Starting phenix.real_space_refine on Thu Feb 5 19:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.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 { model { file = "/net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cye_46041/02_2026/9cye_46041.map" } 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= 0.075 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 Ca 9 9.91 5 S 116 5.16 5 C 12148 2.51 5 N 3260 2.21 5 O 3760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19293 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2980 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 364} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.47, per 1000 atoms: 0.23 Number of scatterers: 19293 At special positions: 0 Unit cell: (138.475, 138.475, 92.8, 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) Ca 9 19.99 S 116 16.00 O 3760 8.00 N 3260 7.00 C 12148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 234 " " NAG A 503 " - " ASN A 146 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 234 " " NAG B 503 " - " ASN B 146 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 234 " " NAG C 503 " - " ASN C 146 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 234 " " NAG D 503 " - " ASN D 146 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 869.2 milliseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 5.9% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.571A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.571A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'J' and resid 50 through 52 No H-bonds generated for 'chain 'J' and resid 50 through 52' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.571A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 197 through 200 Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.571A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.392A pdb=" N SER A 445 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.649A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.426A pdb=" N TYR A 207 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.581A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.599A pdb=" N PHE A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 363 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 372 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY A 399 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 392 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.432A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.096A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG H 94 " --> pdb=" O MET H 100I" (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET H 100I" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP H 96 " --> pdb=" O TYR H 100G" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.391A pdb=" N SER B 445 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.649A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.426A pdb=" N TYR B 207 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB9, first strand: chain 'B' and resid 223 through 224 removed outlier: 6.581A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AC2, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.599A pdb=" N PHE B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 363 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN B 372 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B 399 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 392 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.432A pdb=" N TRP E 35A" --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.096A pdb=" N CYS E 92 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL E 102 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG E 94 " --> pdb=" O MET E 100I" (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET E 100I" --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP E 96 " --> pdb=" O TYR E 100G" (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.391A pdb=" N SER C 445 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.649A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.427A pdb=" N TYR C 207 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD4, first strand: chain 'C' and resid 223 through 224 removed outlier: 6.581A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 279 through 282 Processing sheet with id=AD6, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.599A pdb=" N PHE C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY C 363 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 372 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY C 399 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 392 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.432A pdb=" N TRP F 35A" --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 11 through 12 removed outlier: 7.096A pdb=" N CYS F 92 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL F 102 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG F 94 " --> pdb=" O MET F 100I" (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET F 100I" --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP F 96 " --> pdb=" O TYR F 100G" (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE3, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.391A pdb=" N SER D 445 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.649A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.427A pdb=" N TYR D 207 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AE8, first strand: chain 'D' and resid 223 through 224 removed outlier: 6.581A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 279 through 282 Processing sheet with id=AF1, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.599A pdb=" N PHE D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 363 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN D 372 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY D 399 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 392 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.432A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.095A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG G 94 " --> pdb=" O MET G 100I" (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET G 100I" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP G 96 " --> pdb=" O TYR G 100G" (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5054 1.46 - 1.58: 8453 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 19796 Sorted by residual: bond pdb=" C ARG B 430 " pdb=" N PRO B 431 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.57e+00 bond pdb=" C ARG A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.42e+00 bond pdb=" C ARG D 430 " pdb=" N PRO D 431 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.42e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 ... (remaining 19791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 25667 1.90 - 3.79: 1065 3.79 - 5.69: 144 5.69 - 7.59: 32 7.59 - 9.48: 16 Bond angle restraints: 26924 Sorted by residual: angle pdb=" N LEU A 464 " pdb=" CA LEU A 464 " pdb=" C LEU A 464 " ideal model delta sigma weight residual 109.81 119.15 -9.34 2.21e+00 2.05e-01 1.79e+01 angle pdb=" N LEU C 464 " pdb=" CA LEU C 464 " pdb=" C LEU C 464 " ideal model delta sigma weight residual 109.81 119.10 -9.29 2.21e+00 2.05e-01 1.77e+01 angle pdb=" N LEU D 464 " pdb=" CA LEU D 464 " pdb=" C LEU D 464 " ideal model delta sigma weight residual 109.81 119.10 -9.29 2.21e+00 2.05e-01 1.77e+01 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 109.81 119.10 -9.29 2.21e+00 2.05e-01 1.77e+01 angle pdb=" C ALA K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 26919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 10665 13.49 - 26.97: 798 26.97 - 40.45: 181 40.45 - 53.94: 80 53.94 - 67.42: 24 Dihedral angle restraints: 11748 sinusoidal: 4724 harmonic: 7024 Sorted by residual: dihedral pdb=" CA GLU D 463 " pdb=" C GLU D 463 " pdb=" N LEU D 464 " pdb=" CA LEU D 464 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU B 463 " pdb=" C GLU B 463 " pdb=" N LEU B 464 " pdb=" CA LEU B 464 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU C 463 " pdb=" C GLU C 463 " pdb=" N LEU C 464 " pdb=" CA LEU C 464 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 11745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1744 0.045 - 0.089: 764 0.089 - 0.134: 276 0.134 - 0.178: 98 0.178 - 0.223: 14 Chirality restraints: 2896 Sorted by residual: chirality pdb=" CB ILE D 215 " pdb=" CA ILE D 215 " pdb=" CG1 ILE D 215 " pdb=" CG2 ILE D 215 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE A 215 " pdb=" CA ILE A 215 " pdb=" CG1 ILE A 215 " pdb=" CG2 ILE A 215 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE B 215 " pdb=" CA ILE B 215 " pdb=" CG1 ILE B 215 " pdb=" CG2 ILE B 215 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2893 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 125 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 126 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 125 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO D 126 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 125 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C 126 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " 0.029 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4345 2.79 - 3.32: 16729 3.32 - 3.85: 35316 3.85 - 4.37: 44071 4.37 - 4.90: 74140 Nonbonded interactions: 174601 Sorted by model distance: nonbonded pdb=" OD2 ASP A 293 " pdb=" OH TYR A 316 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP C 293 " pdb=" OH TYR C 316 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP D 293 " pdb=" OH TYR D 316 " model vdw 2.268 3.040 nonbonded pdb=" OD2 ASP B 293 " pdb=" OH TYR B 316 " model vdw 2.268 3.040 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 504 " model vdw 2.332 2.510 ... (remaining 174596 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 83 through 505) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 9.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.140 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.005 0.055 19848 Z= 0.233 Angle : 0.874 9.483 27040 Z= 0.465 Chirality : 0.059 0.223 2896 Planarity : 0.006 0.052 3456 Dihedral : 11.109 67.423 7180 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.76 % Allowed : 4.55 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.97 (0.16), residues: 2464 helix: -1.99 (0.74), residues: 24 sheet: -0.10 (0.17), residues: 840 loop : -0.93 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 94 TYR 0.017 0.002 TYR K 49 PHE 0.026 0.003 PHE C 115 TRP 0.019 0.002 TRP H 103 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00526 (19796) covalent geometry : angle 0.87158 (26924) SS BOND : bond 0.00290 ( 40) SS BOND : angle 1.12934 ( 80) hydrogen bonds : bond 0.16394 ( 672) hydrogen bonds : angle 8.34073 ( 1728) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.52977 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 308 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.7825 (ptpt) cc_final: 0.7593 (pttt) REVERT: A 452 ASP cc_start: 0.8055 (m-30) cc_final: 0.7650 (m-30) REVERT: H 100 MET cc_start: 0.8922 (mtt) cc_final: 0.8573 (mtt) REVERT: B 331 LYS cc_start: 0.7819 (ptpt) cc_final: 0.7592 (pttt) REVERT: B 452 ASP cc_start: 0.8051 (m-30) cc_final: 0.7650 (m-30) REVERT: E 100 MET cc_start: 0.8926 (mtt) cc_final: 0.8581 (mtt) REVERT: C 331 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7580 (pttt) REVERT: C 452 ASP cc_start: 0.8042 (m-30) cc_final: 0.7646 (m-30) REVERT: F 100 MET cc_start: 0.8922 (mtt) cc_final: 0.8573 (mtt) REVERT: D 331 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7582 (pttt) REVERT: D 452 ASP cc_start: 0.8057 (m-30) cc_final: 0.7651 (m-30) REVERT: G 100 MET cc_start: 0.8919 (mtt) cc_final: 0.8579 (mtt) outliers start: 16 outliers final: 4 residues processed: 324 average time/residue: 0.5657 time to fit residues: 209.4217 Evaluate side-chains 234 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 230 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 226 GLN B 220 ASN B 226 GLN C 220 ASN C 226 GLN D 220 ASN D 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111105 restraints weight = 20154.875| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.12 r_work: 0.2876 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19848 Z= 0.162 Angle : 0.614 10.532 27040 Z= 0.321 Chirality : 0.048 0.177 2896 Planarity : 0.004 0.044 3456 Dihedral : 5.940 42.065 2936 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 7.78 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.61 (0.16), residues: 2464 helix: -1.76 (0.78), residues: 24 sheet: 0.18 (0.17), residues: 908 loop : -0.74 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 430 TYR 0.012 0.002 TYR E 91 PHE 0.018 0.002 PHE H 78 TRP 0.015 0.001 TRP C 178 HIS 0.002 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00368 (19796) covalent geometry : angle 0.60884 (26924) SS BOND : bond 0.00242 ( 40) SS BOND : angle 1.34557 ( 80) hydrogen bonds : bond 0.03903 ( 672) hydrogen bonds : angle 6.97116 ( 1728) link_NAG-ASN : bond 0.00166 ( 12) link_NAG-ASN : angle 1.26686 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8666 (mmtp) REVERT: A 267 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: H 100 MET cc_start: 0.8904 (mtt) cc_final: 0.8525 (mtt) REVERT: B 267 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: E 100 MET cc_start: 0.8909 (mtt) cc_final: 0.8536 (mtt) REVERT: C 267 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: F 100 MET cc_start: 0.8911 (mtt) cc_final: 0.8539 (mtt) REVERT: D 261 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8667 (mmtp) REVERT: D 267 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: G 100 MET cc_start: 0.8906 (mtt) cc_final: 0.8532 (mtt) outliers start: 28 outliers final: 12 residues processed: 278 average time/residue: 0.5517 time to fit residues: 176.3142 Evaluate side-chains 254 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 201 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN H 39 GLN B 226 GLN B 296 HIS E 39 GLN C 226 GLN C 296 HIS F 39 GLN D 226 GLN G 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112500 restraints weight = 20387.805| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.15 r_work: 0.3007 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19848 Z= 0.139 Angle : 0.589 10.823 27040 Z= 0.307 Chirality : 0.047 0.170 2896 Planarity : 0.004 0.043 3456 Dihedral : 5.786 36.202 2936 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.80 % Allowed : 8.30 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.54 (0.16), residues: 2464 helix: -1.86 (0.74), residues: 24 sheet: 0.35 (0.17), residues: 884 loop : -0.76 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.013 0.001 TYR H 91 PHE 0.016 0.002 PHE F 78 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00315 (19796) covalent geometry : angle 0.58547 (26924) SS BOND : bond 0.00326 ( 40) SS BOND : angle 1.08861 ( 80) hydrogen bonds : bond 0.03623 ( 672) hydrogen bonds : angle 6.64432 ( 1728) link_NAG-ASN : bond 0.00163 ( 12) link_NAG-ASN : angle 1.23161 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 430 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6145 (tmm-80) REVERT: H 100 MET cc_start: 0.8887 (mtt) cc_final: 0.8500 (mtt) REVERT: B 286 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: B 430 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6145 (tmm-80) REVERT: E 100 MET cc_start: 0.8894 (mtt) cc_final: 0.8511 (mtt) REVERT: C 286 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: C 430 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6145 (tmm-80) REVERT: F 100 MET cc_start: 0.8895 (mtt) cc_final: 0.8514 (mtt) REVERT: D 286 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: D 430 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6141 (tmm-80) REVERT: G 100 MET cc_start: 0.8886 (mtt) cc_final: 0.8498 (mtt) outliers start: 38 outliers final: 8 residues processed: 261 average time/residue: 0.5920 time to fit residues: 175.7361 Evaluate side-chains 233 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 214 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 225 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 39 GLN B 226 GLN B 296 HIS E 39 GLN C 226 GLN C 296 HIS F 39 GLN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 296 HIS G 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110187 restraints weight = 20228.892| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.17 r_work: 0.2858 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 0.043 19848 Z= 0.186 Angle : 0.625 12.041 27040 Z= 0.324 Chirality : 0.048 0.178 2896 Planarity : 0.004 0.044 3456 Dihedral : 5.824 34.694 2936 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.47 % Allowed : 9.44 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.52 (0.16), residues: 2464 helix: -1.79 (0.77), residues: 24 sheet: 0.40 (0.17), residues: 884 loop : -0.78 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.014 0.002 TYR G 91 PHE 0.019 0.002 PHE E 78 TRP 0.015 0.002 TRP A 97 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00428 (19796) covalent geometry : angle 0.62086 (26924) SS BOND : bond 0.00314 ( 40) SS BOND : angle 1.16540 ( 80) hydrogen bonds : bond 0.03784 ( 672) hydrogen bonds : angle 6.70282 ( 1728) link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 1.32809 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: A 286 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: A 430 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6307 (tmm-80) REVERT: H 100 MET cc_start: 0.8956 (mtt) cc_final: 0.8562 (mtt) REVERT: B 267 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: B 286 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 430 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6310 (tmm-80) REVERT: E 100 MET cc_start: 0.8956 (mtt) cc_final: 0.8566 (mtt) REVERT: C 267 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: C 286 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: C 430 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6312 (tmm-80) REVERT: F 100 MET cc_start: 0.8959 (mtt) cc_final: 0.8569 (mtt) REVERT: D 267 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 286 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: D 430 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6306 (tmm-80) REVERT: G 100 MET cc_start: 0.8956 (mtt) cc_final: 0.8564 (mtt) outliers start: 52 outliers final: 16 residues processed: 256 average time/residue: 0.5540 time to fit residues: 162.5913 Evaluate side-chains 248 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 198 optimal weight: 0.0070 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 39 GLN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS E 39 GLN C 296 HIS ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS G 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112083 restraints weight = 20144.590| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.12 r_work: 0.3006 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19848 Z= 0.134 Angle : 0.582 11.310 27040 Z= 0.302 Chirality : 0.046 0.166 2896 Planarity : 0.004 0.043 3456 Dihedral : 5.513 36.056 2936 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 9.68 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.47 (0.16), residues: 2464 helix: -1.93 (0.73), residues: 24 sheet: 0.40 (0.17), residues: 892 loop : -0.72 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 172 TYR 0.012 0.001 TYR F 91 PHE 0.015 0.002 PHE E 78 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00300 (19796) covalent geometry : angle 0.57919 (26924) SS BOND : bond 0.00238 ( 40) SS BOND : angle 0.84737 ( 80) hydrogen bonds : bond 0.03461 ( 672) hydrogen bonds : angle 6.48587 ( 1728) link_NAG-ASN : bond 0.00183 ( 12) link_NAG-ASN : angle 1.23596 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (tp30) REVERT: A 286 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: A 425 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: A 430 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6133 (tmm-80) REVERT: H 100 MET cc_start: 0.8872 (mtt) cc_final: 0.8499 (mtt) REVERT: B 267 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (tp30) REVERT: B 286 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: B 425 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: B 430 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6096 (tmm-80) REVERT: E 100 MET cc_start: 0.8875 (mtt) cc_final: 0.8506 (mtt) REVERT: C 267 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: C 286 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: C 425 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: C 430 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6093 (tmm-80) REVERT: F 100 MET cc_start: 0.8879 (mtt) cc_final: 0.8509 (mtt) REVERT: D 267 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8574 (tp30) REVERT: D 286 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: D 425 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: D 430 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6131 (tmm-80) REVERT: G 100 MET cc_start: 0.8876 (mtt) cc_final: 0.8502 (mtt) outliers start: 44 outliers final: 16 residues processed: 257 average time/residue: 0.5150 time to fit residues: 151.6015 Evaluate side-chains 245 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111543 restraints weight = 20134.677| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.13 r_work: 0.3113 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19848 Z= 0.147 Angle : 0.588 11.655 27040 Z= 0.305 Chirality : 0.047 0.168 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.475 35.562 2936 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 10.58 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.16), residues: 2464 helix: -1.77 (0.77), residues: 24 sheet: 0.43 (0.17), residues: 892 loop : -0.70 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.012 0.002 TYR G 91 PHE 0.017 0.002 PHE H 78 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00334 (19796) covalent geometry : angle 0.58557 (26924) SS BOND : bond 0.00282 ( 40) SS BOND : angle 0.89644 ( 80) hydrogen bonds : bond 0.03517 ( 672) hydrogen bonds : angle 6.46062 ( 1728) link_NAG-ASN : bond 0.00172 ( 12) link_NAG-ASN : angle 1.28709 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: A 430 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6215 (tmm-80) REVERT: H 100 MET cc_start: 0.8942 (mtt) cc_final: 0.8579 (mtt) REVERT: B 425 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: B 430 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6177 (tmm-80) REVERT: E 100 MET cc_start: 0.8950 (mtt) cc_final: 0.8591 (mtt) REVERT: C 425 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8758 (tt0) REVERT: C 430 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6196 (tmm-80) REVERT: F 100 MET cc_start: 0.8948 (mtt) cc_final: 0.8585 (mtt) REVERT: D 425 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: D 430 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6207 (tmm-80) REVERT: G 100 MET cc_start: 0.8941 (mtt) cc_final: 0.8578 (mtt) outliers start: 40 outliers final: 16 residues processed: 238 average time/residue: 0.5004 time to fit residues: 136.7785 Evaluate side-chains 227 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 3 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 99 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS C 296 HIS F 39 GLN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111826 restraints weight = 20253.892| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.16 r_work: 0.2899 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19848 Z= 0.140 Angle : 0.580 11.529 27040 Z= 0.300 Chirality : 0.046 0.165 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.406 35.633 2936 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 11.10 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.38 (0.16), residues: 2464 helix: -1.79 (0.75), residues: 24 sheet: 0.48 (0.17), residues: 892 loop : -0.67 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.012 0.002 TYR G 91 PHE 0.016 0.002 PHE F 78 TRP 0.013 0.001 TRP D 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00318 (19796) covalent geometry : angle 0.57766 (26924) SS BOND : bond 0.00246 ( 40) SS BOND : angle 0.84005 ( 80) hydrogen bonds : bond 0.03443 ( 672) hydrogen bonds : angle 6.42521 ( 1728) link_NAG-ASN : bond 0.00172 ( 12) link_NAG-ASN : angle 1.29913 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: A 425 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: A 430 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6114 (tmm-80) REVERT: H 100 MET cc_start: 0.8853 (mtt) cc_final: 0.8470 (mtt) REVERT: B 267 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: B 425 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: B 430 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6141 (tmm-80) REVERT: E 100 MET cc_start: 0.8857 (mtt) cc_final: 0.8477 (mtt) REVERT: C 267 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: C 425 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: C 430 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6143 (tmm-80) REVERT: F 100 MET cc_start: 0.8858 (mtt) cc_final: 0.8479 (mtt) REVERT: D 267 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: D 425 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: D 430 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6109 (tmm-80) REVERT: G 100 MET cc_start: 0.8855 (mtt) cc_final: 0.8474 (mtt) outliers start: 40 outliers final: 16 residues processed: 241 average time/residue: 0.5174 time to fit residues: 143.1062 Evaluate side-chains 240 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 39 GLN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS E 39 GLN C 296 HIS F 39 GLN ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114119 restraints weight = 20198.303| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.15 r_work: 0.3083 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19848 Z= 0.104 Angle : 0.546 10.227 27040 Z= 0.284 Chirality : 0.046 0.151 2896 Planarity : 0.004 0.041 3456 Dihedral : 5.167 37.200 2936 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.33 % Allowed : 11.67 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.34 (0.16), residues: 2464 helix: -1.79 (0.72), residues: 24 sheet: 0.44 (0.17), residues: 900 loop : -0.60 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 430 TYR 0.011 0.001 TYR C 252 PHE 0.013 0.002 PHE F 78 TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00228 (19796) covalent geometry : angle 0.54386 (26924) SS BOND : bond 0.00286 ( 40) SS BOND : angle 0.65116 ( 80) hydrogen bonds : bond 0.03179 ( 672) hydrogen bonds : angle 6.23799 ( 1728) link_NAG-ASN : bond 0.00131 ( 12) link_NAG-ASN : angle 1.20105 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: A 425 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: A 430 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6110 (tmm-80) REVERT: H 100 MET cc_start: 0.8882 (mtt) cc_final: 0.8516 (mtt) REVERT: B 267 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: B 425 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8717 (tt0) REVERT: B 430 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6126 (tmm-80) REVERT: E 100 MET cc_start: 0.8883 (mtt) cc_final: 0.8520 (mtt) REVERT: C 267 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: C 425 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: C 430 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6113 (tmm-80) REVERT: F 100 MET cc_start: 0.8888 (mtt) cc_final: 0.8525 (mtt) REVERT: D 267 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: D 425 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8716 (tt0) REVERT: D 430 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6106 (tmm-80) REVERT: G 100 MET cc_start: 0.8881 (mtt) cc_final: 0.8512 (mtt) outliers start: 28 outliers final: 12 residues processed: 243 average time/residue: 0.5434 time to fit residues: 151.7767 Evaluate side-chains 227 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 2.9990 chunk 165 optimal weight: 0.2980 chunk 178 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 39 GLN B 296 HIS E 39 GLN C 296 HIS D 296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113312 restraints weight = 20051.973| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.14 r_work: 0.3023 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19848 Z= 0.120 Angle : 0.555 10.789 27040 Z= 0.287 Chirality : 0.046 0.153 2896 Planarity : 0.004 0.041 3456 Dihedral : 5.183 36.291 2936 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 12.62 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.30 (0.16), residues: 2464 helix: -1.97 (0.65), residues: 24 sheet: 0.52 (0.17), residues: 900 loop : -0.60 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.012 0.001 TYR F 91 PHE 0.015 0.002 PHE H 78 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00269 (19796) covalent geometry : angle 0.55274 (26924) SS BOND : bond 0.00244 ( 40) SS BOND : angle 0.73131 ( 80) hydrogen bonds : bond 0.03278 ( 672) hydrogen bonds : angle 6.26468 ( 1728) link_NAG-ASN : bond 0.00142 ( 12) link_NAG-ASN : angle 1.25886 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: A 430 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6074 (tmm-80) REVERT: H 100 MET cc_start: 0.8822 (mtt) cc_final: 0.8458 (mtt) REVERT: B 267 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: B 430 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6083 (tmm-80) REVERT: E 100 MET cc_start: 0.8823 (mtt) cc_final: 0.8459 (mtt) REVERT: C 267 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: C 430 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6078 (tmm-80) REVERT: F 100 MET cc_start: 0.8830 (mtt) cc_final: 0.8468 (mtt) REVERT: D 267 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: D 430 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6071 (tmm-80) REVERT: G 100 MET cc_start: 0.8821 (mtt) cc_final: 0.8456 (mtt) outliers start: 28 outliers final: 8 residues processed: 225 average time/residue: 0.5299 time to fit residues: 137.1779 Evaluate side-chains 213 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 430 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 0.0570 chunk 46 optimal weight: 0.0060 chunk 160 optimal weight: 0.3980 chunk 206 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 296 HIS C 296 HIS D 296 HIS G 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115764 restraints weight = 20178.604| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.18 r_work: 0.3108 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19848 Z= 0.096 Angle : 0.531 9.624 27040 Z= 0.276 Chirality : 0.045 0.142 2896 Planarity : 0.004 0.041 3456 Dihedral : 5.004 37.957 2936 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.76 % Allowed : 13.09 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.17), residues: 2464 helix: -2.03 (0.61), residues: 24 sheet: 0.55 (0.17), residues: 900 loop : -0.54 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 38 TYR 0.011 0.001 TYR F 91 PHE 0.013 0.001 PHE G 78 TRP 0.012 0.001 TRP C 178 HIS 0.001 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00211 (19796) covalent geometry : angle 0.52931 (26924) SS BOND : bond 0.00253 ( 40) SS BOND : angle 0.60978 ( 80) hydrogen bonds : bond 0.03083 ( 672) hydrogen bonds : angle 6.09207 ( 1728) link_NAG-ASN : bond 0.00127 ( 12) link_NAG-ASN : angle 1.19014 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: H 100 MET cc_start: 0.8840 (mtt) cc_final: 0.8512 (mtt) REVERT: B 267 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7986 (tp30) REVERT: E 100 MET cc_start: 0.8838 (mtt) cc_final: 0.8511 (mtt) REVERT: C 267 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: F 100 MET cc_start: 0.8850 (mtt) cc_final: 0.8526 (mtt) REVERT: D 267 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: G 100 MET cc_start: 0.8842 (mtt) cc_final: 0.8505 (mtt) outliers start: 16 outliers final: 8 residues processed: 219 average time/residue: 0.5196 time to fit residues: 131.3905 Evaluate side-chains 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 217 optimal weight: 0.0970 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 128 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS H 39 GLN ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS E 39 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS G 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.108850 restraints weight = 20121.144| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.18 r_work: 0.2853 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19848 Z= 0.245 Angle : 0.660 13.612 27040 Z= 0.340 Chirality : 0.050 0.191 2896 Planarity : 0.004 0.041 3456 Dihedral : 5.751 36.042 2936 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.52 % Allowed : 12.48 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.30 (0.16), residues: 2464 helix: -1.95 (0.68), residues: 24 sheet: 0.65 (0.17), residues: 884 loop : -0.69 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 156 TYR 0.016 0.002 TYR G 91 PHE 0.020 0.003 PHE H 78 TRP 0.018 0.002 TRP A 97 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00573 (19796) covalent geometry : angle 0.65508 (26924) SS BOND : bond 0.00383 ( 40) SS BOND : angle 1.25102 ( 80) hydrogen bonds : bond 0.04030 ( 672) hydrogen bonds : angle 6.66538 ( 1728) link_NAG-ASN : bond 0.00283 ( 12) link_NAG-ASN : angle 1.53720 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6062.11 seconds wall clock time: 104 minutes 29.18 seconds (6269.18 seconds total)