET cc_start: 0.6832 (mmm) cc_final: 0.6374 (tmm) REVERT: I 199 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7154 (tptt) REVERT: J 1 MET cc_start: 0.6996 (mmm) cc_final: 0.6764 (tmm) REVERT: J 199 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7431 (tptt) outliers start: 72 outliers final: 33 residues processed: 195 average time/residue: 1.2794 time to fit residues: 279.3766 Evaluate side-chains 188 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 127 VAL 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 D residue 222 GLN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 198 SER 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 136 HIS 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 136 HIS Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 51 VAL 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 198 SER 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 I residue 199 LYS Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 207 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 chunk 157 optimal weight: 2.9990 chunk 88 optimal weight: 0.0020 chunk 93 optimal weight: 40.0000 chunk 101 optimal weight: 4.9990 chunk 191 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 198 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 16 ASN 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 = 0.4360 r_free = 0.4360 target = 0.208844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109230 restraints weight = 21034.560| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.19 r_work: 0.2961 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18250 Z= 0.198 Angle : 0.503 5.979 24690 Z= 0.279 Chirality : 0.047 0.150 2730 Planarity : 0.003 0.033 3180 Dihedral : 4.513 49.594 2452 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.46 % Allowed : 22.42 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2300 helix: 1.91 (0.17), residues: 920 sheet: 0.07 (0.24), residues: 440 loop : -1.33 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 35 HIS 0.005 0.001 HIS C 136 PHE 0.014 0.002 PHE H 87 TYR 0.007 0.001 TYR E 131 ARG 0.002 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.07184 ( 857) hydrogen bonds : angle 4.30833 ( 2541) SS BOND : bond 0.00027 ( 10) SS BOND : angle 0.16410 ( 20) covalent geometry : bond 0.00502 (18240) covalent geometry : angle 0.50272 (24670) *********************** 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 218 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 135 time to evaluate : 1.839 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: 0.6999 (mmm) cc_final: 0.6526 (tmm) REVERT: B 132 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: C 1 MET cc_start: 0.7177 (mmm) cc_final: 0.6808 (tmm) REVERT: C 136 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8206 (t70) REVERT: C 210 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8661 (tttp) REVERT: D 1 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.5983 (tmm) REVERT: D 121 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: D 222 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: E 1 MET cc_start: 0.6956 (mmm) cc_final: 0.6580 (tmm) REVERT: F 1 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.5716 (tmm) REVERT: F 121 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: F 222 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: G 1 MET cc_start: 0.7062 (mmm) cc_final: 0.6723 (tmm) REVERT: G 136 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8204 (t70) REVERT: H 132 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: I 1 MET cc_start: 0.6915 (mmm) cc_final: 0.6444 (tmm) REVERT: J 1 MET cc_start: 0.6993 (mmm) cc_final: 0.6760 (tmm) REVERT: J 199 LYS cc_start: 0.7708 (tptt) cc_final: 0.7449 (tptt) outliers start: 83 outliers final: 34 residues processed: 208 average time/residue: 1.2554 time to fit residues: 293.0446 Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 198 SER 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 1 MET 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 32 THR 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 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 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 198 SER 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 132 GLU Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 202 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 174 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 73 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 I 208 HIS J 208 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.212591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110545 restraints weight = 20822.575| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.32 r_work: 0.3040 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18250 Z= 0.103 Angle : 0.444 6.502 24690 Z= 0.241 Chirality : 0.044 0.146 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.218 51.822 2452 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.28 % Allowed : 23.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2300 helix: 1.88 (0.17), residues: 950 sheet: 0.21 (0.24), residues: 440 loop : -1.39 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 96 HIS 0.003 0.001 HIS H 218 PHE 0.011 0.001 PHE J 108 TYR 0.005 0.001 TYR I 15 ARG 0.003 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 857) hydrogen bonds : angle 3.93916 ( 2541) SS BOND : bond 0.00018 ( 10) SS BOND : angle 0.10548 ( 20) covalent geometry : bond 0.00217 (18240) covalent geometry : angle 0.44438 (24670) *********************** 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 : 1.915 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: 0.7044 (mmm) cc_final: 0.6562 (tmm) REVERT: B 132 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: C 1 MET cc_start: 0.7207 (mmm) cc_final: 0.6841 (tmm) REVERT: C 136 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8305 (t70) REVERT: C 210 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8670 (tttp) REVERT: D 1 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6026 (tmm) REVERT: D 222 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: E 1 MET cc_start: 0.7229 (mmm) cc_final: 0.6883 (tmm) REVERT: F 1 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6065 (tmm) REVERT: F 222 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: G 1 MET cc_start: 0.6983 (mmm) cc_final: 0.6644 (tmm) REVERT: G 136 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8254 (t70) REVERT: H 132 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: I 1 MET cc_start: 0.6977 (mmm) cc_final: 0.6500 (tmm) REVERT: J 1 MET cc_start: 0.7164 (mmm) cc_final: 0.6913 (tmm) REVERT: J 199 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7400 (tptt) outliers start: 61 outliers final: 30 residues processed: 178 average time/residue: 1.3642 time to fit residues: 270.3142 Evaluate side-chains 174 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 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 1 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 127 VAL 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 199 LYS 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 127 VAL Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 79 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 5 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 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 H 222 GLN 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 = 0.4379 r_free = 0.4379 target = 0.211082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108728 restraints weight = 20900.608| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.31 r_work: 0.3005 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18250 Z= 0.126 Angle : 0.459 6.253 24690 Z= 0.250 Chirality : 0.044 0.146 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.266 50.461 2452 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.39 % Allowed : 23.49 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2300 helix: 2.03 (0.17), residues: 930 sheet: 0.23 (0.24), residues: 440 loop : -1.19 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 31 HIS 0.003 0.001 HIS G 136 PHE 0.010 0.001 PHE J 108 TYR 0.006 0.001 TYR I 15 ARG 0.003 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.05642 ( 857) hydrogen bonds : angle 4.02482 ( 2541) SS BOND : bond 0.00020 ( 10) SS BOND : angle 0.11374 ( 20) covalent geometry : bond 0.00297 (18240) covalent geometry : angle 0.45917 (24670) *********************** 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 194 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 1.751 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: 0.7193 (mmm) cc_final: 0.6684 (tmm) REVERT: B 132 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8140 (mm-30) REVERT: C 1 MET cc_start: 0.7369 (mmm) cc_final: 0.6978 (tmm) REVERT: C 136 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8244 (t70) REVERT: C 210 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8693 (tttp) REVERT: D 1 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6293 (tmm) REVERT: D 121 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: D 222 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: E 1 MET cc_start: 0.7243 (mmm) cc_final: 0.6890 (tmm) REVERT: F 1 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6167 (tmm) REVERT: F 222 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: G 1 MET cc_start: 0.7185 (mmm) cc_final: 0.6814 (tmm) REVERT: G 136 HIS cc_start: 0.8955 (OUTLIER) cc_final: 0.8214 (t70) REVERT: H 132 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: I 1 MET cc_start: 0.7134 (mmm) cc_final: 0.6639 (tmm) REVERT: J 1 MET cc_start: 0.7181 (mmm) cc_final: 0.6930 (tmm) REVERT: J 199 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7408 (tptt) outliers start: 63 outliers final: 30 residues processed: 183 average time/residue: 1.3324 time to fit residues: 271.8853 Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 198 SER 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 1 MET Chi-restraints excluded: chain D residue 32 THR 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 D residue 222 GLN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 127 VAL 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 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 127 VAL Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 205 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 24 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 157 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 E 208 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS G 222 GLN H 178 GLN H 208 HIS J 208 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.212067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110319 restraints weight = 20886.235| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.27 r_work: 0.3033 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18250 Z= 0.114 Angle : 0.453 7.022 24690 Z= 0.246 Chirality : 0.044 0.145 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.217 50.878 2452 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.85 % Allowed : 24.14 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2300 helix: 2.05 (0.17), residues: 930 sheet: 0.28 (0.24), residues: 440 loop : -1.15 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 96 HIS 0.004 0.001 HIS H 218 PHE 0.010 0.001 PHE J 108 TYR 0.006 0.001 TYR I 15 ARG 0.003 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 857) hydrogen bonds : angle 3.95691 ( 2541) SS BOND : bond 0.00018 ( 10) SS BOND : angle 0.10465 ( 20) covalent geometry : bond 0.00260 (18240) covalent geometry : angle 0.45311 (24670) ********************** 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 191 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.758 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: 0.7028 (mmm) cc_final: 0.6499 (tmm) REVERT: B 132 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: C 1 MET cc_start: 0.7201 (mmm) cc_final: 0.6833 (tmm) REVERT: C 136 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8349 (t70) REVERT: C 210 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8687 (tttp) REVERT: D 1 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6088 (tmm) REVERT: D 222 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: E 1 MET cc_start: 0.7071 (mmm) cc_final: 0.6699 (tmm) REVERT: E 199 LYS cc_start: 0.7555 (tptt) cc_final: 0.7353 (tptt) REVERT: F 1 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6097 (tmm) REVERT: F 121 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: F 222 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: G 1 MET cc_start: 0.7089 (mmm) cc_final: 0.6721 (tmm) REVERT: G 136 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8294 (t70) REVERT: H 132 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: I 1 MET cc_start: 0.7013 (mmm) cc_final: 0.6512 (tmm) REVERT: J 1 MET cc_start: 0.7088 (mmm) cc_final: 0.6843 (tmm) outliers start: 53 outliers final: 28 residues processed: 179 average time/residue: 1.4436 time to fit residues: 286.6072 Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 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 1 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain E residue 136 HIS 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 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 127 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 204 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** F 208 HIS G 208 HIS H 178 GLN H 208 HIS J 208 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.319532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 154)---------------| | r_work = 0.4704 r_free = 0.4704 target = 0.250111 restraints weight = 24277.531| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.33 r_work: 0.3094 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18250 Z= 0.143 Angle : 0.473 6.802 24690 Z= 0.259 Chirality : 0.045 0.146 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.327 50.221 2452 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 23.92 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2300 helix: 1.97 (0.17), residues: 930 sheet: 0.26 (0.24), residues: 440 loop : -1.17 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 31 HIS 0.004 0.001 HIS B 218 PHE 0.010 0.001 PHE F 108 TYR 0.006 0.001 TYR I 15 ARG 0.006 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.06080 ( 857) hydrogen bonds : angle 4.08040 ( 2541) SS BOND : bond 0.00023 ( 10) SS BOND : angle 0.12447 ( 20) covalent geometry : bond 0.00347 (18240) covalent geometry : angle 0.47305 (24670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16281.21 seconds wall clock time: 280 minutes 10.70 seconds (16810.70 seconds total)