Starting phenix.real_space_refine on Fri Jun 20 00:08:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.map" model { file = "/net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zp9_14851/06_2025/7zp9_14851.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 14942 2.51 5 N 3628 2.21 5 O 4359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23097 Number of models: 1 Model: "" Number of chains: 34 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: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 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: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3344 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 2 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' K': 1, 'LMT': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 351 Unusual residues: {' K': 1, 'LMT': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 18.16, per 1000 atoms: 0.79 Number of scatterers: 23097 At special positions: 0 Unit cell: (93.903, 115.509, 172.017, 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 4359 8.00 N 3628 7.00 C 14942 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: 6.21 Conformation dependent library (CDL) restraints added in 3.5 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 68.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 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: 4.232A 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: 3.550A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix removed outlier: 3.530A 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: 3.711A 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: 3.841A 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: 3.619A 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: 3.549A 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: 3.771A 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: 3.686A 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: 3.845A 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: 3.593A 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: 3.537A 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: 3.527A 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: 3.612A 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: 3.771A 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: 3.686A 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: 3.845A 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: 6.167A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.192A 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: 6.171A 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: 6.307A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.923A 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: 6.960A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.267A 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 119 through 121 removed outlier: 3.829A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) 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: 6.905A pdb=" N ALA E 54 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 35 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.801A 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: 6.878A pdb=" N ALA F 54 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP F 35 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.464A 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: 6.173A 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: 6.309A 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: 7.841A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.554A 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: 6.285A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.864A 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: 6.388A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.934A 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: 7.985A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 119 through 121 removed outlier: 6.183A 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: 7.130A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) 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: 6.342A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 54 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP J 35 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 121 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: 6.553A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) 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: 6.880A pdb=" N ALA L 54 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP L 35 " --> pdb=" O ALA L 54 " (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: 4.421A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1451 hydrogen bonds defined for protein. 4266 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: 8.30 Time building geometry restraints manager: 7.29 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: 4052 1.33 - 1.45: 5708 1.45 - 1.57: 13429 1.57 - 1.69: 28 1.69 - 1.81: 261 Bond restraints: 23478 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 3.34e+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 3.09e+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 3.00e+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 23473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 29897 2.16 - 4.32: 1407 4.32 - 6.48: 304 6.48 - 8.63: 61 8.63 - 10.79: 83 Bond angle restraints: 31752 Sorted by residual: angle pdb=" N GLU F 93 " pdb=" CA GLU F 93 " pdb=" C GLU F 93 " ideal model delta sigma weight residual 111.69 105.83 5.86 1.23e+00 6.61e-01 2.27e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.37 -8.95 1.99e+00 2.53e-01 2.02e+01 angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.33 -8.91 1.99e+00 2.53e-01 2.01e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.54 5.35 1.24e+00 6.50e-01 1.86e+01 ... (remaining 31747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 14553 33.64 - 67.27: 580 67.27 - 100.91: 106 100.91 - 134.54: 187 134.54 - 168.18: 6 Dihedral angle restraints: 15432 sinusoidal: 7468 harmonic: 7964 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 300.00 131.82 168.18 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 -60.00 100.86 -160.86 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 -60.00 100.11 -160.11 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 15429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3651 0.107 - 0.213: 285 0.213 - 0.320: 42 0.320 - 0.426: 0 0.426 - 0.533: 8 Chirality restraints: 3986 Sorted by residual: 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 0.53 2.00e-01 2.50e+01 7.10e+00 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 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA THR I 288 " pdb=" N THR I 288 " pdb=" C THR I 288 " pdb=" CB THR I 288 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 3983 not shown) Planarity restraints: 3662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C MET M 92 " 0.040 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 2.34e-02 5.47e+00 pdb=" C MET G 92 " -0.040 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=" CA LEU F 86 " -0.010 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C LEU F 86 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU F 86 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA F 87 " -0.013 2.00e-02 2.50e+03 ... (remaining 3659 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.04: 20 2.04 - 2.82: 6254 2.82 - 3.59: 38649 3.59 - 4.37: 70897 4.37 - 5.14: 123080 Nonbonded interactions: 238900 Sorted by model distance: nonbonded pdb=" OE1 GLU F 64 " pdb=" CA GLY C 8 " model vdw 1.266 3.440 nonbonded pdb=" OE1 GLU L 64 " pdb=" CA GLY G 8 " model vdw 1.404 3.440 nonbonded pdb=" OE2 GLU L 64 " pdb=" N GLY G 8 " model vdw 1.471 3.120 nonbonded pdb=" OE2 GLU F 64 " pdb=" N GLY C 8 " model vdw 1.577 3.120 nonbonded pdb=" OE1 GLU L 38 " pdb=" OH TYR G 11 " model vdw 1.778 3.040 ... (remaining 238895 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 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'G' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) selection = (chain 'I' and (resid 7 through 15 or resid 21 through 350 or resid 352 through \ 455 or resid 503 through 510)) selection = (chain 'M' and (resid 7 through 15 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503 through 510)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.650 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.008 0.256 23478 Z= 0.466 Angle : 1.130 10.792 31752 Z= 0.557 Chirality : 0.065 0.533 3986 Planarity : 0.004 0.047 3662 Dihedral : 23.096 168.179 10292 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.21 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 1.14 % Favored : 97.98 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.15), residues: 2766 helix: 1.44 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 337 HIS 0.005 0.001 HIS G 345 PHE 0.026 0.001 PHE I 210 TYR 0.014 0.001 TYR F 70 ARG 0.005 0.000 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.18893 ( 1451) hydrogen bonds : angle 6.61529 ( 4266) covalent geometry : bond 0.00818 (23478) covalent geometry : angle 1.12970 (31752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 516 time to evaluate : 2.572 Fit side-chains revert: symmetry clash REVERT: H 59 GLU cc_start: 0.8137 (pt0) cc_final: 0.7850 (pt0) REVERT: F 130 ARG cc_start: 0.6899 (ttt90) cc_final: 0.6655 (ttt90) REVERT: I 139 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7499 (tptp) REVERT: I 299 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: I 354 ASN cc_start: 0.8260 (p0) cc_final: 0.7879 (p0) REVERT: A 22 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7894 (tptp) REVERT: M 139 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7288 (tptp) REVERT: M 296 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8238 (mt) REVERT: M 299 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: C 139 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7493 (tptp) REVERT: C 299 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 354 ASN cc_start: 0.8247 (p0) cc_final: 0.7855 (p0) REVERT: G 139 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7284 (tptp) REVERT: G 296 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (mt) REVERT: G 299 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7995 (m-80) outliers start: 20 outliers final: 4 residues processed: 532 average time/residue: 1.6518 time to fit residues: 981.5261 Evaluate side-chains 434 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 424 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 GLN D 50 GLN D 113 GLN F 108 GLN I 119 GLN I 263 ASN A 50 GLN A 113 GLN B 30 GLN B 37 ASN B 50 GLN B 113 GLN J 108 GLN M 263 ASN M 301 GLN M 342 GLN C 119 GLN C 263 ASN G 263 ASN G 301 GLN G 342 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104314 restraints weight = 32874.801| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.81 r_work: 0.2992 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23478 Z= 0.151 Angle : 0.768 10.852 31752 Z= 0.338 Chirality : 0.047 0.322 3986 Planarity : 0.004 0.038 3662 Dihedral : 19.762 176.701 5494 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 1.71 % Allowed : 9.40 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.16), residues: 2766 helix: 2.25 (0.12), residues: 1780 sheet: 1.52 (0.27), residues: 286 loop : 0.09 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 227 HIS 0.004 0.001 HIS I 176 PHE 0.035 0.002 PHE C 210 TYR 0.016 0.001 TYR F 70 ARG 0.005 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1451) hydrogen bonds : angle 4.51605 ( 4266) covalent geometry : bond 0.00303 (23478) covalent geometry : angle 0.76775 (31752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 442 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 GLU cc_start: 0.7982 (mp0) cc_final: 0.7741 (mp0) REVERT: H 130 ARG cc_start: 0.8300 (mtp180) cc_final: 0.8035 (mmm160) REVERT: E 38 GLU cc_start: 0.8029 (tt0) cc_final: 0.7742 (tt0) REVERT: I 26 ARG cc_start: 0.7678 (ttt90) cc_final: 0.6935 (ttt-90) REVERT: I 35 VAL cc_start: 0.8836 (t) cc_final: 0.8617 (p) REVERT: I 139 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7544 (tptp) REVERT: I 228 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7765 (ttm110) REVERT: A 22 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8136 (tptp) REVERT: A 40 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8318 (mtt180) REVERT: B 22 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8095 (tptp) REVERT: J 30 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7815 (mm110) REVERT: M 139 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7369 (tptt) REVERT: M 299 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8230 (m-80) REVERT: C 26 ARG cc_start: 0.7681 (ttt90) cc_final: 0.6965 (ttt-90) REVERT: C 35 VAL cc_start: 0.8798 (t) cc_final: 0.8592 (p) REVERT: C 90 CYS cc_start: 0.7958 (m) cc_final: 0.7557 (t) REVERT: C 139 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7527 (tptp) REVERT: C 228 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7733 (ttm110) REVERT: G 139 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7354 (tptt) REVERT: G 299 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (m-80) outliers start: 39 outliers final: 11 residues processed: 465 average time/residue: 1.9716 time to fit residues: 1030.4760 Evaluate side-chains 430 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 415 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 232 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN F 108 GLN I 263 ASN A 113 GLN B 113 GLN L 108 GLN M 198 ASN M 263 ASN C 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102063 restraints weight = 42716.741| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.13 r_work: 0.2973 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23478 Z= 0.127 Angle : 0.684 8.773 31752 Z= 0.301 Chirality : 0.044 0.333 3986 Planarity : 0.003 0.037 3662 Dihedral : 14.344 178.875 5484 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 2.07 % Allowed : 11.47 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2766 helix: 2.51 (0.12), residues: 1778 sheet: 1.50 (0.27), residues: 270 loop : 0.11 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 337 HIS 0.005 0.001 HIS I 176 PHE 0.033 0.001 PHE I 210 TYR 0.015 0.001 TYR F 70 ARG 0.003 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1451) hydrogen bonds : angle 4.20887 ( 4266) covalent geometry : bond 0.00262 (23478) covalent geometry : angle 0.68381 (31752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 456 time to evaluate : 5.780 Fit side-chains REVERT: H 118 ASP cc_start: 0.8761 (m-30) cc_final: 0.8510 (m-30) REVERT: E 38 GLU cc_start: 0.8125 (tt0) cc_final: 0.7890 (tt0) REVERT: E 122 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8436 (mmm) REVERT: F 38 GLU cc_start: 0.7905 (tt0) cc_final: 0.7667 (tt0) REVERT: F 68 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7495 (p0) REVERT: F 69 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: I 26 ARG cc_start: 0.7771 (ttt90) cc_final: 0.6995 (ttt-90) REVERT: I 90 CYS cc_start: 0.8051 (m) cc_final: 0.7598 (t) REVERT: I 139 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7533 (tptp) REVERT: I 228 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7703 (ttm110) REVERT: I 307 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8784 (tpp) REVERT: A 22 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8155 (tptp) REVERT: B 22 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8186 (tptp) REVERT: J 30 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8064 (mm-40) REVERT: M 139 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7307 (tptp) REVERT: M 170 MET cc_start: 0.8377 (mmm) cc_final: 0.8167 (mmp) REVERT: M 296 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8184 (mt) REVERT: M 299 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: C 26 ARG cc_start: 0.7775 (ttt90) cc_final: 0.7017 (ttt-90) REVERT: C 139 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7521 (tptp) REVERT: C 228 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7707 (ttm110) REVERT: C 307 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8796 (tpp) REVERT: G 139 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7285 (tptp) REVERT: G 170 MET cc_start: 0.8344 (mmm) cc_final: 0.8124 (mmp) REVERT: G 296 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8185 (mt) REVERT: G 299 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8202 (m-80) outliers start: 47 outliers final: 18 residues processed: 479 average time/residue: 1.7711 time to fit residues: 954.1307 Evaluate side-chains 446 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 417 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 307 MET Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 108 GLN I 263 ASN A 37 ASN B 113 GLN J 108 GLN L 82 ASN L 108 GLN M 198 ASN M 263 ASN M 292 ASN C 119 GLN C 263 ASN G 198 ASN G 263 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101397 restraints weight = 38692.320| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.06 r_work: 0.2958 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23478 Z= 0.189 Angle : 0.703 8.167 31752 Z= 0.323 Chirality : 0.046 0.246 3986 Planarity : 0.004 0.038 3662 Dihedral : 13.559 178.331 5480 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 12.26 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.16), residues: 2766 helix: 2.45 (0.12), residues: 1774 sheet: 1.13 (0.27), residues: 274 loop : 0.15 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 337 HIS 0.004 0.001 HIS C 345 PHE 0.032 0.002 PHE C 210 TYR 0.011 0.002 TYR M 108 ARG 0.002 0.000 ARG H 125 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1451) hydrogen bonds : angle 4.24768 ( 4266) covalent geometry : bond 0.00439 (23478) covalent geometry : angle 0.70275 (31752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 432 time to evaluate : 2.533 Fit side-chains REVERT: E 38 GLU cc_start: 0.8154 (tt0) cc_final: 0.7930 (tt0) REVERT: F 30 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7912 (mm110) REVERT: F 38 GLU cc_start: 0.8053 (tt0) cc_final: 0.7826 (tt0) REVERT: F 68 ASP cc_start: 0.8065 (p0) cc_final: 0.7631 (p0) REVERT: I 26 ARG cc_start: 0.7839 (ttt90) cc_final: 0.7022 (ttt-90) REVERT: I 139 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7566 (tptp) REVERT: A 22 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8255 (tptp) REVERT: J 30 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7773 (mm110) REVERT: M 139 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7377 (tptp) REVERT: M 170 MET cc_start: 0.8396 (mmm) cc_final: 0.8150 (mmp) REVERT: M 296 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8042 (mt) REVERT: M 299 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: C 26 ARG cc_start: 0.7865 (ttt90) cc_final: 0.7050 (ttt-90) REVERT: C 139 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7593 (tptp) REVERT: C 263 ASN cc_start: 0.8665 (t0) cc_final: 0.8463 (t0) REVERT: G 139 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7372 (tptp) REVERT: G 170 MET cc_start: 0.8369 (mmm) cc_final: 0.8123 (mmp) REVERT: G 296 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8062 (mt) REVERT: G 299 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8163 (m-80) outliers start: 65 outliers final: 28 residues processed: 475 average time/residue: 1.6765 time to fit residues: 901.3125 Evaluate side-chains 451 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 417 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 GLN A 37 ASN J 82 ASN J 108 GLN L 82 ASN L 108 GLN M 263 ASN G 263 ASN G 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103347 restraints weight = 36794.272| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.99 r_work: 0.2958 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23478 Z= 0.122 Angle : 0.629 7.642 31752 Z= 0.287 Chirality : 0.042 0.236 3986 Planarity : 0.003 0.038 3662 Dihedral : 12.647 178.859 5480 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.50 % Allowed : 13.22 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2766 helix: 2.60 (0.12), residues: 1772 sheet: 1.17 (0.27), residues: 270 loop : 0.03 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 337 HIS 0.004 0.001 HIS C 176 PHE 0.032 0.001 PHE I 210 TYR 0.009 0.001 TYR G 108 ARG 0.004 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 1451) hydrogen bonds : angle 4.10972 ( 4266) covalent geometry : bond 0.00261 (23478) covalent geometry : angle 0.62926 (31752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 435 time to evaluate : 2.235 Fit side-chains REVERT: D 130 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8058 (mmm160) REVERT: E 38 GLU cc_start: 0.8167 (tt0) cc_final: 0.7935 (tt0) REVERT: F 38 GLU cc_start: 0.7992 (tt0) cc_final: 0.7756 (tt0) REVERT: F 68 ASP cc_start: 0.8011 (p0) cc_final: 0.7577 (p0) REVERT: I 26 ARG cc_start: 0.7683 (ttt90) cc_final: 0.6865 (ttt-90) REVERT: I 139 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7525 (tptp) REVERT: A 7 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8369 (mt0) REVERT: A 22 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8187 (tptp) REVERT: A 113 GLN cc_start: 0.8747 (mm-40) cc_final: 0.7979 (mt0) REVERT: B 22 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8146 (tptp) REVERT: J 93 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: M 139 LYS cc_start: 0.8083 (ttpt) cc_final: 0.7325 (tptp) REVERT: M 170 MET cc_start: 0.8262 (mmm) cc_final: 0.8011 (mmp) REVERT: M 296 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8148 (mm) REVERT: C 26 ARG cc_start: 0.7706 (ttt90) cc_final: 0.6890 (ttt-90) REVERT: C 139 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7560 (tptp) REVERT: G 139 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7319 (tptp) REVERT: G 170 MET cc_start: 0.8234 (mmm) cc_final: 0.7983 (mmp) REVERT: G 296 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8088 (mm) REVERT: G 299 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8052 (m-80) outliers start: 57 outliers final: 23 residues processed: 468 average time/residue: 1.6039 time to fit residues: 842.1328 Evaluate side-chains 449 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 421 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 360 LYS Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 360 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 3 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN D 113 GLN E 82 ASN F 108 GLN A 37 ASN J 82 ASN J 108 GLN L 82 ASN L 108 GLN G 282 GLN G 292 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095912 restraints weight = 38125.466| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.99 r_work: 0.2881 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 23478 Z= 0.312 Angle : 0.800 9.096 31752 Z= 0.373 Chirality : 0.051 0.266 3986 Planarity : 0.004 0.051 3662 Dihedral : 13.017 172.974 5478 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 3.12 % Allowed : 13.71 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 2766 helix: 2.10 (0.12), residues: 1764 sheet: 0.65 (0.27), residues: 286 loop : 0.12 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 337 HIS 0.005 0.001 HIS E 58 PHE 0.032 0.002 PHE C 210 TYR 0.012 0.002 TYR J 70 ARG 0.004 0.001 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 1451) hydrogen bonds : angle 4.39810 ( 4266) covalent geometry : bond 0.00744 (23478) covalent geometry : angle 0.79998 (31752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 431 time to evaluate : 2.434 Fit side-chains REVERT: E 30 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7635 (mp-120) REVERT: E 38 GLU cc_start: 0.8272 (tt0) cc_final: 0.8032 (tt0) REVERT: F 38 GLU cc_start: 0.8196 (tt0) cc_final: 0.7925 (tt0) REVERT: F 72 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8419 (mtp) REVERT: I 26 ARG cc_start: 0.7822 (ttt90) cc_final: 0.6693 (ttt90) REVERT: I 139 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7548 (tptp) REVERT: A 7 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8406 (mt0) REVERT: A 113 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8068 (mt0) REVERT: B 113 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8116 (mt0) REVERT: J 93 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: M 139 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7360 (tptp) REVERT: M 265 ASN cc_start: 0.7793 (m110) cc_final: 0.7577 (m-40) REVERT: M 299 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: C 26 ARG cc_start: 0.7848 (ttt90) cc_final: 0.6737 (ttt90) REVERT: C 139 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7552 (tptp) REVERT: G 139 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7315 (tptp) REVERT: G 299 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8047 (m-10) REVERT: G 451 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8256 (p) outliers start: 71 outliers final: 37 residues processed: 479 average time/residue: 2.0435 time to fit residues: 1103.2587 Evaluate side-chains 457 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 414 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 283 SER Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 179 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 ASN E 82 ASN F 108 GLN A 37 ASN J 82 ASN J 108 GLN L 82 ASN L 108 GLN G 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104642 restraints weight = 28248.717| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.69 r_work: 0.2988 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23478 Z= 0.127 Angle : 0.636 7.788 31752 Z= 0.293 Chirality : 0.042 0.248 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.947 171.059 5478 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.15 % Rotamer: Outliers : 1.93 % Allowed : 15.51 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.16), residues: 2766 helix: 2.47 (0.12), residues: 1776 sheet: 0.77 (0.28), residues: 286 loop : 0.09 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 337 HIS 0.004 0.001 HIS C 176 PHE 0.031 0.001 PHE C 210 TYR 0.010 0.001 TYR G 108 ARG 0.004 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1451) hydrogen bonds : angle 4.14757 ( 4266) covalent geometry : bond 0.00272 (23478) covalent geometry : angle 0.63614 (31752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 433 time to evaluate : 3.924 Fit side-chains REVERT: F 38 GLU cc_start: 0.8036 (tt0) cc_final: 0.7757 (tt0) REVERT: I 26 ARG cc_start: 0.7807 (ttt90) cc_final: 0.6683 (ttt90) REVERT: I 139 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7538 (tptp) REVERT: A 7 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8333 (mt0) REVERT: A 22 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8088 (tptp) REVERT: A 113 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8085 (mt0) REVERT: B 22 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: B 113 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8090 (mt0) REVERT: J 93 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: M 139 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7343 (tptp) REVERT: M 299 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: C 26 ARG cc_start: 0.7831 (ttt90) cc_final: 0.6718 (ttt90) REVERT: C 139 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7551 (tptp) REVERT: G 139 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7331 (tptp) REVERT: G 299 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7999 (m-80) outliers start: 44 outliers final: 22 residues processed: 461 average time/residue: 1.5285 time to fit residues: 795.1154 Evaluate side-chains 447 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 421 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 150 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 257 optimal weight: 0.3980 chunk 231 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 ASN A 37 ASN J 82 ASN L 82 ASN L 108 GLN C 263 ASN G 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098738 restraints weight = 36937.006| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.97 r_work: 0.2921 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23478 Z= 0.171 Angle : 0.675 8.060 31752 Z= 0.313 Chirality : 0.044 0.237 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.598 171.469 5478 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 2.02 % Allowed : 15.64 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.16), residues: 2766 helix: 2.43 (0.12), residues: 1774 sheet: 0.68 (0.28), residues: 282 loop : 0.17 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 337 HIS 0.004 0.001 HIS C 176 PHE 0.031 0.002 PHE C 210 TYR 0.011 0.002 TYR G 108 ARG 0.005 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1451) hydrogen bonds : angle 4.16846 ( 4266) covalent geometry : bond 0.00396 (23478) covalent geometry : angle 0.67522 (31752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 2.343 Fit side-chains REVERT: D 113 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8055 (mt0) REVERT: F 38 GLU cc_start: 0.8113 (tt0) cc_final: 0.7844 (tt0) REVERT: I 26 ARG cc_start: 0.7797 (ttt90) cc_final: 0.6593 (ttt90) REVERT: I 139 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7539 (tptp) REVERT: A 7 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8415 (mt0) REVERT: A 22 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8119 (tptp) REVERT: A 113 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8108 (mt0) REVERT: B 113 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8118 (mt0) REVERT: J 93 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: M 139 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7336 (tptp) REVERT: M 299 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: C 26 ARG cc_start: 0.7774 (ttt90) cc_final: 0.6624 (ttt90) REVERT: C 139 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7503 (tptp) REVERT: G 139 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7315 (tptp) REVERT: G 299 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8132 (m-80) outliers start: 46 outliers final: 25 residues processed: 450 average time/residue: 1.5871 time to fit residues: 801.2613 Evaluate side-chains 440 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 412 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 ASN F 82 ASN A 37 ASN J 82 ASN L 82 ASN L 108 GLN C 263 ASN G 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104258 restraints weight = 28320.273| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.70 r_work: 0.2962 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23478 Z= 0.163 Angle : 0.659 7.984 31752 Z= 0.306 Chirality : 0.043 0.258 3986 Planarity : 0.003 0.038 3662 Dihedral : 11.204 170.088 5478 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 2.02 % Allowed : 15.91 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.16), residues: 2766 helix: 2.42 (0.12), residues: 1774 sheet: 0.64 (0.28), residues: 286 loop : 0.15 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 337 HIS 0.004 0.001 HIS G 176 PHE 0.031 0.002 PHE C 210 TYR 0.010 0.001 TYR M 108 ARG 0.005 0.000 ARG J 106 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1451) hydrogen bonds : angle 4.15716 ( 4266) covalent geometry : bond 0.00375 (23478) covalent geometry : angle 0.65870 (31752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 418 time to evaluate : 3.263 Fit side-chains REVERT: D 113 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8131 (mt0) REVERT: F 38 GLU cc_start: 0.8041 (tt0) cc_final: 0.7777 (tt0) REVERT: I 26 ARG cc_start: 0.7691 (ttt90) cc_final: 0.6610 (ttt90) REVERT: I 139 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7545 (tptp) REVERT: A 22 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8110 (tptp) REVERT: A 113 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8126 (mt0) REVERT: B 22 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8124 (tptp) REVERT: B 113 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8108 (mt0) REVERT: J 93 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: M 139 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7341 (tptp) REVERT: M 299 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: C 26 ARG cc_start: 0.7717 (ttt90) cc_final: 0.6656 (ttt90) REVERT: C 139 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7503 (tptp) REVERT: G 139 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7313 (tptp) REVERT: G 299 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: G 451 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8267 (p) outliers start: 46 outliers final: 29 residues processed: 447 average time/residue: 1.5887 time to fit residues: 800.6900 Evaluate side-chains 444 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 410 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 72 MET Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 ASN J 82 ASN L 82 ASN L 108 GLN C 263 ASN G 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102381 restraints weight = 41606.201| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.14 r_work: 0.2945 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23478 Z= 0.126 Angle : 0.621 7.521 31752 Z= 0.289 Chirality : 0.042 0.247 3986 Planarity : 0.003 0.038 3662 Dihedral : 10.766 169.470 5478 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Rotamer: Outliers : 1.67 % Allowed : 16.61 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.16), residues: 2766 helix: 2.56 (0.12), residues: 1776 sheet: 0.78 (0.28), residues: 270 loop : 0.09 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 337 HIS 0.004 0.001 HIS C 176 PHE 0.032 0.001 PHE I 210 TYR 0.009 0.001 TYR G 108 ARG 0.009 0.000 ARG F 106 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1451) hydrogen bonds : angle 4.07387 ( 4266) covalent geometry : bond 0.00276 (23478) covalent geometry : angle 0.62119 (31752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 426 time to evaluate : 2.447 Fit side-chains REVERT: D 113 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8016 (mt0) REVERT: F 38 GLU cc_start: 0.7816 (tt0) cc_final: 0.7597 (tt0) REVERT: I 26 ARG cc_start: 0.7517 (ttt90) cc_final: 0.6515 (ttt90) REVERT: I 139 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7495 (tptp) REVERT: I 307 MET cc_start: 0.8917 (ttp) cc_final: 0.8621 (tpp) REVERT: A 22 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8039 (tptp) REVERT: A 113 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8020 (mt0) REVERT: B 22 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8050 (tptp) REVERT: B 113 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8035 (mt0) REVERT: J 93 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: M 139 LYS cc_start: 0.8042 (ttpt) cc_final: 0.7301 (tptp) REVERT: M 299 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: C 26 ARG cc_start: 0.7505 (ttt90) cc_final: 0.6508 (ttt90) REVERT: C 139 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7461 (tptp) REVERT: C 295 ASP cc_start: 0.8261 (t0) cc_final: 0.8040 (t0) REVERT: G 139 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7277 (tptp) REVERT: G 299 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: G 451 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8220 (p) outliers start: 38 outliers final: 25 residues processed: 448 average time/residue: 1.5401 time to fit residues: 775.9153 Evaluate side-chains 451 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 421 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 142 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 171 optimal weight: 0.0010 chunk 146 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN A 37 ASN ** L 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101691 restraints weight = 39792.542| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.07 r_work: 0.3000 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23478 Z= 0.111 Angle : 0.599 7.469 31752 Z= 0.279 Chirality : 0.041 0.264 3986 Planarity : 0.003 0.038 3662 Dihedral : 10.309 170.513 5478 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.54 % Allowed : 16.65 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.16), residues: 2766 helix: 2.68 (0.12), residues: 1766 sheet: 0.93 (0.29), residues: 270 loop : -0.01 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 337 HIS 0.004 0.001 HIS C 176 PHE 0.032 0.001 PHE I 210 TYR 0.010 0.001 TYR I 108 ARG 0.007 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1451) hydrogen bonds : angle 3.99839 ( 4266) covalent geometry : bond 0.00235 (23478) covalent geometry : angle 0.59871 (31752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22134.30 seconds wall clock time: 385 minutes 16.54 seconds (23116.54 seconds total)