Starting phenix.real_space_refine on Sun Jun 15 19:53:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uaw_42073/06_2025/8uaw_42073.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uaw_42073/06_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_42073/06_2025/8uaw_42073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uaw_42073/06_2025/8uaw_42073.map" model { file = "/net/cci-nas-00/data/ceres_data/8uaw_42073/06_2025/8uaw_42073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uaw_42073/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.09, per 1000 atoms: 0.57 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: 4.62 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: 1.76 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: 5.09 Time building geometry restraints manager: 5.43 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.410 Find NCS groups from input model: 0.650 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:15.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- 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 : 1.778 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: 1.8415 time to fit residues: 332.2667 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 : 1.918 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112439 restraints weight = 20958.216| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.26 r_work: 0.3039 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 2.487 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: 0.8963 (OUTLIER) cc_final: 0.8376 (t70) REVERT: C 200 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: E 126 ASP cc_start: 0.8968 (m-30) cc_final: 0.8747 (m-30) REVERT: F 187 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9179 (t) REVERT: F 199 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7186 (pptt) REVERT: G 136 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8342 (t70) REVERT: G 199 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6973 (pptt) REVERT: G 200 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7415 (mt-10) outliers start: 79 outliers final: 18 residues processed: 200 average time/residue: 1.8087 time to fit residues: 403.6599 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 : 3.086 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 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: 2.9990 chunk 104 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 208 HIS B 45 GLN B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 208 HIS H 16 ASN H 178 GLN H 208 HIS I 38 GLN I 208 HIS J 208 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.209245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109846 restraints weight = 20977.206| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.19 r_work: 0.2952 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18250 Z= 0.217 Angle : 0.524 5.865 24690 Z= 0.291 Chirality : 0.047 0.151 2730 Planarity : 0.004 0.033 3180 Dihedral : 4.514 49.344 2452 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.44 % Allowed : 22.58 % Favored : 73.98 % 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: 0.19 (0.17), residues: 2300 helix: 1.75 (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 136 PHE 0.014 0.002 PHE H 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 0.07599 ( 857) hydrogen bonds : angle 4.48950 ( 2541) SS BOND : bond 0.00026 ( 10) SS BOND : angle 0.19277 ( 20) covalent geometry : bond 0.00548 (18240) covalent geometry : angle 0.52370 (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 199 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 2.032 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: 0.6778 (mmm) cc_final: 0.6356 (tmm) REVERT: A 85 THR cc_start: 0.4418 (OUTLIER) cc_final: 0.4061 (p) REVERT: B 85 THR cc_start: 0.4351 (OUTLIER) cc_final: 0.4043 (p) REVERT: B 132 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: C 1 MET cc_start: 0.7034 (mmm) cc_final: 0.6698 (tmm) REVERT: C 136 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8173 (t70) REVERT: D 121 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: E 1 MET cc_start: 0.6818 (mmm) cc_final: 0.6509 (tmm) REVERT: F 121 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: G 1 MET cc_start: 0.6971 (mmm) cc_final: 0.6606 (tmm) REVERT: G 136 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8159 (t70) REVERT: H 85 THR cc_start: 0.4355 (OUTLIER) cc_final: 0.4054 (p) REVERT: I 1 MET cc_start: 0.6785 (mmm) cc_final: 0.6349 (tmm) REVERT: J 1 MET cc_start: 0.6961 (mmm) cc_final: 0.6685 (tmm) outliers start: 64 outliers final: 23 residues processed: 195 average time/residue: 1.6482 time to fit residues: 356.7116 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 : 2.243 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 48 optimal weight: 40.0000 chunk 185 optimal weight: 50.0000 chunk 77 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 178 GLN B 208 HIS C 208 HIS D 208 HIS E 208 HIS F 208 HIS G 208 HIS H 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 = 0.4364 r_free = 0.4364 target = 0.209066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109235 restraints weight = 20969.445| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.19 r_work: 0.2951 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18250 Z= 0.210 Angle : 0.516 5.969 24690 Z= 0.286 Chirality : 0.047 0.151 2730 Planarity : 0.004 0.034 3180 Dihedral : 4.535 49.446 2452 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.98 % Allowed : 21.83 % 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: 0.11 (0.17), residues: 2300 helix: 1.70 (0.17), residues: 920 sheet: 0.18 (0.29), residues: 290 loop : -1.46 (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 F 136 PHE 0.013 0.002 PHE B 87 TYR 0.007 0.001 TYR D 131 ARG 0.004 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.07384 ( 857) hydrogen bonds : angle 4.43182 ( 2541) SS BOND : bond 0.00027 ( 10) SS BOND : angle 0.19116 ( 20) covalent geometry : bond 0.00530 (18240) covalent geometry : angle 0.51662 (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 206 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 132 time to evaluate : 1.746 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: 0.6878 (mmm) cc_final: 0.6436 (tmm) REVERT: B 132 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: C 1 MET cc_start: 0.7132 (mmm) cc_final: 0.6790 (tmm) REVERT: C 136 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8173 (t70) REVERT: C 199 LYS cc_start: 0.7536 (tptt) cc_final: 0.7322 (tptt) REVERT: C 210 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (tttp) REVERT: D 1 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5818 (tmm) REVERT: D 121 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: D 222 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: E 1 MET cc_start: 0.6908 (mmm) cc_final: 0.6588 (tmm) REVERT: F 1 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.5684 (tmm) REVERT: F 121 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: F 222 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: G 1 MET cc_start: 0.7018 (mmm) cc_final: 0.6701 (tmm) REVERT: G 136 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8154 (t70) REVERT: G 199 LYS cc_start: 0.7567 (tptt) cc_final: 0.7358 (tptt) REVERT: H 132 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: I 1 MET cc_start: 0.6855 (mmm) cc_final: 0.6408 (tmm) REVERT: J 1 MET cc_start: 0.6952 (mmm) cc_final: 0.6721 (tmm) outliers start: 74 outliers final: 30 residues processed: 193 average time/residue: 1.6525 time to fit residues: 354.7498 Evaluate side-chains 177 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 3.391 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.209709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106324 restraints weight = 20940.717| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.28 r_work: 0.2976 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18250 Z= 0.156 Angle : 0.481 6.259 24690 Z= 0.264 Chirality : 0.045 0.151 2730 Planarity : 0.003 0.033 3180 Dihedral : 4.420 49.593 2452 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.62 % Allowed : 21.18 % 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: 0.21 (0.17), residues: 2300 helix: 1.83 (0.17), residues: 920 sheet: 0.26 (0.29), residues: 290 loop : -1.45 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 31 HIS 0.004 0.001 HIS D 136 PHE 0.011 0.001 PHE F 108 TYR 0.005 0.001 TYR D 131 ARG 0.005 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.06470 ( 857) hydrogen bonds : angle 4.23779 ( 2541) SS BOND : bond 0.00024 ( 10) SS BOND : angle 0.15442 ( 20) covalent geometry : bond 0.00378 (18240) covalent geometry : angle 0.48116 (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 221 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 135 time to evaluate : 1.773 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: 0.6737 (mmm) cc_final: 0.6299 (tmm) REVERT: B 132 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: C 1 MET cc_start: 0.6953 (mmm) cc_final: 0.6614 (tmm) REVERT: C 136 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8293 (t70) REVERT: C 210 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (tttp) REVERT: D 1 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5435 (tmm) REVERT: D 121 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: D 210 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8677 (tmtt) REVERT: D 222 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: E 1 MET cc_start: 0.6752 (mmm) cc_final: 0.6418 (tmm) REVERT: E 142 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8706 (mtm-85) REVERT: E 199 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7639 (tptt) REVERT: F 1 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.5458 (tmm) REVERT: F 121 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: F 222 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: G 1 MET cc_start: 0.6837 (mmm) cc_final: 0.6530 (tmm) REVERT: G 136 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8291 (t70) REVERT: H 132 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: I 1 MET cc_start: 0.6712 (mmm) cc_final: 0.6268 (tmm) REVERT: J 1 MET cc_start: 0.6780 (mmm) cc_final: 0.6575 (tmm) REVERT: J 142 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8699 (mtm-85) REVERT: J 199 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7659 (tptt) outliers start: 86 outliers final: 29 residues processed: 202 average time/residue: 1.3889 time to fit residues: 312.9084 Evaluate side-chains 174 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL 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 132 GLU Chi-restraints excluded: chain E residue 136 HIS 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 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 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 115 LYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain J residue 132 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 207 optimal weight: 0.0370 chunk 221 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 0.0000 chunk 195 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 98 optimal weight: 50.0000 chunk 110 optimal weight: 3.9990 overall best weight: 0.8068 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.211846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109661 restraints weight = 20944.698| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.28 r_work: 0.3026 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18250 Z= 0.110 Angle : 0.451 6.456 24690 Z= 0.245 Chirality : 0.044 0.146 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.011 50.205 2448 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.76 % Allowed : 23.12 % 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: 0.52 (0.17), residues: 2300 helix: 1.96 (0.17), residues: 930 sheet: 0.11 (0.24), residues: 440 loop : -1.24 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 96 HIS 0.002 0.000 HIS G 136 PHE 0.011 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 0.05197 ( 857) hydrogen bonds : angle 4.00962 ( 2541) SS BOND : bond 0.00013 ( 10) SS BOND : angle 0.11091 ( 20) covalent geometry : bond 0.00238 (18240) covalent geometry : angle 0.45143 (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 200 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 1.939 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: 0.6964 (mmm) cc_final: 0.6503 (tmm) REVERT: B 132 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: C 1 MET cc_start: 0.7131 (mmm) cc_final: 0.6774 (tmm) REVERT: C 136 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8372 (t70) REVERT: C 210 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8720 (tttp) REVERT: D 1 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.5913 (tmm) REVERT: D 121 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: D 222 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: E 1 MET cc_start: 0.6995 (mmm) cc_final: 0.6628 (tmm) REVERT: E 199 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7510 (tptt) REVERT: F 1 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.5648 (tmm) REVERT: F 121 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: F 222 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: G 1 MET cc_start: 0.7031 (mmm) cc_final: 0.6699 (tmm) REVERT: G 136 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8353 (t70) REVERT: H 132 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: I 1 MET cc_start: 0.6902 (mmm) cc_final: 0.6440 (tmm) REVERT: J 1 MET cc_start: 0.6996 (mmm) cc_final: 0.6762 (tmm) REVERT: J 199 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7512 (tptt) outliers start: 70 outliers final: 33 residues processed: 187 average time/residue: 1.4031 time to fit residues: 292.3781 Evaluate side-chains 184 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 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 199 LYS 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 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 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 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 198 SER Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain J residue 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: 40.0000 chunk 23 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 88 optimal weight: 0.0000 chunk 93 optimal weight: 50.0000 chunk 101 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 209 optimal weight: 50.0000 chunk 198 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.210673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107716 restraints weight = 20853.053| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.28 r_work: 0.2997 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18250 Z= 0.138 Angle : 0.466 6.227 24690 Z= 0.255 Chirality : 0.045 0.149 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.104 50.132 2448 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.82 % Allowed : 23.06 % 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: 0.52 (0.17), residues: 2300 helix: 1.96 (0.17), residues: 930 sheet: 0.13 (0.24), residues: 440 loop : -1.26 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 31 HIS 0.003 0.001 HIS G 136 PHE 0.010 0.001 PHE D 108 TYR 0.005 0.001 TYR I 15 ARG 0.003 0.000 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.05979 ( 857) hydrogen bonds : angle 4.10287 ( 2541) SS BOND : bond 0.00021 ( 10) SS BOND : angle 0.13170 ( 20) covalent geometry : bond 0.00329 (18240) covalent geometry : angle 0.46579 (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 199 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 128 time to evaluate : 1.982 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: 0.6988 (mmm) cc_final: 0.6515 (tmm) REVERT: B 132 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: C 1 MET cc_start: 0.7116 (mmm) cc_final: 0.6761 (tmm) REVERT: C 136 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8273 (t70) REVERT: D 1 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.5904 (tmm) REVERT: D 121 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: D 222 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: E 1 MET cc_start: 0.6984 (mmm) cc_final: 0.6603 (tmm) REVERT: F 1 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.5739 (tmm) REVERT: F 121 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: F 222 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: G 1 MET cc_start: 0.6987 (mmm) cc_final: 0.6657 (tmm) REVERT: G 136 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8256 (t70) REVERT: H 132 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: I 1 MET cc_start: 0.6913 (mmm) cc_final: 0.6446 (tmm) REVERT: J 1 MET cc_start: 0.7017 (mmm) cc_final: 0.6781 (tmm) outliers start: 71 outliers final: 33 residues processed: 186 average time/residue: 1.4264 time to fit residues: 297.0348 Evaluate side-chains 172 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 143 THR 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 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 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 G residue 143 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 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 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: 2.9990 chunk 157 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 142 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.210103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106887 restraints weight = 20820.627| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.27 r_work: 0.2983 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18250 Z= 0.152 Angle : 0.477 6.185 24690 Z= 0.262 Chirality : 0.045 0.148 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.171 49.994 2448 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.66 % Allowed : 23.17 % Favored : 73.17 % 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: 0.48 (0.17), residues: 2300 helix: 1.89 (0.17), residues: 930 sheet: 0.15 (0.24), residues: 440 loop : -1.26 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 31 HIS 0.004 0.001 HIS D 136 PHE 0.011 0.001 PHE D 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 0.06321 ( 857) hydrogen bonds : angle 4.15112 ( 2541) SS BOND : bond 0.00024 ( 10) SS BOND : angle 0.14646 ( 20) covalent geometry : bond 0.00374 (18240) covalent geometry : angle 0.47753 (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: 68 poor density : 128 time to evaluate : 1.846 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: 0.6960 (mmm) cc_final: 0.6480 (tmm) REVERT: B 132 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: C 1 MET cc_start: 0.7133 (mmm) cc_final: 0.6774 (tmm) REVERT: C 136 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8294 (t70) REVERT: C 210 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8729 (tttp) REVERT: D 1 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.5889 (tmm) REVERT: D 121 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: D 222 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 1 MET cc_start: 0.6978 (mmm) cc_final: 0.6639 (tmm) REVERT: F 1 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.5948 (tmm) REVERT: F 121 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: F 222 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: G 1 MET cc_start: 0.6926 (mmm) cc_final: 0.6595 (tmm) REVERT: G 136 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8282 (t70) REVERT: H 132 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: I 1 MET cc_start: 0.6906 (mmm) cc_final: 0.6432 (tmm) REVERT: J 1 MET cc_start: 0.7070 (mmm) cc_final: 0.6832 (tmm) outliers start: 68 outliers final: 32 residues processed: 186 average time/residue: 1.3818 time to fit residues: 286.6947 Evaluate side-chains 173 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 143 THR 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 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 G residue 171 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 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 136 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 40.0000 chunk 5 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 166 optimal weight: 0.0270 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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 16 ASN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 208 HIS H 178 GLN H 208 HIS I 208 HIS J 208 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.212760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111074 restraints weight = 20884.406| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.31 r_work: 0.3040 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18250 Z= 0.106 Angle : 0.448 6.473 24690 Z= 0.242 Chirality : 0.044 0.146 2730 Planarity : 0.003 0.031 3180 Dihedral : 3.934 51.113 2448 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.12 % Allowed : 23.87 % 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: 2.07 (0.17), residues: 930 sheet: 0.27 (0.24), residues: 440 loop : -1.18 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 96 HIS 0.003 0.001 HIS H 218 PHE 0.011 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 0.04861 ( 857) hydrogen bonds : angle 3.90457 ( 2541) SS BOND : bond 0.00017 ( 10) SS BOND : angle 0.09988 ( 20) covalent geometry : bond 0.00232 (18240) covalent geometry : angle 0.44831 (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 199 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 1.885 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: 0.7200 (mmm) cc_final: 0.6686 (tmm) REVERT: B 132 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: C 1 MET cc_start: 0.7396 (mmm) cc_final: 0.7003 (tmm) REVERT: C 136 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8322 (t70) REVERT: C 210 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8665 (tttp) REVERT: D 1 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6317 (tmm) REVERT: D 222 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: E 1 MET cc_start: 0.7188 (mmm) cc_final: 0.6821 (tmm) REVERT: F 1 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6343 (tmm) REVERT: F 222 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: G 1 MET cc_start: 0.7208 (mmm) cc_final: 0.6840 (tmm) REVERT: G 136 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8265 (t70) REVERT: H 132 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: I 1 MET cc_start: 0.7153 (mmm) cc_final: 0.6656 (tmm) REVERT: J 1 MET cc_start: 0.7217 (mmm) cc_final: 0.6959 (tmm) outliers start: 58 outliers final: 31 residues processed: 185 average time/residue: 1.3695 time to fit residues: 282.9337 Evaluate side-chains 177 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain D residue 1 MET 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 E residue 198 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 171 ILE 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 J residue 32 THR Chi-restraints excluded: chain J residue 136 HIS Chi-restraints excluded: chain J residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 205 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 141 optimal weight: 40.0000 chunk 36 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.5041 r_free = 0.5041 target = 0.317437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4818 r_free = 0.4818 target = 0.252922 restraints weight = 24347.509| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.41 r_work: 0.3112 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18250 Z= 0.215 Angle : 0.519 7.325 24690 Z= 0.287 Chirality : 0.047 0.151 2730 Planarity : 0.004 0.032 3180 Dihedral : 4.303 49.534 2448 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.12 % Allowed : 24.03 % Favored : 72.85 % 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: 0.43 (0.17), residues: 2300 helix: 1.87 (0.17), residues: 920 sheet: 0.14 (0.24), residues: 440 loop : -1.28 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 96 HIS 0.006 0.001 HIS G 136 PHE 0.014 0.002 PHE H 87 TYR 0.009 0.001 TYR E 131 ARG 0.006 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.07347 ( 857) hydrogen bonds : angle 4.29473 ( 2541) SS BOND : bond 0.00029 ( 10) SS BOND : angle 0.17272 ( 20) covalent geometry : bond 0.00548 (18240) covalent geometry : angle 0.51942 (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: 58 poor density : 133 time to evaluate : 1.785 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: 0.5749 (mmm) cc_final: 0.5336 (tmm) REVERT: B 132 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: C 1 MET cc_start: 0.5936 (mmm) cc_final: 0.5697 (tmm) REVERT: C 136 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8353 (t70) REVERT: C 210 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8710 (tttp) REVERT: D 1 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.4776 (tmm) REVERT: D 132 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8690 (mm-30) REVERT: D 222 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: E 1 MET cc_start: 0.5660 (mmm) cc_final: 0.5448 (tmm) REVERT: E 142 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8640 (mtm-85) REVERT: F 1 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.4959 (tmm) REVERT: F 132 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: F 222 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: G 136 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8357 (t70) REVERT: H 132 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: I 1 MET cc_start: 0.5716 (mmm) cc_final: 0.5327 (tmm) REVERT: J 142 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8637 (mtm-85) outliers start: 58 outliers final: 31 residues processed: 182 average time/residue: 1.3369 time to fit residues: 271.6087 Evaluate side-chains 176 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 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 132 GLU 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 136 HIS 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 127 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 136 HIS Chi-restraints excluded: chain 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 J residue 32 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 204 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.319067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 280)---------------| | r_work = 0.5024 r_free = 0.5024 target = 0.259319 restraints weight = 24238.514| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.82 r_work: 0.3224 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.2892 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18250 Z= 0.155 Angle : 0.489 7.441 24690 Z= 0.268 Chirality : 0.045 0.149 2730 Planarity : 0.003 0.031 3180 Dihedral : 4.193 50.059 2448 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.12 % Allowed : 23.87 % 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: 0.45 (0.17), residues: 2300 helix: 1.81 (0.17), residues: 930 sheet: 0.18 (0.24), residues: 440 loop : -1.22 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 96 HIS 0.004 0.001 HIS D 136 PHE 0.011 0.001 PHE D 108 TYR 0.006 0.001 TYR I 15 ARG 0.005 0.000 ARG J 142 Details of bonding type rmsd hydrogen bonds : bond 0.06397 ( 857) hydrogen bonds : angle 4.14299 ( 2541) SS BOND : bond 0.00025 ( 10) SS BOND : angle 0.16496 ( 20) covalent geometry : bond 0.00380 (18240) covalent geometry : angle 0.48914 (24670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17183.70 seconds wall clock time: 303 minutes 19.55 seconds (18199.55 seconds total)