Starting phenix.real_space_refine on Sat Jul 4 09:16:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cye_46041/07_2026/9cye_46041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cye_46041/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cye_46041/07_2026/9cye_46041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cye_46041/07_2026/9cye_46041.map" model { file = "/net/cci-nas-00/data/ceres_data/9cye_46041/07_2026/9cye_46041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cye_46041/07_2026/9cye_46041.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.09, per 1000 atoms: 0.21 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: 1.76 Conformation dependent library (CDL) restraints added in 938.9 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: 0.71 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: 3.55 Time building geometry restraints manager: 2.33 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 3.250 ... (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: 10.770 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: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.140 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 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/Z covalent geometry : bond 0.00526 / 0.23 (19796) covalent geometry : angle 0.87158 / 0.47 (26924) SS BOND : bond 0.00290 / 0.19 ( 40) SS BOND : angle 1.12934 / 0.76 ( 80) hydrogen bonds : bond 0.16394 / 10.89 ( 672) hydrogen bonds : angle 8.34073 / 5.90 ( 1728) link_NAG-ASN : bond 0.00221 / 0.16 ( 12) link_NAG-ASN : angle 1.52977 / 0.99 ( 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 : 0.712 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: 0.4855 time to fit residues: 180.7107 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 : 0.769 ------------------------------------------------------------------------------- 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... 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 = 0.3552 r_free = 0.3552 target = 0.140617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111618 restraints weight = 20206.986| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.19 r_work: 0.3094 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19848 Z= 0.164 Angle : 0.617 10.535 27040 Z= 0.323 Chirality : 0.048 0.178 2896 Planarity : 0.004 0.045 3456 Dihedral : 5.924 41.411 2936 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.38 % Allowed : 7.92 % Favored : 90.70 % 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: -1.70 (0.80), 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 0.011 0.002 TYR F 91 PHE 0.018 0.002 PHE H 78 TRP 0.016 0.002 TRP C 178 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (19796) covalent geometry : angle 0.61268 / 0.32 (26924) SS BOND : bond 0.00337 / 0.23 ( 40) SS BOND : angle 1.29166 / 0.93 ( 80) hydrogen bonds : bond 0.03894 / 2.61 ( 672) hydrogen bonds : angle 6.96072 / 4.95 ( 1728) link_NAG-ASN : bond 0.00210 / 0.13 ( 12) link_NAG-ASN : angle 1.30344 / 0.86 ( 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 278 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: A 324 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: H 100 MET cc_start: 0.8989 (mtt) cc_final: 0.8634 (mtt) REVERT: L 21 ILE cc_start: 0.8238 (mt) cc_final: 0.8035 (mt) REVERT: B 267 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: B 324 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: E 100 MET cc_start: 0.8997 (mtt) cc_final: 0.8645 (mtt) REVERT: I 21 ILE cc_start: 0.8223 (mt) cc_final: 0.8022 (mt) REVERT: C 267 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: C 324 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: F 100 MET cc_start: 0.8999 (mtt) cc_final: 0.8649 (mtt) REVERT: J 21 ILE cc_start: 0.8251 (mt) cc_final: 0.8047 (mt) REVERT: D 267 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: D 324 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: G 100 MET cc_start: 0.8991 (mtt) cc_final: 0.8639 (mtt) REVERT: K 21 ILE cc_start: 0.8240 (mt) cc_final: 0.8039 (mt) outliers start: 29 outliers final: 8 residues processed: 274 average time/residue: 0.4917 time to fit residues: 155.9291 Evaluate side-chains 250 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 3.9990 chunk 148 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3564 r_free = 0.3564 target = 0.141628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113033 restraints weight = 20467.004| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.16 r_work: 0.3133 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19848 Z= 0.140 Angle : 0.590 10.860 27040 Z= 0.307 Chirality : 0.047 0.171 2896 Planarity : 0.004 0.043 3456 Dihedral : 5.789 36.020 2936 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.99 % Allowed : 8.25 % Favored : 89.75 % 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: -0.55 (0.16), residues: 2464 helix: -1.86 (0.74), residues: 24 sheet: 0.36 (0.17), residues: 884 loop : -0.78 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.013 0.001 TYR G 91 PHE 0.016 0.002 PHE G 78 TRP 0.015 0.001 TRP C 178 HIS 0.002 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19796) covalent geometry : angle 0.58647 / 0.31 (26924) SS BOND : bond 0.00289 / 0.19 ( 40) SS BOND : angle 1.11689 / 0.81 ( 80) hydrogen bonds : bond 0.03646 / 2.44 ( 672) hydrogen bonds : angle 6.66718 / 4.74 ( 1728) link_NAG-ASN : bond 0.00165 / 0.11 ( 12) link_NAG-ASN : angle 1.21915 / 0.81 ( 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 279 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 324 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 430 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6241 (tmm-80) REVERT: H 100 MET cc_start: 0.8973 (mtt) cc_final: 0.8582 (mtt) REVERT: B 286 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: B 324 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: B 430 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6244 (tmm-80) REVERT: E 100 MET cc_start: 0.8984 (mtt) cc_final: 0.8600 (mtt) REVERT: C 286 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 324 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: C 430 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6245 (tmm-80) REVERT: F 100 MET cc_start: 0.8979 (mtt) cc_final: 0.8593 (mtt) REVERT: D 286 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: D 324 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: D 430 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6240 (tmm-80) REVERT: G 100 MET cc_start: 0.8976 (mtt) cc_final: 0.8605 (mtt) outliers start: 42 outliers final: 8 residues processed: 271 average time/residue: 0.5083 time to fit residues: 158.1571 Evaluate side-chains 231 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 324 ASP 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 324 ASP 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 324 ASP 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 324 ASP 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: 0.7980 chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 225 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 296 HIS B 226 GLN B 296 HIS C 226 GLN C 296 HIS F 39 GLN D 226 GLN D 296 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112545 restraints weight = 20284.523| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.19 r_work: 0.3116 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19848 Z= 0.141 Angle : 0.587 11.113 27040 Z= 0.305 Chirality : 0.047 0.168 2896 Planarity : 0.004 0.043 3456 Dihedral : 5.605 35.842 2936 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.28 % Allowed : 9.35 % Favored : 88.38 % 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: -1.82 (0.76), residues: 24 sheet: 0.40 (0.17), residues: 892 loop : -0.73 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.013 0.001 TYR G 91 PHE 0.016 0.002 PHE E 78 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (19796) covalent geometry : angle 0.58390 / 0.30 (26924) SS BOND : bond 0.00224 / 0.14 ( 40) SS BOND : angle 0.95346 / 0.68 ( 80) hydrogen bonds : bond 0.03520 / 2.35 ( 672) hydrogen bonds : angle 6.55400 / 4.66 ( 1728) link_NAG-ASN : bond 0.00172 / 0.12 ( 12) link_NAG-ASN : angle 1.23804 / 0.82 ( 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 259 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 286 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: A 324 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: A 430 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6319 (tmm-80) REVERT: H 100 MET cc_start: 0.8985 (mtt) cc_final: 0.8617 (mtt) REVERT: B 267 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: B 286 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: B 324 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: B 430 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6293 (tmm-80) REVERT: E 100 MET cc_start: 0.8993 (mtt) cc_final: 0.8628 (mtt) REVERT: C 267 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: C 286 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: C 324 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: C 430 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6286 (tmm-80) REVERT: F 100 MET cc_start: 0.8994 (mtt) cc_final: 0.8628 (mtt) REVERT: D 267 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: D 286 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 324 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: D 430 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6283 (tmm-80) REVERT: G 100 MET cc_start: 0.8985 (mtt) cc_final: 0.8616 (mtt) outliers start: 48 outliers final: 12 residues processed: 243 average time/residue: 0.4883 time to fit residues: 136.9908 Evaluate side-chains 237 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 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 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 430 ARG 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: 0.6980 chunk 12 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS 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 = 0.3545 r_free = 0.3545 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111125 restraints weight = 20183.663| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.19 r_work: 0.2968 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19848 Z= 0.163 Angle : 0.602 11.824 27040 Z= 0.312 Chirality : 0.047 0.172 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.592 35.115 2936 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 9.44 % Favored : 88.28 % 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: -1.72 (0.80), residues: 24 sheet: 0.41 (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 156 TYR 0.013 0.002 TYR G 91 PHE 0.018 0.002 PHE F 78 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (19796) covalent geometry : angle 0.59893 / 0.31 (26924) SS BOND : bond 0.00301 / 0.19 ( 40) SS BOND : angle 0.97437 / 0.69 ( 80) hydrogen bonds : bond 0.03629 / 2.42 ( 672) hydrogen bonds : angle 6.56668 / 4.67 ( 1728) link_NAG-ASN : bond 0.00192 / 0.14 ( 12) link_NAG-ASN : angle 1.30253 / 0.86 ( 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 258 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8564 (tp30) REVERT: A 286 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 324 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: A 430 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6177 (tmm-80) REVERT: H 100 MET cc_start: 0.8889 (mtt) cc_final: 0.8500 (mtt) REVERT: B 267 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: B 286 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: B 324 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: B 430 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6181 (tmm-80) REVERT: E 100 MET cc_start: 0.8890 (mtt) cc_final: 0.8505 (mtt) REVERT: C 267 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8560 (tp30) REVERT: C 286 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: C 324 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: C 430 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6197 (tmm-80) REVERT: F 100 MET cc_start: 0.8892 (mtt) cc_final: 0.8507 (mtt) REVERT: D 267 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: D 286 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 324 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: D 430 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6175 (tmm-80) REVERT: G 100 MET cc_start: 0.8893 (mtt) cc_final: 0.8504 (mtt) outliers start: 48 outliers final: 16 residues processed: 242 average time/residue: 0.5343 time to fit residues: 148.4166 Evaluate side-chains 239 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 324 ASP 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 324 ASP 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 324 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3543 r_free = 0.3543 target = 0.139954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110981 restraints weight = 20186.461| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.19 r_work: 0.3094 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 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 : 0.004 0.036 19848 Z= 0.163 Angle : 0.600 11.954 27040 Z= 0.311 Chirality : 0.047 0.173 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.557 35.273 2936 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.09 % Allowed : 10.39 % 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: -0.42 (0.16), residues: 2464 helix: -1.78 (0.77), residues: 24 sheet: 0.45 (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 B 156 TYR 0.013 0.002 TYR F 91 PHE 0.017 0.002 PHE E 78 TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (19796) covalent geometry : angle 0.59688 / 0.31 (26924) SS BOND : bond 0.00251 / 0.16 ( 40) SS BOND : angle 0.97145 / 0.69 ( 80) hydrogen bonds : bond 0.03620 / 2.42 ( 672) hydrogen bonds : angle 6.54685 / 4.66 ( 1728) link_NAG-ASN : bond 0.00196 / 0.14 ( 12) link_NAG-ASN : angle 1.32708 / 0.88 ( 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 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: A 286 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: A 324 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: A 430 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6321 (tmm-80) REVERT: H 100 MET cc_start: 0.9002 (mtt) cc_final: 0.8615 (mtt) REVERT: B 267 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8611 (tp30) REVERT: B 286 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 324 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 430 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6318 (tmm-80) REVERT: E 100 MET cc_start: 0.8999 (mtt) cc_final: 0.8612 (mtt) REVERT: C 267 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: C 286 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 324 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: C 430 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6320 (tmm-80) REVERT: F 100 MET cc_start: 0.9003 (mtt) cc_final: 0.8615 (mtt) REVERT: D 267 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (tp30) REVERT: D 286 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: D 324 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: D 430 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6325 (tmm-80) REVERT: G 100 MET cc_start: 0.9001 (mtt) cc_final: 0.8614 (mtt) outliers start: 44 outliers final: 16 residues processed: 243 average time/residue: 0.5000 time to fit residues: 139.2338 Evaluate side-chains 239 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 324 ASP 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 324 ASP 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 324 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 3 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 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: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3529 r_free = 0.3529 target = 0.138920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109771 restraints weight = 20288.075| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.21 r_work: 0.2935 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19848 Z= 0.193 Angle : 0.624 12.703 27040 Z= 0.323 Chirality : 0.048 0.182 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.687 34.435 2936 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.28 % Allowed : 10.58 % Favored : 87.14 % 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: -0.42 (0.16), residues: 2464 helix: -1.75 (0.79), residues: 24 sheet: 0.49 (0.17), residues: 892 loop : -0.73 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.013 0.002 TYR G 91 PHE 0.019 0.002 PHE E 78 TRP 0.015 0.001 TRP A 97 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (19796) covalent geometry : angle 0.62066 / 0.32 (26924) SS BOND : bond 0.00318 / 0.20 ( 40) SS BOND : angle 1.09712 / 0.78 ( 80) hydrogen bonds : bond 0.03807 / 2.54 ( 672) hydrogen bonds : angle 6.65747 / 4.74 ( 1728) link_NAG-ASN : bond 0.00235 / 0.17 ( 12) link_NAG-ASN : angle 1.41478 / 0.95 ( 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 260 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 286 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 324 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: A 430 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6181 (tmm-80) REVERT: H 100 MET cc_start: 0.8895 (mtt) cc_final: 0.8486 (mtt) REVERT: B 267 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: B 286 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: B 324 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: B 430 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6185 (tmm-80) REVERT: E 100 MET cc_start: 0.8897 (mtt) cc_final: 0.8488 (mtt) REVERT: C 267 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: C 286 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: C 324 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: C 430 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6179 (tmm-80) REVERT: F 100 MET cc_start: 0.8897 (mtt) cc_final: 0.8490 (mtt) REVERT: D 267 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 286 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: D 324 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: D 430 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6176 (tmm-80) REVERT: G 100 MET cc_start: 0.8895 (mtt) cc_final: 0.8487 (mtt) outliers start: 48 outliers final: 16 residues processed: 244 average time/residue: 0.4851 time to fit residues: 136.9951 Evaluate side-chains 236 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 324 ASP 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 324 ASP 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 324 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3533 r_free = 0.3533 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110022 restraints weight = 20254.158| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.19 r_work: 0.2878 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19848 Z= 0.181 Angle : 0.613 12.555 27040 Z= 0.317 Chirality : 0.048 0.179 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.651 34.784 2936 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.04 % Allowed : 11.95 % 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: -0.40 (0.16), residues: 2464 helix: -1.83 (0.77), residues: 24 sheet: 0.50 (0.17), residues: 892 loop : -0.71 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.013 0.002 TYR E 91 PHE 0.018 0.002 PHE E 78 TRP 0.015 0.001 TRP B 178 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (19796) covalent geometry : angle 0.60975 / 0.32 (26924) SS BOND : bond 0.00294 / 0.18 ( 40) SS BOND : angle 1.02683 / 0.73 ( 80) hydrogen bonds : bond 0.03726 / 2.49 ( 672) hydrogen bonds : angle 6.62066 / 4.71 ( 1728) link_NAG-ASN : bond 0.00226 / 0.16 ( 12) link_NAG-ASN : angle 1.40760 / 0.95 ( 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: 43 poor density : 204 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: A 286 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: A 324 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: A 425 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: A 430 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6241 (tmm-80) REVERT: H 100 MET cc_start: 0.8907 (mtt) cc_final: 0.8522 (mtt) REVERT: B 267 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: B 286 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: B 324 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: B 425 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: B 430 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6248 (tmm-80) REVERT: E 100 MET cc_start: 0.8902 (mtt) cc_final: 0.8493 (mtt) REVERT: E 102 VAL cc_start: 0.8956 (t) cc_final: 0.8755 (t) REVERT: C 267 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: C 286 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: C 324 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 425 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8789 (tt0) REVERT: C 430 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6247 (tmm-80) REVERT: F 100 MET cc_start: 0.8912 (mtt) cc_final: 0.8527 (mtt) REVERT: F 102 VAL cc_start: 0.8959 (t) cc_final: 0.8758 (t) REVERT: D 267 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: D 286 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: D 324 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: D 425 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: D 430 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6239 (tmm-80) REVERT: G 100 MET cc_start: 0.8909 (mtt) cc_final: 0.8523 (mtt) outliers start: 43 outliers final: 19 residues processed: 235 average time/residue: 0.5330 time to fit residues: 144.3536 Evaluate side-chains 235 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 A residue 463 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 LEU 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 B residue 463 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain I residue 33 LEU 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 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 324 ASP Chi-restraints excluded: chain D residue 425 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 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: 0.9980 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3533 r_free = 0.3533 target = 0.139180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110103 restraints weight = 20123.071| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.16 r_work: 0.2956 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19848 Z= 0.181 Angle : 0.615 12.546 27040 Z= 0.318 Chirality : 0.048 0.178 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.641 34.716 2936 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.13 % Allowed : 12.00 % Favored : 85.86 % 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: -0.39 (0.16), residues: 2464 helix: -1.81 (0.78), residues: 24 sheet: 0.52 (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 D 156 TYR 0.014 0.002 TYR H 91 PHE 0.018 0.002 PHE E 78 TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (19796) covalent geometry : angle 0.61158 / 0.32 (26924) SS BOND : bond 0.00312 / 0.20 ( 40) SS BOND : angle 1.02601 / 0.73 ( 80) hydrogen bonds : bond 0.03738 / 2.50 ( 672) hydrogen bonds : angle 6.62811 / 4.71 ( 1728) link_NAG-ASN : bond 0.00227 / 0.16 ( 12) link_NAG-ASN : angle 1.40400 / 0.94 ( 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 250 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: A 286 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 324 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: A 425 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8787 (tt0) REVERT: A 430 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6181 (tmm-80) REVERT: H 100 MET cc_start: 0.8872 (mtt) cc_final: 0.8478 (mtt) REVERT: B 267 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: B 286 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 324 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: B 425 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: B 430 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6184 (tmm-80) REVERT: E 100 MET cc_start: 0.8879 (mtt) cc_final: 0.8490 (mtt) REVERT: C 267 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: C 286 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: C 324 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: C 425 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: C 430 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6201 (tmm-80) REVERT: F 100 MET cc_start: 0.8881 (mtt) cc_final: 0.8489 (mtt) REVERT: D 267 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: D 286 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: D 324 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: D 425 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: D 430 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6181 (tmm-80) REVERT: G 100 MET cc_start: 0.8872 (mtt) cc_final: 0.8477 (mtt) outliers start: 45 outliers final: 16 residues processed: 234 average time/residue: 0.5175 time to fit residues: 138.8588 Evaluate side-chains 237 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 324 ASP Chi-restraints excluded: chain B residue 425 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 324 ASP Chi-restraints excluded: chain C residue 425 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 324 ASP Chi-restraints excluded: chain D residue 425 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3509 r_free = 0.3509 target = 0.137315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108184 restraints weight = 20271.139| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.20 r_work: 0.2907 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19848 Z= 0.264 Angle : 0.680 13.819 27040 Z= 0.352 Chirality : 0.051 0.198 2896 Planarity : 0.005 0.041 3456 Dihedral : 5.974 33.122 2936 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.04 % Allowed : 12.10 % Favored : 85.86 % 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: -0.44 (0.16), residues: 2464 helix: -1.67 (0.85), residues: 24 sheet: 0.53 (0.17), residues: 884 loop : -0.78 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.015 0.002 TYR H 91 PHE 0.020 0.003 PHE H 78 TRP 0.019 0.002 TRP A 97 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (19796) covalent geometry : angle 0.67508 / 0.35 (26924) SS BOND : bond 0.00403 / 0.25 ( 40) SS BOND : angle 1.38822 / 0.98 ( 80) hydrogen bonds : bond 0.04177 / 2.79 ( 672) hydrogen bonds : angle 6.83516 / 4.86 ( 1728) link_NAG-ASN : bond 0.00309 / 0.22 ( 12) link_NAG-ASN : angle 1.50689 / 1.03 ( 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 242 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 286 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 430 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6271 (tmm-80) REVERT: H 100 MET cc_start: 0.8917 (mtt) cc_final: 0.8501 (mtt) REVERT: B 267 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: B 286 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: B 324 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: B 430 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6276 (tmm-80) REVERT: E 100 MET cc_start: 0.8918 (mtt) cc_final: 0.8498 (mtt) REVERT: C 267 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 286 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: C 324 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: C 430 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6276 (tmm-80) REVERT: F 100 MET cc_start: 0.8919 (mtt) cc_final: 0.8498 (mtt) REVERT: D 267 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: D 286 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: D 324 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: D 430 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6277 (tmm-80) REVERT: G 100 MET cc_start: 0.8918 (mtt) cc_final: 0.8501 (mtt) outliers start: 43 outliers final: 19 residues processed: 230 average time/residue: 0.4720 time to fit residues: 124.7603 Evaluate side-chains 225 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 L residue 33 LEU 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 430 ARG Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain I residue 33 LEU 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 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 324 ASP Chi-restraints excluded: chain D residue 430 ARG Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3541 r_free = 0.3541 target = 0.139881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110999 restraints weight = 20146.415| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.19 r_work: 0.2885 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19848 Z= 0.153 Angle : 0.598 12.174 27040 Z= 0.310 Chirality : 0.047 0.171 2896 Planarity : 0.004 0.042 3456 Dihedral : 5.598 35.585 2936 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.80 % Allowed : 12.90 % Favored : 85.29 % 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: -0.37 (0.16), residues: 2464 helix: -1.90 (0.74), residues: 24 sheet: 0.56 (0.17), residues: 892 loop : -0.71 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 300 TYR 0.012 0.002 TYR E 91 PHE 0.017 0.002 PHE F 78 TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19796) covalent geometry : angle 0.59482 / 0.31 (26924) SS BOND : bond 0.00257 / 0.16 ( 40) SS BOND : angle 0.88799 / 0.63 ( 80) hydrogen bonds : bond 0.03588 / 2.40 ( 672) hydrogen bonds : angle 6.57663 / 4.68 ( 1728) link_NAG-ASN : bond 0.00210 / 0.15 ( 12) link_NAG-ASN : angle 1.37596 / 0.92 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5879.47 seconds wall clock time: 101 minutes 13.89 seconds (6073.89 seconds total)