Starting phenix.real_space_refine on Sun Sep 13 05:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpr_14862/09_2026/7zpr_14862.map" } resolution = 3.56 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= 0.004 sd= 0.009 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 13782 2.51 5 N 3576 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21350 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "G" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.30 Number of scatterers: 21350 At special positions: 0 Unit cell: (95.9651, 110.921, 173.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 3824 8.00 N 3576 7.00 C 13782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 69.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'H' and resid 14 through 27 removed outlier: 3.520A pdb=" N SER H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.713A pdb=" N GLY H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 122 through 137 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.762A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 37 through 46 removed outlier: 4.231A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 37 through 46 removed outlier: 4.024A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 67 through 70 Processing helix chain 'F' and resid 80 through 95 Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'I' and resid 23 through 44 removed outlier: 3.527A pdb=" N PHE I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix removed outlier: 3.531A pdb=" N THR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 122 Processing helix chain 'I' and resid 133 through 165 removed outlier: 3.710A pdb=" N ARG I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 167 through 182 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 230 through 234 Processing helix chain 'I' and resid 235 through 261 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 271 through 286 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 300 through 314 Processing helix chain 'I' and resid 325 through 341 Processing helix chain 'I' and resid 354 through 383 Processing helix chain 'I' and resid 386 through 399 Processing helix chain 'I' and resid 407 through 411 Processing helix chain 'I' and resid 412 through 439 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.842A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.684A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.535A pdb=" N SER J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 removed outlier: 4.242A pdb=" N GLY J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 65 Processing helix chain 'J' and resid 80 through 94 Processing helix chain 'J' and resid 105 through 116 Processing helix chain 'J' and resid 122 through 137 Processing helix chain 'L' and resid 14 through 28 removed outlier: 3.618A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 4.247A pdb=" N GLY L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 Processing helix chain 'L' and resid 67 through 70 Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.548A pdb=" N SER L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 116 Processing helix chain 'L' and resid 122 through 137 Processing helix chain 'M' and resid 23 through 45 Proline residue: M 38 - end of helix removed outlier: 3.770A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 67 Processing helix chain 'M' and resid 75 through 80 removed outlier: 3.687A pdb=" N PHE M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 122 removed outlier: 3.582A pdb=" N GLN M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 165 removed outlier: 3.846A pdb=" N ARG M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Proline residue: M 162 - end of helix Processing helix chain 'M' and resid 165 through 182 removed outlier: 3.594A pdb=" N PHE M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 214 Processing helix chain 'M' and resid 216 through 227 Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 235 through 261 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 286 Processing helix chain 'M' and resid 295 through 299 Processing helix chain 'M' and resid 300 through 314 Processing helix chain 'M' and resid 325 through 342 Processing helix chain 'M' and resid 354 through 383 Processing helix chain 'M' and resid 386 through 399 Processing helix chain 'M' and resid 412 through 439 removed outlier: 3.536A pdb=" N TYR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) Proline residue: M 430 - end of helix Processing helix chain 'C' and resid 23 through 44 removed outlier: 3.525A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.530A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.611A pdb=" N PHE C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 122 Processing helix chain 'C' and resid 133 through 165 removed outlier: 3.711A pdb=" N ARG C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 235 through 261 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 354 through 383 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 439 Proline residue: C 430 - end of helix Processing helix chain 'G' and resid 23 through 45 Proline residue: G 38 - end of helix removed outlier: 3.770A pdb=" N THR G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 75 through 80 removed outlier: 3.685A pdb=" N PHE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 122 removed outlier: 3.581A pdb=" N GLN G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 165 removed outlier: 3.846A pdb=" N ARG G 159 " --> pdb=" O PHE G 155 " (cutoff:3.500A) Proline residue: G 162 - end of helix Processing helix chain 'G' and resid 165 through 182 removed outlier: 3.593A pdb=" N PHE G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 214 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 235 through 261 Proline residue: G 246 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 300 through 314 Processing helix chain 'G' and resid 325 through 342 Processing helix chain 'G' and resid 354 through 383 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 412 through 439 removed outlier: 3.537A pdb=" N TYR G 417 " --> pdb=" O GLU G 413 " (cutoff:3.500A) Proline residue: G 430 - end of helix Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 53 removed outlier: 6.168A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA H 33 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET H 72 " --> pdb=" O GLN H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 50 through 53 removed outlier: 6.172A pdb=" N VAL D 31 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE D 52 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL D 34 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 10 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N MET D 74 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 9 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 99 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 121 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 101 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 53 removed outlier: 6.253A pdb=" N VAL E 31 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 52 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 33 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 50 through 53 removed outlier: 6.419A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE F 52 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 33 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.466A pdb=" N VAL I 346 " --> pdb=" O VAL I 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR I 352 " --> pdb=" O ASP M 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.257A pdb=" N VAL A 31 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 52 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 33 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A 7 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N MET A 74 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 9 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 99 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 101 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.120A pdb=" N VAL B 31 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 52 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 8 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 34 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 7 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET B 74 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 9 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 99 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 50 through 53 removed outlier: 6.329A pdb=" N VAL J 31 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE J 52 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 50 through 53 removed outlier: 6.448A pdb=" N VAL L 31 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE L 52 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA L 33 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL L 99 " --> pdb=" O HIS L 119 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE L 121 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL C 346 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR C 352 " --> pdb=" O ASP G 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 346 through 347 removed outlier: 4.420A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1443 hydrogen bonds defined for protein. 4242 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: 3.99 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4195 1.33 - 1.45: 4835 1.45 - 1.57: 12413 1.57 - 1.69: 24 1.69 - 1.82: 261 Bond restraints: 21728 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.35e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 21723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 28501 2.16 - 4.32: 817 4.32 - 6.48: 113 6.48 - 8.64: 16 8.64 - 10.80: 11 Bond angle restraints: 29458 Sorted by residual: angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.31 -8.89 1.99e+00 2.53e-01 2.00e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.50 5.39 1.24e+00 6.50e-01 1.89e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N LEU C 296 " pdb=" CA LEU C 296 " pdb=" C LEU C 296 " ideal model delta sigma weight residual 112.89 107.71 5.18 1.24e+00 6.50e-01 1.75e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 12514 33.64 - 67.28: 281 67.28 - 100.92: 16 100.92 - 134.56: 5 134.56 - 168.20: 6 Dihedral angle restraints: 12822 sinusoidal: 4956 harmonic: 7866 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.80 168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.80 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.02 -160.01 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3354 0.108 - 0.215: 188 0.215 - 0.322: 2 0.322 - 0.430: 0 0.430 - 0.537: 4 Chirality restraints: 3548 Sorted by residual: chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA THR C 288 " pdb=" N THR C 288 " pdb=" C THR C 288 " pdb=" CB THR C 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 3545 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C MET M 92 " 0.041 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET G 92 " -0.041 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 122 " 0.032 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 123 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.026 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 141 2.56 - 3.21: 19848 3.21 - 3.85: 43220 3.85 - 4.50: 61039 4.50 - 5.14: 95532 Nonbonded interactions: 219780 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O3B ADP A1002 " model vdw 1.919 2.170 nonbonded pdb=" OD1 ASN H 82 " pdb=" ND2 ASN B 82 " model vdw 1.954 3.120 nonbonded pdb=" O2B ADP L 301 " pdb="MG MG L 302 " model vdw 1.977 2.170 nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 301 " pdb="MG MG E 302 " model vdw 1.988 2.170 ... (remaining 219775 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 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 21 through 350 or resid 352 through 601)) selection = (chain 'G' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 501)) selection = (chain 'I' and (resid 21 through 350 or resid 352 through 601)) selection = (chain 'M' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 501)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.700 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.256 21728 Z= 0.358 Angle : 0.800 10.803 29458 Z= 0.497 Chirality : 0.053 0.537 3548 Planarity : 0.004 0.047 3608 Dihedral : 14.454 168.201 7742 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 1.16 % Favored : 97.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 2736 helix: 1.46 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 130 TYR 0.014 0.002 TYR F 70 PHE 0.026 0.001 PHE I 210 TRP 0.011 0.001 TRP M 337 HIS 0.005 0.001 HIS G 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.36 (21728) covalent geometry : angle 0.80015 / 0.50 (29458) hydrogen bonds : bond 0.18822 / 12.48 ( 1443) hydrogen bonds : angle 6.57781 / 4.64 ( 4242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 772 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7987 (tp30) cc_final: 0.7137 (tp30) REVERT: H 127 MET cc_start: 0.8929 (tpt) cc_final: 0.8175 (tpp) REVERT: D 110 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8189 (mtm180) REVERT: D 133 ARG cc_start: 0.7368 (mtt90) cc_final: 0.7027 (mtm-85) REVERT: E 29 SER cc_start: 0.7901 (m) cc_final: 0.7693 (p) REVERT: E 96 VAL cc_start: 0.8462 (t) cc_final: 0.8255 (t) REVERT: E 127 MET cc_start: 0.8340 (mmm) cc_final: 0.8094 (mmm) REVERT: I 92 MET cc_start: 0.7593 (ptt) cc_final: 0.7338 (ptt) REVERT: I 387 PHE cc_start: 0.7513 (t80) cc_final: 0.7042 (t80) REVERT: I 389 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7597 (ttmt) REVERT: I 420 ILE cc_start: 0.7474 (mt) cc_final: 0.7061 (mt) REVERT: I 447 TYR cc_start: 0.8776 (m-80) cc_final: 0.8502 (m-80) REVERT: A 23 GLU cc_start: 0.7777 (tp30) cc_final: 0.7219 (tp30) REVERT: A 133 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7215 (mtm180) REVERT: B 23 GLU cc_start: 0.7382 (tp30) cc_final: 0.7021 (tp30) REVERT: B 127 MET cc_start: 0.9040 (tpt) cc_final: 0.8792 (tpp) REVERT: B 133 ARG cc_start: 0.7328 (mtt90) cc_final: 0.7041 (mtm-85) REVERT: J 122 MET cc_start: 0.7679 (mtp) cc_final: 0.6735 (mtm) REVERT: J 126 ASP cc_start: 0.7860 (m-30) cc_final: 0.7546 (m-30) REVERT: L 98 SER cc_start: 0.7307 (p) cc_final: 0.6758 (p) REVERT: L 122 MET cc_start: 0.7622 (mtp) cc_final: 0.6897 (mtm) REVERT: M 76 THR cc_start: 0.7360 (m) cc_final: 0.7106 (m) REVERT: M 93 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6899 (tp-100) REVERT: M 298 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: M 420 ILE cc_start: 0.7844 (mt) cc_final: 0.7506 (mt) REVERT: M 447 TYR cc_start: 0.8739 (m-80) cc_final: 0.8473 (m-80) REVERT: C 92 MET cc_start: 0.7635 (ptt) cc_final: 0.7376 (ptt) REVERT: C 93 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7235 (tp-100) REVERT: C 108 TYR cc_start: 0.7607 (t80) cc_final: 0.7367 (t80) REVERT: C 136 ARG cc_start: 0.5225 (ttt180) cc_final: 0.4998 (tpt170) REVERT: C 387 PHE cc_start: 0.7614 (t80) cc_final: 0.7199 (t80) REVERT: C 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7642 (ttmt) REVERT: C 420 ILE cc_start: 0.7642 (mt) cc_final: 0.7245 (mt) REVERT: C 447 TYR cc_start: 0.8841 (m-80) cc_final: 0.8597 (m-80) REVERT: C 449 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6444 (mt-10) REVERT: G 93 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6853 (tp-100) REVERT: G 277 LEU cc_start: 0.8276 (tp) cc_final: 0.7862 (tt) REVERT: G 298 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: G 400 THR cc_start: 0.8878 (m) cc_final: 0.8573 (m) REVERT: G 420 ILE cc_start: 0.7862 (mt) cc_final: 0.7613 (mt) REVERT: G 447 TYR cc_start: 0.8782 (m-80) cc_final: 0.8549 (m-80) outliers start: 20 outliers final: 2 residues processed: 782 average time/residue: 0.1687 time to fit residues: 199.9793 Evaluate side-chains 479 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 473 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 50 GLN D 50 GLN I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN I 301 GLN A 50 GLN B 50 GLN J 30 GLN J 108 GLN J 113 GLN M 93 GLN M 262 HIS C 78 GLN C 282 GLN C 301 GLN G 345 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119498 restraints weight = 30160.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123255 restraints weight = 16140.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125757 restraints weight = 10295.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127312 restraints weight = 7438.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128480 restraints weight = 5964.808| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21728 Z= 0.233 Angle : 0.734 8.381 29458 Z= 0.367 Chirality : 0.048 0.169 3548 Planarity : 0.005 0.048 3608 Dihedral : 9.752 179.729 3010 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.98 % Favored : 97.95 % Rotamer: Outliers : 3.16 % Allowed : 11.53 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2736 helix: 1.89 (0.12), residues: 1782 sheet: 1.31 (0.27), residues: 274 loop : -0.14 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 427 TYR 0.012 0.002 TYR G 447 PHE 0.040 0.003 PHE I 210 TRP 0.019 0.002 TRP G 257 HIS 0.008 0.002 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (21728) covalent geometry : angle 0.73393 / 0.37 (29458) hydrogen bonds : bond 0.04663 / 3.16 ( 1443) hydrogen bonds : angle 4.48726 / 3.21 ( 4242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 513 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7910 (tp30) cc_final: 0.7131 (tp30) REVERT: H 40 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7503 (mtt180) REVERT: H 134 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8285 (mtpt) REVERT: D 40 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7931 (mtt180) REVERT: D 107 PHE cc_start: 0.8499 (m-80) cc_final: 0.8258 (m-10) REVERT: D 133 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6931 (mtm-85) REVERT: E 72 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6289 (mmm) REVERT: F 122 MET cc_start: 0.7550 (mtm) cc_final: 0.6772 (mtm) REVERT: F 126 ASP cc_start: 0.8049 (m-30) cc_final: 0.7729 (m-30) REVERT: I 139 LYS cc_start: 0.7292 (ttpp) cc_final: 0.6740 (ttmt) REVERT: I 217 PHE cc_start: 0.8136 (t80) cc_final: 0.7931 (t80) REVERT: I 389 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7517 (ttmt) REVERT: I 420 ILE cc_start: 0.8497 (mt) cc_final: 0.8182 (mt) REVERT: A 23 GLU cc_start: 0.7711 (tp30) cc_final: 0.7355 (tp30) REVERT: A 133 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7037 (mtm-85) REVERT: B 23 GLU cc_start: 0.7629 (tp30) cc_final: 0.7349 (tp30) REVERT: B 127 MET cc_start: 0.8877 (tpt) cc_final: 0.8675 (tpp) REVERT: B 133 ARG cc_start: 0.7360 (mtt90) cc_final: 0.7122 (mtm-85) REVERT: L 23 GLU cc_start: 0.7702 (tp30) cc_final: 0.7498 (tp30) REVERT: L 35 ASP cc_start: 0.7821 (t70) cc_final: 0.7557 (t70) REVERT: L 122 MET cc_start: 0.7570 (mtp) cc_final: 0.6893 (mtm) REVERT: L 126 ASP cc_start: 0.7528 (m-30) cc_final: 0.7295 (m-30) REVERT: M 193 MET cc_start: 0.8140 (mmt) cc_final: 0.7926 (mmt) REVERT: M 241 MET cc_start: 0.8145 (mmt) cc_final: 0.7818 (mmt) REVERT: C 139 LYS cc_start: 0.7334 (ttpp) cc_final: 0.7008 (ttmt) REVERT: C 292 ASN cc_start: 0.7471 (p0) cc_final: 0.7150 (p0) REVERT: C 295 ASP cc_start: 0.6219 (m-30) cc_final: 0.5815 (m-30) REVERT: C 299 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: C 388 ASP cc_start: 0.7154 (p0) cc_final: 0.6846 (p0) REVERT: C 389 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7501 (ttmt) REVERT: C 420 ILE cc_start: 0.8550 (mt) cc_final: 0.8264 (mt) REVERT: G 228 ARG cc_start: 0.6840 (ptp-110) cc_final: 0.6605 (ptp-110) REVERT: G 241 MET cc_start: 0.8059 (mmt) cc_final: 0.7771 (mmt) REVERT: G 298 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7478 (mt0) outliers start: 71 outliers final: 52 residues processed: 561 average time/residue: 0.1488 time to fit residues: 131.2161 Evaluate side-chains 496 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 441 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 GLN Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 109 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 179 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.8282 > 50:) chunk 257 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 ASN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN M 265 ASN M 282 GLN G 93 GLN G 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116032 restraints weight = 38735.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120548 restraints weight = 18356.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123691 restraints weight = 10981.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125673 restraints weight = 7492.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127077 restraints weight = 5707.381| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21728 Z= 0.165 Angle : 0.633 7.041 29458 Z= 0.310 Chirality : 0.044 0.167 3548 Planarity : 0.004 0.036 3608 Dihedral : 9.108 173.409 3004 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 13.89 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.16), residues: 2736 helix: 2.23 (0.12), residues: 1770 sheet: 1.28 (0.28), residues: 274 loop : -0.23 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 427 TYR 0.010 0.001 TYR I 158 PHE 0.035 0.002 PHE C 210 TRP 0.011 0.001 TRP G 257 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (21728) covalent geometry : angle 0.63276 / 0.31 (29458) hydrogen bonds : bond 0.04177 / 2.83 ( 1443) hydrogen bonds : angle 4.29491 / 3.06 ( 4242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 483 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7899 (tp30) cc_final: 0.7189 (tp30) REVERT: H 40 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7410 (mtt180) REVERT: H 134 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8312 (mtpt) REVERT: D 40 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7896 (mtt180) REVERT: D 133 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6777 (mtm-85) REVERT: E 72 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6578 (mmm) REVERT: E 124 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7996 (mm-30) REVERT: I 139 LYS cc_start: 0.7258 (ttpp) cc_final: 0.6875 (ttmt) REVERT: I 217 PHE cc_start: 0.8396 (t80) cc_final: 0.8182 (t80) REVERT: I 228 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6883 (ptp-110) REVERT: I 241 MET cc_start: 0.8247 (tpp) cc_final: 0.7841 (mmt) REVERT: I 292 ASN cc_start: 0.7179 (p0) cc_final: 0.6771 (p0) REVERT: I 389 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7523 (ttmt) REVERT: I 420 ILE cc_start: 0.8606 (mt) cc_final: 0.8331 (mt) REVERT: A 23 GLU cc_start: 0.7792 (tp30) cc_final: 0.7303 (tp30) REVERT: A 42 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8163 (mtpt) REVERT: A 133 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6885 (mmm-85) REVERT: B 23 GLU cc_start: 0.7636 (tp30) cc_final: 0.7324 (tp30) REVERT: L 35 ASP cc_start: 0.7841 (t70) cc_final: 0.7595 (t70) REVERT: L 122 MET cc_start: 0.7643 (mtp) cc_final: 0.7289 (mtm) REVERT: M 241 MET cc_start: 0.7996 (mmt) cc_final: 0.7665 (mmt) REVERT: M 265 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (t0) REVERT: M 292 ASN cc_start: 0.7212 (p0) cc_final: 0.6716 (p0) REVERT: M 410 GLU cc_start: 0.7009 (pp20) cc_final: 0.6709 (pt0) REVERT: M 446 LYS cc_start: 0.8585 (tttt) cc_final: 0.8094 (tttm) REVERT: C 139 LYS cc_start: 0.7450 (ttpp) cc_final: 0.7066 (ttmt) REVERT: C 241 MET cc_start: 0.8262 (tpp) cc_final: 0.7810 (mmt) REVERT: C 292 ASN cc_start: 0.7307 (p0) cc_final: 0.6767 (p0) REVERT: C 295 ASP cc_start: 0.6492 (m-30) cc_final: 0.6200 (m-30) REVERT: C 389 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7517 (ttmt) REVERT: G 228 ARG cc_start: 0.7154 (ptp-110) cc_final: 0.6710 (ptp-110) REVERT: G 241 MET cc_start: 0.8003 (mmt) cc_final: 0.7702 (mmt) REVERT: G 277 LEU cc_start: 0.8927 (tp) cc_final: 0.8669 (tt) REVERT: G 292 ASN cc_start: 0.7287 (p0) cc_final: 0.6802 (p0) REVERT: G 410 GLU cc_start: 0.6932 (pp20) cc_final: 0.6729 (pt0) REVERT: G 423 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7193 (mtm) REVERT: G 446 LYS cc_start: 0.8691 (tttt) cc_final: 0.8180 (tttm) outliers start: 65 outliers final: 41 residues processed: 525 average time/residue: 0.1506 time to fit residues: 124.8997 Evaluate side-chains 494 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 449 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 396 SER Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 64 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 267 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 HIS G 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116039 restraints weight = 46898.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122303 restraints weight = 21939.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124247 restraints weight = 11345.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125946 restraints weight = 8520.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126856 restraints weight = 6535.595| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21728 Z= 0.134 Angle : 0.600 7.482 29458 Z= 0.292 Chirality : 0.043 0.157 3548 Planarity : 0.003 0.040 3608 Dihedral : 8.410 172.241 3001 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.23 % Allowed : 15.36 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.16), residues: 2736 helix: 2.36 (0.12), residues: 1780 sheet: 1.30 (0.28), residues: 274 loop : -0.25 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 427 TYR 0.007 0.001 TYR I 158 PHE 0.033 0.002 PHE C 210 TRP 0.009 0.001 TRP M 257 HIS 0.005 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21728) covalent geometry : angle 0.59951 / 0.29 (29458) hydrogen bonds : bond 0.03724 / 2.52 ( 1443) hydrogen bonds : angle 4.18476 / 2.98 ( 4242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 481 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7921 (tp30) cc_final: 0.7281 (tp30) REVERT: H 40 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7401 (mtt180) REVERT: H 134 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8326 (mtpt) REVERT: D 40 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7916 (mtt180) REVERT: D 133 ARG cc_start: 0.7243 (mtt90) cc_final: 0.6774 (mtm-85) REVERT: E 50 GLN cc_start: 0.7853 (tt0) cc_final: 0.7596 (tt0) REVERT: E 72 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6715 (mmp) REVERT: E 126 ASP cc_start: 0.8002 (m-30) cc_final: 0.7186 (m-30) REVERT: I 228 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6997 (ptp-110) REVERT: I 292 ASN cc_start: 0.7095 (p0) cc_final: 0.6636 (p0) REVERT: I 419 MET cc_start: 0.8711 (tpp) cc_final: 0.8494 (tpt) REVERT: I 420 ILE cc_start: 0.8541 (mt) cc_final: 0.8260 (mt) REVERT: A 23 GLU cc_start: 0.7751 (tp30) cc_final: 0.7285 (tp30) REVERT: A 42 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8064 (mtpt) REVERT: A 133 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7025 (mmm-85) REVERT: L 35 ASP cc_start: 0.7825 (t70) cc_final: 0.7589 (t70) REVERT: L 50 GLN cc_start: 0.7809 (tt0) cc_final: 0.7567 (tt0) REVERT: L 122 MET cc_start: 0.7629 (mtp) cc_final: 0.7282 (mtm) REVERT: M 99 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: M 199 ASP cc_start: 0.7061 (t0) cc_final: 0.6807 (t0) REVERT: M 241 MET cc_start: 0.7922 (mmt) cc_final: 0.7670 (mmt) REVERT: M 292 ASN cc_start: 0.7071 (p0) cc_final: 0.6578 (p0) REVERT: M 446 LYS cc_start: 0.8443 (tttt) cc_final: 0.7963 (tttm) REVERT: C 241 MET cc_start: 0.8307 (tpp) cc_final: 0.8015 (mmt) REVERT: C 292 ASN cc_start: 0.7297 (p0) cc_final: 0.6916 (p0) REVERT: C 295 ASP cc_start: 0.6452 (m-30) cc_final: 0.5951 (m-30) REVERT: C 389 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7572 (ttmt) REVERT: C 419 MET cc_start: 0.8699 (tpp) cc_final: 0.8470 (tpt) REVERT: G 144 PHE cc_start: 0.8011 (t80) cc_final: 0.7700 (t80) REVERT: G 228 ARG cc_start: 0.7269 (ptp-110) cc_final: 0.7063 (ptp-170) REVERT: G 241 MET cc_start: 0.8042 (mmt) cc_final: 0.7728 (mmt) REVERT: G 277 LEU cc_start: 0.8923 (tp) cc_final: 0.8680 (tt) REVERT: G 292 ASN cc_start: 0.7199 (p0) cc_final: 0.6690 (p0) REVERT: G 423 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7167 (mtm) REVERT: G 446 LYS cc_start: 0.8451 (tttt) cc_final: 0.7975 (tttm) outliers start: 50 outliers final: 34 residues processed: 518 average time/residue: 0.1439 time to fit residues: 119.0297 Evaluate side-chains 499 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 178 optimal weight: 0.1980 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN G 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115165 restraints weight = 32938.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119325 restraints weight = 16415.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122097 restraints weight = 10118.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123768 restraints weight = 7112.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124856 restraints weight = 5603.220| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21728 Z= 0.175 Angle : 0.633 7.453 29458 Z= 0.309 Chirality : 0.044 0.164 3548 Planarity : 0.004 0.040 3608 Dihedral : 8.112 171.329 2998 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.80 % Allowed : 15.54 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.16), residues: 2736 helix: 2.37 (0.12), residues: 1764 sheet: 1.11 (0.28), residues: 274 loop : -0.29 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 427 TYR 0.008 0.001 TYR L 70 PHE 0.037 0.002 PHE I 217 TRP 0.008 0.001 TRP M 257 HIS 0.004 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (21728) covalent geometry : angle 0.63276 / 0.31 (29458) hydrogen bonds : bond 0.03874 / 2.63 ( 1443) hydrogen bonds : angle 4.19007 / 3.00 ( 4242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 482 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7902 (tp30) cc_final: 0.7257 (tp30) REVERT: H 40 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7451 (mtt180) REVERT: H 74 MET cc_start: 0.7795 (tpp) cc_final: 0.7577 (tpp) REVERT: H 134 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8321 (mtpt) REVERT: D 27 SER cc_start: 0.8455 (t) cc_final: 0.8072 (t) REVERT: D 133 ARG cc_start: 0.7268 (mtt90) cc_final: 0.6777 (mtm-85) REVERT: E 50 GLN cc_start: 0.7848 (tt0) cc_final: 0.7633 (tt0) REVERT: E 72 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6622 (mmp) REVERT: E 124 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 126 ASP cc_start: 0.8040 (m-30) cc_final: 0.7675 (m-30) REVERT: F 113 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7258 (tm-30) REVERT: I 139 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7103 (ttmt) REVERT: I 292 ASN cc_start: 0.7057 (p0) cc_final: 0.6795 (p0) REVERT: I 388 ASP cc_start: 0.7205 (p0) cc_final: 0.6805 (p0) REVERT: I 419 MET cc_start: 0.8736 (tpp) cc_final: 0.8501 (tpt) REVERT: I 446 LYS cc_start: 0.8592 (tttt) cc_final: 0.8018 (tttm) REVERT: A 23 GLU cc_start: 0.7639 (tp30) cc_final: 0.7211 (tp30) REVERT: A 133 ARG cc_start: 0.7436 (mtt90) cc_final: 0.7111 (mmm-85) REVERT: B 23 GLU cc_start: 0.7608 (tp30) cc_final: 0.7292 (tp30) REVERT: B 127 MET cc_start: 0.8644 (tpp) cc_final: 0.8415 (tpp) REVERT: L 35 ASP cc_start: 0.7835 (t70) cc_final: 0.7634 (t0) REVERT: M 199 ASP cc_start: 0.7137 (t0) cc_final: 0.6868 (t0) REVERT: M 241 MET cc_start: 0.8022 (mmt) cc_final: 0.7725 (mmt) REVERT: M 292 ASN cc_start: 0.7168 (p0) cc_final: 0.6702 (p0) REVERT: M 423 MET cc_start: 0.7650 (mtm) cc_final: 0.7424 (mtm) REVERT: M 446 LYS cc_start: 0.8628 (tttt) cc_final: 0.8110 (tttm) REVERT: C 194 MET cc_start: 0.6988 (mmm) cc_final: 0.6779 (mmt) REVERT: C 241 MET cc_start: 0.8338 (tpp) cc_final: 0.7989 (mmt) REVERT: C 292 ASN cc_start: 0.7379 (p0) cc_final: 0.6889 (p0) REVERT: G 241 MET cc_start: 0.8140 (mmt) cc_final: 0.7825 (mmt) REVERT: G 292 ASN cc_start: 0.7170 (p0) cc_final: 0.6931 (p0) REVERT: G 388 ASP cc_start: 0.7455 (p0) cc_final: 0.7194 (p0) REVERT: G 446 LYS cc_start: 0.8612 (tttt) cc_final: 0.8026 (tttm) outliers start: 63 outliers final: 47 residues processed: 527 average time/residue: 0.1460 time to fit residues: 121.9776 Evaluate side-chains 509 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 461 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 64 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS L 7 GLN C 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112079 restraints weight = 49054.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118085 restraints weight = 23091.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120436 restraints weight = 10601.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121135 restraints weight = 7394.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121478 restraints weight = 6657.698| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21728 Z= 0.191 Angle : 0.647 8.008 29458 Z= 0.317 Chirality : 0.045 0.169 3548 Planarity : 0.004 0.040 3608 Dihedral : 7.901 165.547 2998 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.21 % Allowed : 16.92 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2736 helix: 2.31 (0.12), residues: 1758 sheet: 0.93 (0.29), residues: 270 loop : -0.40 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 427 TYR 0.028 0.001 TYR I 158 PHE 0.033 0.002 PHE C 210 TRP 0.021 0.001 TRP G 227 HIS 0.004 0.001 HIS I 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (21728) covalent geometry : angle 0.64741 / 0.32 (29458) hydrogen bonds : bond 0.03902 / 2.65 ( 1443) hydrogen bonds : angle 4.22595 / 3.03 ( 4242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 488 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7940 (tp30) cc_final: 0.7319 (tp30) REVERT: H 40 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7483 (mtt180) REVERT: H 134 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8364 (mtpt) REVERT: D 133 ARG cc_start: 0.7306 (mtt90) cc_final: 0.6939 (mtm-85) REVERT: E 50 GLN cc_start: 0.7796 (tt0) cc_final: 0.7546 (tt0) REVERT: E 72 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6626 (mmp) REVERT: E 113 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7198 (tm-30) REVERT: E 126 ASP cc_start: 0.8065 (m-30) cc_final: 0.7719 (m-30) REVERT: F 50 GLN cc_start: 0.7846 (tt0) cc_final: 0.7532 (tt0) REVERT: F 82 ASN cc_start: 0.8472 (t0) cc_final: 0.8102 (t0) REVERT: I 227 TRP cc_start: 0.7832 (p-90) cc_final: 0.7628 (p-90) REVERT: I 292 ASN cc_start: 0.7160 (p0) cc_final: 0.6801 (p0) REVERT: I 446 LYS cc_start: 0.8633 (tttt) cc_final: 0.8065 (tttm) REVERT: A 23 GLU cc_start: 0.7658 (tp30) cc_final: 0.7257 (tp30) REVERT: A 133 ARG cc_start: 0.7471 (mtt90) cc_final: 0.7097 (mmm-85) REVERT: B 23 GLU cc_start: 0.7672 (tp30) cc_final: 0.7470 (tp30) REVERT: L 50 GLN cc_start: 0.8050 (tt0) cc_final: 0.7633 (tt0) REVERT: M 35 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7624 (p) REVERT: M 241 MET cc_start: 0.8099 (mmt) cc_final: 0.7699 (mmt) REVERT: M 292 ASN cc_start: 0.7176 (p0) cc_final: 0.6922 (p0) REVERT: M 343 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8402 (mtpt) REVERT: M 388 ASP cc_start: 0.7419 (p0) cc_final: 0.7217 (p0) REVERT: M 446 LYS cc_start: 0.8694 (tttt) cc_final: 0.8153 (tttm) REVERT: C 139 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7238 (ttmt) REVERT: C 194 MET cc_start: 0.7164 (mmm) cc_final: 0.6953 (mmm) REVERT: C 241 MET cc_start: 0.8382 (tpp) cc_final: 0.7949 (mmt) REVERT: C 292 ASN cc_start: 0.7725 (p0) cc_final: 0.7297 (p0) REVERT: C 388 ASP cc_start: 0.7183 (p0) cc_final: 0.6818 (p0) REVERT: G 35 VAL cc_start: 0.8017 (m) cc_final: 0.7759 (p) REVERT: G 241 MET cc_start: 0.8164 (mmt) cc_final: 0.7838 (mmt) REVERT: G 292 ASN cc_start: 0.7038 (p0) cc_final: 0.6813 (p0) REVERT: G 446 LYS cc_start: 0.8662 (tttt) cc_final: 0.8093 (tttm) outliers start: 72 outliers final: 57 residues processed: 537 average time/residue: 0.1503 time to fit residues: 126.9729 Evaluate side-chains 507 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 448 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 255 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110452 restraints weight = 35144.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114549 restraints weight = 17362.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117118 restraints weight = 10707.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118952 restraints weight = 7604.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120027 restraints weight = 5901.660| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21728 Z= 0.249 Angle : 0.707 8.644 29458 Z= 0.348 Chirality : 0.047 0.208 3548 Planarity : 0.004 0.037 3608 Dihedral : 7.954 156.159 2998 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.29 % Allowed : 18.21 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.16), residues: 2736 helix: 2.10 (0.12), residues: 1760 sheet: 0.60 (0.30), residues: 270 loop : -0.59 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 427 TYR 0.008 0.001 TYR I 447 PHE 0.034 0.002 PHE C 210 TRP 0.015 0.001 TRP G 227 HIS 0.004 0.001 HIS C 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (21728) covalent geometry : angle 0.70703 / 0.35 (29458) hydrogen bonds : bond 0.04156 / 2.83 ( 1443) hydrogen bonds : angle 4.33404 / 3.11 ( 4242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 469 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7943 (tp30) cc_final: 0.7522 (tp30) REVERT: H 40 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7582 (mtt180) REVERT: H 134 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8403 (mtpt) REVERT: D 25 GLN cc_start: 0.8625 (tp40) cc_final: 0.8405 (tp40) REVERT: D 133 ARG cc_start: 0.7311 (mtt90) cc_final: 0.6849 (mtm-85) REVERT: E 50 GLN cc_start: 0.7691 (tt0) cc_final: 0.7303 (tt0) REVERT: E 72 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6655 (mmp) REVERT: E 124 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7860 (mm-30) REVERT: F 50 GLN cc_start: 0.7897 (tt0) cc_final: 0.7659 (tt0) REVERT: F 82 ASN cc_start: 0.8501 (t0) cc_final: 0.8215 (t0) REVERT: F 97 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7377 (mmtt) REVERT: A 23 GLU cc_start: 0.7706 (tp30) cc_final: 0.7369 (tp30) REVERT: A 133 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7080 (mmm-85) REVERT: J 23 GLU cc_start: 0.7806 (tp30) cc_final: 0.7537 (tp30) REVERT: L 23 GLU cc_start: 0.7855 (tp30) cc_final: 0.7493 (tp30) REVERT: L 50 GLN cc_start: 0.8029 (tt0) cc_final: 0.7637 (tt0) REVERT: M 241 MET cc_start: 0.8173 (mmt) cc_final: 0.7810 (mmt) REVERT: M 343 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8314 (mtmt) REVERT: M 410 GLU cc_start: 0.6506 (pt0) cc_final: 0.6204 (pt0) REVERT: M 446 LYS cc_start: 0.8745 (tttt) cc_final: 0.8224 (tttm) REVERT: C 139 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7317 (ttmt) REVERT: C 194 MET cc_start: 0.7021 (mmm) cc_final: 0.6569 (mmt) REVERT: C 292 ASN cc_start: 0.7797 (p0) cc_final: 0.7387 (p0) REVERT: C 388 ASP cc_start: 0.7293 (p0) cc_final: 0.7012 (p0) REVERT: C 410 GLU cc_start: 0.6249 (pt0) cc_final: 0.5912 (pt0) REVERT: G 97 LEU cc_start: 0.8470 (tp) cc_final: 0.8249 (tp) REVERT: G 241 MET cc_start: 0.8185 (mmt) cc_final: 0.7801 (mmt) REVERT: G 343 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8471 (mtpt) REVERT: G 410 GLU cc_start: 0.6466 (pt0) cc_final: 0.6163 (pt0) REVERT: G 446 LYS cc_start: 0.8735 (tttt) cc_final: 0.8200 (tttm) outliers start: 74 outliers final: 62 residues processed: 521 average time/residue: 0.1525 time to fit residues: 124.6600 Evaluate side-chains 516 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 453 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 347 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 28 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.0050 chunk 86 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115733 restraints weight = 37562.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120138 restraints weight = 17616.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122902 restraints weight = 10426.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124872 restraints weight = 7207.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126068 restraints weight = 5453.111| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21728 Z= 0.122 Angle : 0.619 10.176 29458 Z= 0.300 Chirality : 0.043 0.192 3548 Planarity : 0.003 0.042 3608 Dihedral : 7.481 147.359 2998 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 19.90 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.16), residues: 2736 helix: 2.33 (0.12), residues: 1758 sheet: 0.94 (0.30), residues: 270 loop : -0.58 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.023 0.001 TYR I 158 PHE 0.030 0.001 PHE C 210 TRP 0.013 0.001 TRP G 227 HIS 0.003 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (21728) covalent geometry : angle 0.61926 / 0.30 (29458) hydrogen bonds : bond 0.03506 / 2.38 ( 1443) hydrogen bonds : angle 4.17760 / 2.98 ( 4242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 495 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7854 (tp30) cc_final: 0.7397 (tp30) REVERT: H 40 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7561 (mtt180) REVERT: H 110 ARG cc_start: 0.8851 (mtm110) cc_final: 0.8497 (mtm110) REVERT: H 134 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8427 (mtpt) REVERT: D 133 ARG cc_start: 0.7252 (mtt90) cc_final: 0.6832 (mtm-85) REVERT: E 50 GLN cc_start: 0.7569 (tt0) cc_final: 0.7165 (tt0) REVERT: E 126 ASP cc_start: 0.7977 (m-30) cc_final: 0.7619 (m-30) REVERT: F 82 ASN cc_start: 0.8435 (t0) cc_final: 0.8114 (t0) REVERT: F 97 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7391 (mmtt) REVERT: I 292 ASN cc_start: 0.7489 (p0) cc_final: 0.7192 (p0) REVERT: A 23 GLU cc_start: 0.7475 (tp30) cc_final: 0.7152 (tp30) REVERT: J 23 GLU cc_start: 0.7788 (tp30) cc_final: 0.7496 (tp30) REVERT: J 50 GLN cc_start: 0.7878 (tt0) cc_final: 0.7592 (tt0) REVERT: J 126 ASP cc_start: 0.7784 (m-30) cc_final: 0.7495 (m-30) REVERT: L 23 GLU cc_start: 0.7890 (tp30) cc_final: 0.7576 (tp30) REVERT: L 50 GLN cc_start: 0.7863 (tt0) cc_final: 0.7484 (tt0) REVERT: M 241 MET cc_start: 0.8108 (mmt) cc_final: 0.7702 (mmt) REVERT: M 292 ASN cc_start: 0.7145 (p0) cc_final: 0.6921 (p0) REVERT: M 343 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8315 (mtpt) REVERT: M 446 LYS cc_start: 0.8593 (tttt) cc_final: 0.8156 (tttm) REVERT: C 194 MET cc_start: 0.6944 (mmm) cc_final: 0.6735 (mmm) REVERT: C 292 ASN cc_start: 0.7620 (p0) cc_final: 0.7322 (p0) REVERT: C 388 ASP cc_start: 0.7247 (p0) cc_final: 0.6949 (p0) REVERT: G 48 PHE cc_start: 0.6788 (m-80) cc_final: 0.6457 (m-80) REVERT: G 241 MET cc_start: 0.8087 (mmt) cc_final: 0.7705 (mmt) REVERT: G 419 MET cc_start: 0.8751 (tpp) cc_final: 0.8527 (tpt) REVERT: G 446 LYS cc_start: 0.8557 (tttt) cc_final: 0.8107 (tttm) outliers start: 37 outliers final: 30 residues processed: 522 average time/residue: 0.1465 time to fit residues: 122.1925 Evaluate side-chains 493 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 463 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 189 optimal weight: 0.4980 chunk 251 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 244 optimal weight: 0.0030 chunk 133 optimal weight: 10.0000 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 ASN F 7 GLN ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125846 restraints weight = 36294.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130653 restraints weight = 16316.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133605 restraints weight = 9364.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135753 restraints weight = 6365.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136914 restraints weight = 4745.024| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21728 Z= 0.127 Angle : 0.634 9.672 29458 Z= 0.308 Chirality : 0.043 0.217 3548 Planarity : 0.003 0.044 3608 Dihedral : 7.142 143.245 2998 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 20.61 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.16), residues: 2736 helix: 2.36 (0.12), residues: 1750 sheet: 1.20 (0.30), residues: 268 loop : -0.62 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 427 TYR 0.007 0.001 TYR I 447 PHE 0.030 0.001 PHE C 210 TRP 0.011 0.001 TRP G 227 HIS 0.003 0.001 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (21728) covalent geometry : angle 0.63427 / 0.31 (29458) hydrogen bonds : bond 0.03476 / 2.36 ( 1443) hydrogen bonds : angle 4.13786 / 2.96 ( 4242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 476 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7875 (tp30) cc_final: 0.7413 (tp30) REVERT: H 40 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7620 (mtt180) REVERT: H 110 ARG cc_start: 0.8799 (mtm110) cc_final: 0.8523 (mtm110) REVERT: H 134 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8393 (mtpt) REVERT: D 133 ARG cc_start: 0.7112 (mtt90) cc_final: 0.6837 (mtm-85) REVERT: E 74 MET cc_start: 0.7397 (tpp) cc_final: 0.7039 (ttm) REVERT: E 126 ASP cc_start: 0.7900 (m-30) cc_final: 0.7543 (m-30) REVERT: F 43 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7070 (mt-10) REVERT: F 50 GLN cc_start: 0.8052 (tt0) cc_final: 0.7648 (tt0) REVERT: F 82 ASN cc_start: 0.8374 (t0) cc_final: 0.8082 (t0) REVERT: F 97 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7370 (mmtt) REVERT: F 126 ASP cc_start: 0.7697 (m-30) cc_final: 0.7352 (m-30) REVERT: I 199 ASP cc_start: 0.6802 (t0) cc_final: 0.6545 (t0) REVERT: I 292 ASN cc_start: 0.7589 (p0) cc_final: 0.7305 (p0) REVERT: A 23 GLU cc_start: 0.7386 (tp30) cc_final: 0.7096 (tp30) REVERT: J 23 GLU cc_start: 0.7699 (tp30) cc_final: 0.7487 (tp30) REVERT: J 50 GLN cc_start: 0.7857 (tt0) cc_final: 0.7205 (tt0) REVERT: J 126 ASP cc_start: 0.7724 (m-30) cc_final: 0.7376 (m-30) REVERT: L 23 GLU cc_start: 0.7703 (tp30) cc_final: 0.7410 (tp30) REVERT: L 50 GLN cc_start: 0.7836 (tt0) cc_final: 0.7483 (tt0) REVERT: L 126 ASP cc_start: 0.7348 (m-30) cc_final: 0.7058 (m-30) REVERT: M 48 PHE cc_start: 0.6937 (m-80) cc_final: 0.6631 (m-80) REVERT: M 194 MET cc_start: 0.7286 (mmm) cc_final: 0.6816 (mmt) REVERT: M 241 MET cc_start: 0.8158 (mmt) cc_final: 0.7745 (mmt) REVERT: M 388 ASP cc_start: 0.7352 (p0) cc_final: 0.6945 (p0) REVERT: M 419 MET cc_start: 0.8822 (tpp) cc_final: 0.8595 (tpt) REVERT: M 446 LYS cc_start: 0.8569 (tttt) cc_final: 0.8159 (tttm) REVERT: C 30 LEU cc_start: 0.8201 (mm) cc_final: 0.7952 (pp) REVERT: C 48 PHE cc_start: 0.6787 (m-80) cc_final: 0.6505 (m-80) REVERT: C 92 MET cc_start: 0.8460 (ptp) cc_final: 0.7870 (ptp) REVERT: C 117 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6422 (mtp85) REVERT: C 241 MET cc_start: 0.8345 (tpp) cc_final: 0.7817 (mmt) REVERT: C 292 ASN cc_start: 0.7449 (p0) cc_final: 0.7157 (p0) REVERT: G 48 PHE cc_start: 0.6614 (m-80) cc_final: 0.6325 (m-80) REVERT: G 241 MET cc_start: 0.8100 (mmt) cc_final: 0.7721 (mmt) REVERT: G 419 MET cc_start: 0.8732 (tpp) cc_final: 0.8490 (tpt) REVERT: G 446 LYS cc_start: 0.8542 (tttt) cc_final: 0.8144 (tttm) outliers start: 32 outliers final: 26 residues processed: 500 average time/residue: 0.1422 time to fit residues: 114.2987 Evaluate side-chains 479 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 453 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 292 ASN Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 ASN ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 ASN M 298 GLN G 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124032 restraints weight = 34406.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128660 restraints weight = 15826.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131635 restraints weight = 9219.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133516 restraints weight = 6258.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134774 restraints weight = 4783.722| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21728 Z= 0.155 Angle : 0.654 10.704 29458 Z= 0.320 Chirality : 0.045 0.193 3548 Planarity : 0.004 0.043 3608 Dihedral : 7.064 139.305 2998 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.47 % Allowed : 21.15 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.16), residues: 2736 helix: 2.29 (0.12), residues: 1766 sheet: 1.23 (0.30), residues: 270 loop : -0.56 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 427 TYR 0.026 0.001 TYR I 158 PHE 0.030 0.002 PHE C 210 TRP 0.011 0.001 TRP G 227 HIS 0.003 0.001 HIS M 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (21728) covalent geometry : angle 0.65368 / 0.32 (29458) hydrogen bonds : bond 0.03629 / 2.47 ( 1443) hydrogen bonds : angle 4.16993 / 2.98 ( 4242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 461 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7907 (tp30) cc_final: 0.7364 (tp30) REVERT: H 40 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7563 (mtt180) REVERT: H 110 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8322 (mtm110) REVERT: H 134 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8413 (mtpt) REVERT: D 133 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6845 (mtm-85) REVERT: E 50 GLN cc_start: 0.7734 (tt0) cc_final: 0.7330 (tt0) REVERT: E 126 ASP cc_start: 0.8012 (m-30) cc_final: 0.7642 (m-30) REVERT: F 43 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7097 (mt-10) REVERT: F 50 GLN cc_start: 0.8069 (tt0) cc_final: 0.7691 (tt0) REVERT: F 82 ASN cc_start: 0.8433 (t0) cc_final: 0.8131 (t0) REVERT: F 97 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7395 (mmtm) REVERT: I 24 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: I 30 LEU cc_start: 0.8244 (mm) cc_final: 0.7956 (pp) REVERT: I 48 PHE cc_start: 0.6973 (m-80) cc_final: 0.6577 (m-80) REVERT: I 92 MET cc_start: 0.8457 (ptp) cc_final: 0.7821 (ptp) REVERT: I 199 ASP cc_start: 0.6928 (t0) cc_final: 0.6688 (t0) REVERT: I 292 ASN cc_start: 0.7561 (p0) cc_final: 0.7314 (p0) REVERT: A 23 GLU cc_start: 0.7475 (tp30) cc_final: 0.7219 (tp30) REVERT: B 127 MET cc_start: 0.8695 (mmm) cc_final: 0.8425 (tpp) REVERT: J 23 GLU cc_start: 0.7833 (tp30) cc_final: 0.7531 (tp30) REVERT: J 50 GLN cc_start: 0.7746 (tt0) cc_final: 0.7123 (tt0) REVERT: L 50 GLN cc_start: 0.7801 (tt0) cc_final: 0.7425 (tt0) REVERT: L 126 ASP cc_start: 0.7454 (m-30) cc_final: 0.7092 (m-30) REVERT: M 48 PHE cc_start: 0.6998 (m-80) cc_final: 0.6706 (m-80) REVERT: M 241 MET cc_start: 0.8168 (mmt) cc_final: 0.7731 (mmt) REVERT: M 343 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8304 (mtpt) REVERT: M 388 ASP cc_start: 0.7379 (p0) cc_final: 0.7036 (p0) REVERT: M 419 MET cc_start: 0.8822 (tpp) cc_final: 0.8578 (tpt) REVERT: M 446 LYS cc_start: 0.8597 (tttt) cc_final: 0.8159 (tttm) REVERT: C 24 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: C 30 LEU cc_start: 0.8162 (mm) cc_final: 0.7935 (pp) REVERT: C 48 PHE cc_start: 0.6753 (m-80) cc_final: 0.6433 (m-80) REVERT: C 92 MET cc_start: 0.8514 (ptp) cc_final: 0.7888 (ptp) REVERT: C 117 ARG cc_start: 0.6998 (ttp-170) cc_final: 0.6412 (mtp85) REVERT: G 48 PHE cc_start: 0.6709 (m-80) cc_final: 0.6422 (m-80) REVERT: G 241 MET cc_start: 0.8170 (mmt) cc_final: 0.7766 (mmt) REVERT: G 343 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8288 (mtpt) REVERT: G 446 LYS cc_start: 0.8576 (tttt) cc_final: 0.8128 (tttm) outliers start: 33 outliers final: 28 residues processed: 484 average time/residue: 0.1413 time to fit residues: 109.2951 Evaluate side-chains 482 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 452 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 292 ASN Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 292 ASN Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 71 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 246 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN M 292 ASN M 298 GLN C 292 ASN G 93 GLN G 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127402 restraints weight = 32600.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131932 restraints weight = 14996.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134818 restraints weight = 8764.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136585 restraints weight = 5947.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137972 restraints weight = 4598.379| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21728 Z= 0.125 Angle : 0.635 10.802 29458 Z= 0.308 Chirality : 0.043 0.215 3548 Planarity : 0.003 0.044 3608 Dihedral : 6.806 130.899 2998 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.51 % Allowed : 21.10 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.16), residues: 2736 helix: 2.37 (0.12), residues: 1754 sheet: 1.36 (0.31), residues: 274 loop : -0.63 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 427 TYR 0.007 0.001 TYR M 108 PHE 0.029 0.001 PHE C 210 TRP 0.011 0.001 TRP G 227 HIS 0.004 0.001 HIS G 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21728) covalent geometry : angle 0.63497 / 0.31 (29458) hydrogen bonds : bond 0.03418 / 2.31 ( 1443) hydrogen bonds : angle 4.13618 / 2.96 ( 4242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.50 seconds wall clock time: 68 minutes 56.18 seconds (4136.18 seconds total)