Starting phenix.real_space_refine on Wed Feb 4 11:15:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzj_47331/02_2026/9dzj_47331.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.164 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 Cl 2 4.86 5 C 6535 2.51 5 N 1755 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10145 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 762 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 759 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3188 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 27, 'TRANS': 399} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 13, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3185 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 399} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 13, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 135 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10145 At special positions: 0 Unit cell: (97.37, 108.07, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 47 16.00 O 1806 8.00 N 1755 7.00 C 6535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 23 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A1102 " - " ASN A 354 " " NAG B1102 " - " ASN B 354 " " NAG D 1 " - " ASN A 395 " " NAG E 1 " - " ASN A 13 " " NAG F 1 " - " ASN A 2 " " NAG I 1 " - " ASN B 395 " " NAG J 1 " - " ASN B 2 " " NAG M 1 " - " ASN B 13 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 611.4 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 20 sheets defined 30.9% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.528A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.086A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.850A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.100A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 37 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 130 through 145 removed outlier: 3.707A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.562A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.711A pdb=" N GLN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.617A pdb=" N ARG A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.545A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 337 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 63 through 77 Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.892A pdb=" N LEU B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.926A pdb=" N GLN B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.578A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.548A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 337 Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.741A pdb=" N GLY C 16 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.839A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR H 32 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LYS H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 57 " --> pdb=" O LYS H 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.966A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.640A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.470A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N TYR G 32 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 57 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.470A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL G 113 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 6 removed outlier: 12.047A pdb=" N CYS K 23 " --> pdb=" O THR K 74 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N THR K 74 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 11.828A pdb=" N ALA K 25 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N THR K 72 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N GLN K 27 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP K 70 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.677A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 11 through 13 Processing sheet with id=AB6, first strand: chain 'A' and resid 44 through 52 removed outlier: 9.128A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 182 through 189 removed outlier: 6.511A pdb=" N ALA A 150 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU A 186 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 152 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 188 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A 154 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 356 through 359 Processing sheet with id=AB9, first strand: chain 'B' and resid 44 through 52 removed outlier: 9.141A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 81 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.511A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 358 468 hydrogen bonds defined for protein. 1254 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: 1.79 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1632 1.32 - 1.45: 3050 1.45 - 1.57: 5660 1.57 - 1.69: 0 1.69 - 1.82: 74 Bond restraints: 10416 Sorted by residual: bond pdb=" C LYS B 298 " pdb=" O LYS B 298 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 1.541 1.521 0.020 1.20e-02 6.94e+03 2.82e+00 bond pdb=" N ALA B -1 " pdb=" CA ALA B -1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N ALA A -1 " pdb=" CA ALA A -1 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.20e+00 bond pdb=" C LEU B 297 " pdb=" N LYS B 298 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.36e-02 5.41e+03 2.12e+00 ... (remaining 10411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 13986 2.29 - 4.58: 209 4.58 - 6.86: 25 6.86 - 9.15: 2 9.15 - 11.44: 3 Bond angle restraints: 14225 Sorted by residual: angle pdb=" CG1 VAL B 70 " pdb=" CB VAL B 70 " pdb=" CG2 VAL B 70 " ideal model delta sigma weight residual 110.80 122.24 -11.44 2.20e+00 2.07e-01 2.70e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 109.41 4.76 1.14e+00 7.69e-01 1.74e+01 angle pdb=" CA VAL B 70 " pdb=" CB VAL B 70 " pdb=" CG2 VAL B 70 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 angle pdb=" CA VAL B 70 " pdb=" CB VAL B 70 " pdb=" CG1 VAL B 70 " ideal model delta sigma weight residual 110.40 116.86 -6.46 1.70e+00 3.46e-01 1.44e+01 angle pdb=" N ASN K 1 " pdb=" CA ASN K 1 " pdb=" C ASN K 1 " ideal model delta sigma weight residual 111.00 121.15 -10.15 2.80e+00 1.28e-01 1.31e+01 ... (remaining 14220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 5689 21.81 - 43.63: 438 43.63 - 65.44: 78 65.44 - 87.25: 34 87.25 - 109.06: 17 Dihedral angle restraints: 6256 sinusoidal: 2445 harmonic: 3811 Sorted by residual: dihedral pdb=" CA TRP H 47 " pdb=" C TRP H 47 " pdb=" N MET H 48 " pdb=" CA MET H 48 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP G 47 " pdb=" C TRP G 47 " pdb=" N MET G 48 " pdb=" CA MET G 48 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.65 109.06 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 6253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1622 0.339 - 0.678: 2 0.678 - 1.016: 0 1.016 - 1.355: 0 1.355 - 1.694: 2 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CG LEU A 105 " pdb=" CB LEU A 105 " pdb=" CD1 LEU A 105 " pdb=" CD2 LEU A 105 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.17e+01 chirality pdb=" CB VAL B 70 " pdb=" CA VAL B 70 " pdb=" CG1 VAL B 70 " pdb=" CG2 VAL B 70 " both_signs ideal model delta sigma weight residual False -2.63 -1.05 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" CA ASN K 1 " pdb=" N ASN K 1 " pdb=" C ASN K 1 " pdb=" CB ASN K 1 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 1623 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 322 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C HIS B 322 " 0.030 2.00e-02 2.50e+03 pdb=" O HIS B 322 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 323 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 322 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C HIS A 322 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 322 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 323 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE K 94 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO K 95 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " -0.023 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 109 2.66 - 3.22: 8990 3.22 - 3.78: 15517 3.78 - 4.34: 22890 4.34 - 4.90: 37962 Nonbonded interactions: 85468 Sorted by model distance: nonbonded pdb=" O ASN B 13 " pdb=" OG SER B 19 " model vdw 2.096 3.040 nonbonded pdb=" OE1 GLU H 46 " pdb=" NH1 ARG H 63 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR H 33 " pdb=" O HOH H 301 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR G 33 " pdb=" O HOH G 301 " model vdw 2.299 3.040 nonbonded pdb=" OE1 GLU G 46 " pdb=" NH1 ARG G 63 " model vdw 2.309 3.120 ... (remaining 85463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid -1 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 1102)) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'G' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 124)) selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 106)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.006 0.042 10441 Z= 0.253 Angle : 0.706 11.439 14293 Z= 0.345 Chirality : 0.076 1.694 1626 Planarity : 0.004 0.053 1796 Dihedral : 17.712 109.065 3817 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.53 % Allowed : 16.23 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1320 helix: 0.26 (0.28), residues: 332 sheet: -0.19 (0.26), residues: 420 loop : -0.81 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 85 TYR 0.016 0.002 TYR B 154 PHE 0.016 0.001 PHE B 172 TRP 0.011 0.002 TRP B 379 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00579 (10416) covalent geometry : angle 0.69510 (14225) SS BOND : bond 0.00652 ( 7) SS BOND : angle 1.29957 ( 14) hydrogen bonds : bond 0.15344 ( 427) hydrogen bonds : angle 7.39982 ( 1254) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.80088 ( 30) link_NAG-ASN : bond 0.00442 ( 8) link_NAG-ASN : angle 2.24860 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.306 Fit side-chains REVERT: L 61 ARG cc_start: 0.8580 (ptt-90) cc_final: 0.8326 (ptt90) REVERT: K 61 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8432 (ptt90) REVERT: K 72 THR cc_start: 0.9135 (m) cc_final: 0.8925 (t) outliers start: 14 outliers final: 9 residues processed: 190 average time/residue: 0.6669 time to fit residues: 134.7336 Evaluate side-chains 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 39 GLN A 195 HIS A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105581 restraints weight = 11893.397| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.08 r_work: 0.3154 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10441 Z= 0.127 Angle : 0.588 7.119 14293 Z= 0.294 Chirality : 0.043 0.144 1626 Planarity : 0.004 0.041 1796 Dihedral : 10.685 70.023 1851 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.49 % Allowed : 14.60 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1320 helix: 1.68 (0.29), residues: 328 sheet: -0.10 (0.26), residues: 416 loop : -0.44 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.011 0.001 TYR H 108 PHE 0.013 0.001 PHE A 172 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00287 (10416) covalent geometry : angle 0.57452 (14225) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.73652 ( 14) hydrogen bonds : bond 0.04036 ( 427) hydrogen bonds : angle 5.09927 ( 1254) link_BETA1-4 : bond 0.00450 ( 10) link_BETA1-4 : angle 2.27455 ( 30) link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 1.91739 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.359 Fit side-chains REVERT: H 21 SER cc_start: 0.9058 (p) cc_final: 0.8691 (m) REVERT: H 77 SER cc_start: 0.8279 (m) cc_final: 0.7969 (t) REVERT: H 109 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7351 (t80) REVERT: L 61 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8341 (ptt90) REVERT: G 65 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6252 (mt0) REVERT: A 300 LEU cc_start: 0.8353 (tp) cc_final: 0.7909 (tp) REVERT: A 304 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6105 (mp10) REVERT: A 419 ASP cc_start: 0.8862 (p0) cc_final: 0.8569 (p0) REVERT: C 12 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6732 (mtm) outliers start: 32 outliers final: 16 residues processed: 191 average time/residue: 0.6291 time to fit residues: 128.2307 Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 104 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS A 393 ASN B 299 HIS B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103894 restraints weight = 11901.981| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.09 r_work: 0.3132 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10441 Z= 0.168 Angle : 0.599 7.724 14293 Z= 0.295 Chirality : 0.044 0.139 1626 Planarity : 0.004 0.041 1796 Dihedral : 8.377 59.777 1845 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.58 % Allowed : 15.69 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1320 helix: 1.76 (0.29), residues: 326 sheet: -0.07 (0.26), residues: 416 loop : -0.51 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.012 0.001 TYR G 109 PHE 0.016 0.001 PHE A 172 TRP 0.010 0.001 TRP B 379 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00405 (10416) covalent geometry : angle 0.58379 (14225) SS BOND : bond 0.00370 ( 7) SS BOND : angle 1.04615 ( 14) hydrogen bonds : bond 0.04189 ( 427) hydrogen bonds : angle 4.88714 ( 1254) link_BETA1-4 : bond 0.00334 ( 10) link_BETA1-4 : angle 2.30163 ( 30) link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 2.04197 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.407 Fit side-chains REVERT: H 21 SER cc_start: 0.9027 (p) cc_final: 0.8621 (m) REVERT: H 109 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7391 (t80) REVERT: L 61 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.8295 (ptt90) REVERT: G 65 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6159 (mt0) REVERT: A 202 THR cc_start: 0.7837 (t) cc_final: 0.7602 (p) REVERT: A 300 LEU cc_start: 0.8231 (tp) cc_final: 0.7791 (tp) REVERT: A 304 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6014 (mp10) REVERT: A 419 ASP cc_start: 0.8795 (p0) cc_final: 0.8524 (p0) REVERT: B 176 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7802 (mtp85) REVERT: C 12 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6719 (mtm) outliers start: 42 outliers final: 16 residues processed: 193 average time/residue: 0.6122 time to fit residues: 126.3708 Evaluate side-chains 186 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS B 299 HIS B 338 HIS B 385 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105599 restraints weight = 12073.770| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.11 r_work: 0.3092 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10441 Z= 0.129 Angle : 0.554 7.758 14293 Z= 0.276 Chirality : 0.043 0.138 1626 Planarity : 0.004 0.040 1796 Dihedral : 6.474 56.727 1842 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.92 % Allowed : 16.99 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1320 helix: 1.80 (0.29), residues: 326 sheet: -0.00 (0.26), residues: 416 loop : -0.52 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 24 TYR 0.009 0.001 TYR K 49 PHE 0.016 0.001 PHE B 172 TRP 0.009 0.001 TRP H 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00302 (10416) covalent geometry : angle 0.54052 (14225) SS BOND : bond 0.00265 ( 7) SS BOND : angle 0.74566 ( 14) hydrogen bonds : bond 0.03665 ( 427) hydrogen bonds : angle 4.66333 ( 1254) link_BETA1-4 : bond 0.00364 ( 10) link_BETA1-4 : angle 2.10786 ( 30) link_NAG-ASN : bond 0.00239 ( 8) link_NAG-ASN : angle 1.90219 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.418 Fit side-chains REVERT: H 21 SER cc_start: 0.9021 (p) cc_final: 0.8658 (m) REVERT: H 77 SER cc_start: 0.8162 (m) cc_final: 0.7834 (t) REVERT: H 109 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7320 (t80) REVERT: G 21 SER cc_start: 0.9082 (p) cc_final: 0.8651 (m) REVERT: G 65 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5830 (mt0) REVERT: K 27 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: A 201 ARG cc_start: 0.7761 (ptp90) cc_final: 0.7543 (ptp-110) REVERT: A 202 THR cc_start: 0.7649 (t) cc_final: 0.7405 (p) REVERT: A 300 LEU cc_start: 0.8150 (tp) cc_final: 0.7688 (tp) REVERT: A 304 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.5935 (mp10) REVERT: A 372 ARG cc_start: 0.8472 (ttp-170) cc_final: 0.8159 (tmm-80) REVERT: B 45 THR cc_start: 0.8846 (m) cc_final: 0.8463 (t) REVERT: C 12 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6548 (mtm) outliers start: 36 outliers final: 16 residues processed: 192 average time/residue: 0.6395 time to fit residues: 131.0857 Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 87 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100695 restraints weight = 12076.079| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.09 r_work: 0.3067 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 10441 Z= 0.339 Angle : 0.723 9.940 14293 Z= 0.356 Chirality : 0.049 0.182 1626 Planarity : 0.005 0.046 1796 Dihedral : 6.880 49.654 1842 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.01 % Allowed : 17.21 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1320 helix: 1.42 (0.28), residues: 324 sheet: -0.20 (0.25), residues: 418 loop : -0.74 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.023 0.002 TYR G 109 PHE 0.022 0.002 PHE B 172 TRP 0.014 0.002 TRP A 379 HIS 0.009 0.002 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00820 (10416) covalent geometry : angle 0.70678 (14225) SS BOND : bond 0.00681 ( 7) SS BOND : angle 1.83962 ( 14) hydrogen bonds : bond 0.05083 ( 427) hydrogen bonds : angle 5.09227 ( 1254) link_BETA1-4 : bond 0.00206 ( 10) link_BETA1-4 : angle 2.47649 ( 30) link_NAG-ASN : bond 0.00766 ( 8) link_NAG-ASN : angle 2.37682 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.388 Fit side-chains REVERT: H 76 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7272 (pp) REVERT: H 109 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7308 (t80) REVERT: G 109 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7250 (t80) REVERT: K 27 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8364 (mt0) REVERT: A 202 THR cc_start: 0.8192 (t) cc_final: 0.7960 (p) REVERT: A 300 LEU cc_start: 0.8201 (tp) cc_final: 0.7739 (tp) REVERT: A 304 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6136 (mp10) REVERT: B 74 TRP cc_start: 0.7582 (m-90) cc_final: 0.6899 (m-10) REVERT: B 176 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7789 (mtp85) REVERT: C 12 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7042 (mtm) outliers start: 46 outliers final: 25 residues processed: 186 average time/residue: 0.6575 time to fit residues: 130.4700 Evaluate side-chains 186 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN A 299 HIS A 338 HIS B 299 HIS B 338 HIS B 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104608 restraints weight = 12097.960| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.12 r_work: 0.3146 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10441 Z= 0.130 Angle : 0.568 8.418 14293 Z= 0.286 Chirality : 0.043 0.146 1626 Planarity : 0.004 0.040 1796 Dihedral : 5.916 43.208 1842 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.59 % Allowed : 18.74 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1320 helix: 1.73 (0.29), residues: 326 sheet: -0.05 (0.26), residues: 416 loop : -0.63 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 24 TYR 0.010 0.001 TYR A 154 PHE 0.017 0.001 PHE B 172 TRP 0.012 0.001 TRP H 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00302 (10416) covalent geometry : angle 0.55610 (14225) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.75044 ( 14) hydrogen bonds : bond 0.03707 ( 427) hydrogen bonds : angle 4.70844 ( 1254) link_BETA1-4 : bond 0.00393 ( 10) link_BETA1-4 : angle 1.94610 ( 30) link_NAG-ASN : bond 0.00214 ( 8) link_NAG-ASN : angle 1.95525 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.489 Fit side-chains REVERT: H 6 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: H 21 SER cc_start: 0.9002 (p) cc_final: 0.8655 (m) REVERT: H 76 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7306 (pp) REVERT: H 109 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7282 (t80) REVERT: L 24 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8136 (ttm110) REVERT: L 89 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: G 21 SER cc_start: 0.9041 (p) cc_final: 0.8665 (m) REVERT: G 67 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6784 (mtp180) REVERT: G 109 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7252 (t80) REVERT: K 27 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: A 202 THR cc_start: 0.8152 (t) cc_final: 0.7946 (p) REVERT: A 300 LEU cc_start: 0.8287 (tp) cc_final: 0.7855 (tp) REVERT: A 304 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: A 372 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.8198 (tmm-80) REVERT: B 176 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7753 (mtp85) REVERT: B 202 THR cc_start: 0.7807 (m) cc_final: 0.7560 (p) REVERT: C 12 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6734 (mtm) outliers start: 33 outliers final: 19 residues processed: 182 average time/residue: 0.7148 time to fit residues: 138.3422 Evaluate side-chains 190 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 338 HIS A 385 ASN B 299 HIS B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105650 restraints weight = 11933.872| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.11 r_work: 0.3165 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10441 Z= 0.116 Angle : 0.551 7.848 14293 Z= 0.277 Chirality : 0.042 0.148 1626 Planarity : 0.004 0.040 1796 Dihedral : 5.504 43.042 1842 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.27 % Favored : 97.58 % Rotamer: Outliers : 3.92 % Allowed : 19.17 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.24), residues: 1320 helix: 1.77 (0.28), residues: 332 sheet: -0.02 (0.26), residues: 416 loop : -0.55 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 24 TYR 0.010 0.001 TYR A 154 PHE 0.018 0.001 PHE B 172 TRP 0.009 0.001 TRP G 50 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00269 (10416) covalent geometry : angle 0.53972 (14225) SS BOND : bond 0.00210 ( 7) SS BOND : angle 0.73316 ( 14) hydrogen bonds : bond 0.03533 ( 427) hydrogen bonds : angle 4.60046 ( 1254) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 1.87204 ( 30) link_NAG-ASN : bond 0.00198 ( 8) link_NAG-ASN : angle 1.93438 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.410 Fit side-chains REVERT: H 21 SER cc_start: 0.8986 (p) cc_final: 0.8705 (m) REVERT: H 63 ARG cc_start: 0.7621 (ttt180) cc_final: 0.7378 (ttp-170) REVERT: H 76 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7308 (pp) REVERT: H 109 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7280 (t80) REVERT: L 89 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: G 21 SER cc_start: 0.9038 (p) cc_final: 0.8674 (m) REVERT: G 65 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.5812 (mt0) REVERT: G 67 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6699 (mtp180) REVERT: G 109 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7219 (t80) REVERT: K 27 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: A 202 THR cc_start: 0.8139 (t) cc_final: 0.7921 (p) REVERT: A 300 LEU cc_start: 0.8315 (tp) cc_final: 0.7844 (tp) REVERT: A 304 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6170 (mp10) REVERT: B 45 THR cc_start: 0.8744 (m) cc_final: 0.8469 (t) REVERT: B 176 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7773 (mtp85) REVERT: B 202 THR cc_start: 0.7785 (m) cc_final: 0.7557 (p) REVERT: C 12 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6570 (mtm) outliers start: 36 outliers final: 19 residues processed: 186 average time/residue: 0.7020 time to fit residues: 139.0880 Evaluate side-chains 191 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106177 restraints weight = 11909.270| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.11 r_work: 0.3098 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10441 Z= 0.118 Angle : 0.540 7.636 14293 Z= 0.272 Chirality : 0.042 0.146 1626 Planarity : 0.004 0.039 1796 Dihedral : 5.111 42.888 1842 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.12 % Favored : 97.73 % Rotamer: Outliers : 3.70 % Allowed : 19.93 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1320 helix: 1.82 (0.28), residues: 332 sheet: 0.06 (0.26), residues: 416 loop : -0.49 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 24 TYR 0.009 0.001 TYR A 154 PHE 0.020 0.001 PHE B 172 TRP 0.008 0.001 TRP G 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00277 (10416) covalent geometry : angle 0.52919 (14225) SS BOND : bond 0.00252 ( 7) SS BOND : angle 0.74565 ( 14) hydrogen bonds : bond 0.03447 ( 427) hydrogen bonds : angle 4.51279 ( 1254) link_BETA1-4 : bond 0.00387 ( 10) link_BETA1-4 : angle 1.78085 ( 30) link_NAG-ASN : bond 0.00207 ( 8) link_NAG-ASN : angle 1.90923 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.390 Fit side-chains REVERT: H 21 SER cc_start: 0.8998 (p) cc_final: 0.8696 (m) REVERT: H 76 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6894 (pp) REVERT: H 109 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7282 (t80) REVERT: L 89 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8742 (tt0) REVERT: G 21 SER cc_start: 0.8986 (p) cc_final: 0.8619 (m) REVERT: G 63 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7317 (ttp-170) REVERT: G 65 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6058 (mt0) REVERT: G 67 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6283 (mtp180) REVERT: G 109 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7347 (t80) REVERT: K 27 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: A 202 THR cc_start: 0.8070 (t) cc_final: 0.7846 (p) REVERT: A 300 LEU cc_start: 0.8090 (tp) cc_final: 0.7661 (tp) REVERT: A 304 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6086 (mp10) REVERT: B 45 THR cc_start: 0.8815 (m) cc_final: 0.8438 (t) REVERT: B 202 THR cc_start: 0.7692 (m) cc_final: 0.7401 (p) REVERT: C 12 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6866 (mtm) outliers start: 34 outliers final: 18 residues processed: 186 average time/residue: 0.6263 time to fit residues: 124.4080 Evaluate side-chains 194 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103088 restraints weight = 11963.172| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.07 r_work: 0.3061 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10441 Z= 0.219 Angle : 0.627 9.321 14293 Z= 0.312 Chirality : 0.045 0.150 1626 Planarity : 0.005 0.041 1796 Dihedral : 5.499 42.469 1842 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.73 % Favored : 97.12 % Rotamer: Outliers : 3.92 % Allowed : 19.39 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1320 helix: 1.63 (0.28), residues: 332 sheet: -0.03 (0.26), residues: 416 loop : -0.53 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.018 0.002 TYR G 109 PHE 0.022 0.002 PHE B 172 TRP 0.011 0.002 TRP B 379 HIS 0.009 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00529 (10416) covalent geometry : angle 0.61375 (14225) SS BOND : bond 0.00524 ( 7) SS BOND : angle 1.33728 ( 14) hydrogen bonds : bond 0.04253 ( 427) hydrogen bonds : angle 4.74024 ( 1254) link_BETA1-4 : bond 0.00287 ( 10) link_BETA1-4 : angle 1.98834 ( 30) link_NAG-ASN : bond 0.00471 ( 8) link_NAG-ASN : angle 2.17112 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.413 Fit side-chains REVERT: H 21 SER cc_start: 0.9040 (p) cc_final: 0.8690 (m) REVERT: H 76 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7144 (pp) REVERT: H 77 SER cc_start: 0.8481 (p) cc_final: 0.8263 (p) REVERT: H 109 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7274 (t80) REVERT: L 89 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: G 21 SER cc_start: 0.9069 (p) cc_final: 0.8678 (m) REVERT: G 63 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7303 (ttp-170) REVERT: G 67 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6696 (mtp180) REVERT: G 109 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7264 (t80) REVERT: K 27 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: A 202 THR cc_start: 0.8125 (t) cc_final: 0.7903 (p) REVERT: A 300 LEU cc_start: 0.8150 (tp) cc_final: 0.7741 (tp) REVERT: A 304 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6397 (mp10) REVERT: B 176 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7760 (mtp85) REVERT: B 202 THR cc_start: 0.7651 (m) cc_final: 0.7348 (p) REVERT: C 12 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6801 (mtm) outliers start: 36 outliers final: 22 residues processed: 184 average time/residue: 0.5998 time to fit residues: 117.6704 Evaluate side-chains 191 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 119 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106665 restraints weight = 11830.344| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.10 r_work: 0.3104 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10441 Z= 0.109 Angle : 0.543 7.710 14293 Z= 0.274 Chirality : 0.042 0.142 1626 Planarity : 0.004 0.055 1796 Dihedral : 5.077 43.259 1842 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.05 % Favored : 97.80 % Rotamer: Outliers : 3.59 % Allowed : 20.15 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1320 helix: 1.82 (0.28), residues: 332 sheet: 0.07 (0.26), residues: 416 loop : -0.48 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.010 0.001 TYR A 154 PHE 0.018 0.001 PHE B 172 TRP 0.008 0.001 TRP G 50 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00250 (10416) covalent geometry : angle 0.53231 (14225) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.72623 ( 14) hydrogen bonds : bond 0.03387 ( 427) hydrogen bonds : angle 4.51074 ( 1254) link_BETA1-4 : bond 0.00409 ( 10) link_BETA1-4 : angle 1.70229 ( 30) link_NAG-ASN : bond 0.00165 ( 8) link_NAG-ASN : angle 1.88041 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.328 Fit side-chains REVERT: H 21 SER cc_start: 0.8967 (p) cc_final: 0.8656 (m) REVERT: H 76 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7134 (pp) REVERT: H 77 SER cc_start: 0.8440 (p) cc_final: 0.8221 (p) REVERT: H 109 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7251 (t80) REVERT: L 89 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8712 (tt0) REVERT: G 21 SER cc_start: 0.9003 (p) cc_final: 0.8647 (m) REVERT: G 63 ARG cc_start: 0.7668 (ttt180) cc_final: 0.7304 (ttp-170) REVERT: G 67 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6538 (mtp180) REVERT: G 109 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7215 (t80) REVERT: K 27 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: A 202 THR cc_start: 0.8071 (t) cc_final: 0.7848 (p) REVERT: A 300 LEU cc_start: 0.8071 (tp) cc_final: 0.7619 (tp) REVERT: A 304 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6041 (mp10) REVERT: B 45 THR cc_start: 0.8732 (m) cc_final: 0.8386 (t) REVERT: B 176 ARG cc_start: 0.7951 (mtp-110) cc_final: 0.7704 (mtp85) REVERT: B 202 THR cc_start: 0.7680 (m) cc_final: 0.7348 (p) REVERT: C 12 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6580 (mtm) outliers start: 33 outliers final: 18 residues processed: 186 average time/residue: 0.5545 time to fit residues: 110.1904 Evaluate side-chains 192 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 12 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 338 HIS B 299 HIS B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104327 restraints weight = 11963.045| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.08 r_work: 0.3075 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10441 Z= 0.184 Angle : 0.592 8.522 14293 Z= 0.295 Chirality : 0.044 0.148 1626 Planarity : 0.005 0.060 1796 Dihedral : 5.236 42.384 1842 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.35 % Favored : 97.50 % Rotamer: Outliers : 3.49 % Allowed : 20.59 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1320 helix: 1.72 (0.28), residues: 332 sheet: 0.03 (0.26), residues: 416 loop : -0.49 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.015 0.001 TYR G 109 PHE 0.021 0.001 PHE B 172 TRP 0.010 0.001 TRP B 379 HIS 0.008 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00444 (10416) covalent geometry : angle 0.57985 (14225) SS BOND : bond 0.00425 ( 7) SS BOND : angle 1.12359 ( 14) hydrogen bonds : bond 0.03905 ( 427) hydrogen bonds : angle 4.60935 ( 1254) link_BETA1-4 : bond 0.00329 ( 10) link_BETA1-4 : angle 1.86117 ( 30) link_NAG-ASN : bond 0.00359 ( 8) link_NAG-ASN : angle 2.04475 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.22 seconds wall clock time: 66 minutes 23.64 seconds (3983.64 seconds total)