Starting phenix.real_space_refine on Wed Jun 18 12:02:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpr_14862/06_2025/7zpr_14862.cif" } resolution = 3.56 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= 0.004 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 13782 2.51 5 N 3576 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21350 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "G" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.11, per 1000 atoms: 0.71 Number of scatterers: 21350 At special positions: 0 Unit cell: (95.9651, 110.921, 173.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 3824 8.00 N 3576 7.00 C 13782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 4.1 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 69.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'H' and resid 14 through 27 removed outlier: 3.520A pdb=" N SER H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.713A pdb=" N GLY H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 80 through 94 Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 122 through 137 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.762A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 80 through 95 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'E' and resid 14 through 28 Processing helix chain 'E' and resid 37 through 46 removed outlier: 4.231A pdb=" N GLY E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 37 through 46 removed outlier: 4.024A pdb=" N GLY F 46 " --> pdb=" O LYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 67 through 70 Processing helix chain 'F' and resid 80 through 95 Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'I' and resid 23 through 44 removed outlier: 3.527A pdb=" N PHE I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) Proline residue: I 38 - end of helix removed outlier: 3.531A pdb=" N THR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 67 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.612A pdb=" N PHE I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 122 Processing helix chain 'I' and resid 133 through 165 removed outlier: 3.710A pdb=" N ARG I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 167 through 182 Processing helix chain 'I' and resid 199 through 214 Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 230 through 234 Processing helix chain 'I' and resid 235 through 261 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 271 through 286 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 300 through 314 Processing helix chain 'I' and resid 325 through 341 Processing helix chain 'I' and resid 354 through 383 Processing helix chain 'I' and resid 386 through 399 Processing helix chain 'I' and resid 407 through 411 Processing helix chain 'I' and resid 412 through 439 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.842A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'B' and resid 14 through 27 Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.684A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'J' and resid 14 through 27 removed outlier: 3.535A pdb=" N SER J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 removed outlier: 4.242A pdb=" N GLY J 46 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 65 Processing helix chain 'J' and resid 80 through 94 Processing helix chain 'J' and resid 105 through 116 Processing helix chain 'J' and resid 122 through 137 Processing helix chain 'L' and resid 14 through 28 removed outlier: 3.618A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 4.247A pdb=" N GLY L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 Processing helix chain 'L' and resid 67 through 70 Processing helix chain 'L' and resid 80 through 94 removed outlier: 3.548A pdb=" N SER L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 116 Processing helix chain 'L' and resid 122 through 137 Processing helix chain 'M' and resid 23 through 45 Proline residue: M 38 - end of helix removed outlier: 3.770A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 67 Processing helix chain 'M' and resid 75 through 80 removed outlier: 3.687A pdb=" N PHE M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 122 removed outlier: 3.582A pdb=" N GLN M 99 " --> pdb=" O GLY M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 165 removed outlier: 3.846A pdb=" N ARG M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) Proline residue: M 162 - end of helix Processing helix chain 'M' and resid 165 through 182 removed outlier: 3.594A pdb=" N PHE M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 214 Processing helix chain 'M' and resid 216 through 227 Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 235 through 261 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 286 Processing helix chain 'M' and resid 295 through 299 Processing helix chain 'M' and resid 300 through 314 Processing helix chain 'M' and resid 325 through 342 Processing helix chain 'M' and resid 354 through 383 Processing helix chain 'M' and resid 386 through 399 Processing helix chain 'M' and resid 412 through 439 removed outlier: 3.536A pdb=" N TYR M 417 " --> pdb=" O GLU M 413 " (cutoff:3.500A) Proline residue: M 430 - end of helix Processing helix chain 'C' and resid 23 through 44 removed outlier: 3.525A pdb=" N PHE C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.530A pdb=" N THR C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.611A pdb=" N PHE C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 122 Processing helix chain 'C' and resid 133 through 165 removed outlier: 3.711A pdb=" N ARG C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 235 through 261 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 354 through 383 Processing helix chain 'C' and resid 386 through 399 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 439 Proline residue: C 430 - end of helix Processing helix chain 'G' and resid 23 through 45 Proline residue: G 38 - end of helix removed outlier: 3.770A pdb=" N THR G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 75 through 80 removed outlier: 3.685A pdb=" N PHE G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 122 removed outlier: 3.581A pdb=" N GLN G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 165 removed outlier: 3.846A pdb=" N ARG G 159 " --> pdb=" O PHE G 155 " (cutoff:3.500A) Proline residue: G 162 - end of helix Processing helix chain 'G' and resid 165 through 182 removed outlier: 3.593A pdb=" N PHE G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 214 Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 235 through 261 Proline residue: G 246 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 300 through 314 Processing helix chain 'G' and resid 325 through 342 Processing helix chain 'G' and resid 354 through 383 Processing helix chain 'G' and resid 386 through 399 Processing helix chain 'G' and resid 412 through 439 removed outlier: 3.537A pdb=" N TYR G 417 " --> pdb=" O GLU G 413 " (cutoff:3.500A) Proline residue: G 430 - end of helix Processing sheet with id=AA1, first strand: chain 'H' and resid 50 through 53 removed outlier: 6.168A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA H 33 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET H 72 " --> pdb=" O GLN H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 50 through 53 removed outlier: 6.172A pdb=" N VAL D 31 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE D 52 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA D 33 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE D 8 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL D 34 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 10 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN D 7 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N MET D 74 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 9 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 99 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE D 121 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 101 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 53 removed outlier: 6.253A pdb=" N VAL E 31 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE E 52 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA E 33 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 50 through 53 removed outlier: 6.419A pdb=" N VAL F 31 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE F 52 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 33 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.466A pdb=" N VAL I 346 " --> pdb=" O VAL I 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR I 352 " --> pdb=" O ASP M 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.257A pdb=" N VAL A 31 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 52 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 33 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A 7 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N MET A 74 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 9 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 99 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 101 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.120A pdb=" N VAL B 31 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 52 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 8 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 34 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 10 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 7 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N MET B 74 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA B 9 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 99 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 50 through 53 removed outlier: 6.329A pdb=" N VAL J 31 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE J 52 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 50 through 53 removed outlier: 6.448A pdb=" N VAL L 31 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE L 52 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA L 33 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET L 72 " --> pdb=" O GLN L 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL L 73 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL L 99 " --> pdb=" O HIS L 119 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE L 121 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL L 101 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 346 through 347 removed outlier: 4.421A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 347 removed outlier: 4.464A pdb=" N VAL C 346 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR C 352 " --> pdb=" O ASP G 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 346 through 347 removed outlier: 4.420A pdb=" N VAL G 346 " --> pdb=" O VAL G 353 " (cutoff:3.500A) 1443 hydrogen bonds defined for protein. 4242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4195 1.33 - 1.45: 4835 1.45 - 1.57: 12413 1.57 - 1.69: 24 1.69 - 1.82: 261 Bond restraints: 21728 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.35e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 21723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 28501 2.16 - 4.32: 817 4.32 - 6.48: 113 6.48 - 8.64: 16 8.64 - 10.80: 11 Bond angle restraints: 29458 Sorted by residual: angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.31 -8.89 1.99e+00 2.53e-01 2.00e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.50 5.39 1.24e+00 6.50e-01 1.89e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N LEU C 296 " pdb=" CA LEU C 296 " pdb=" C LEU C 296 " ideal model delta sigma weight residual 112.89 107.71 5.18 1.24e+00 6.50e-01 1.75e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 12514 33.64 - 67.28: 281 67.28 - 100.92: 16 100.92 - 134.56: 5 134.56 - 168.20: 6 Dihedral angle restraints: 12822 sinusoidal: 4956 harmonic: 7866 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.80 168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.80 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.02 -160.01 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3354 0.108 - 0.215: 188 0.215 - 0.322: 2 0.322 - 0.430: 0 0.430 - 0.537: 4 Chirality restraints: 3548 Sorted by residual: chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA THR C 288 " pdb=" N THR C 288 " pdb=" C THR C 288 " pdb=" CB THR C 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 3545 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C MET M 92 " 0.041 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET G 92 " -0.041 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 122 " 0.032 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 123 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.026 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 141 2.56 - 3.21: 19848 3.21 - 3.85: 43220 3.85 - 4.50: 61039 4.50 - 5.14: 95532 Nonbonded interactions: 219780 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O3B ADP A1002 " model vdw 1.919 2.170 nonbonded pdb=" OD1 ASN H 82 " pdb=" ND2 ASN B 82 " model vdw 1.954 3.120 nonbonded pdb=" O2B ADP L 301 " pdb="MG MG L 302 " model vdw 1.977 2.170 nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 301 " pdb="MG MG E 302 " model vdw 1.988 2.170 ... (remaining 219775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'G' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) selection = (chain 'I' and (resid 21 through 350 or resid 352 through 455 or resid 601)) selection = (chain 'M' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 455 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 52.810 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 21728 Z= 0.358 Angle : 0.800 10.803 29458 Z= 0.497 Chirality : 0.053 0.537 3548 Planarity : 0.004 0.047 3608 Dihedral : 14.454 168.201 7742 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 1.16 % Favored : 97.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2736 helix: 1.46 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 337 HIS 0.005 0.001 HIS G 345 PHE 0.026 0.001 PHE I 210 TYR 0.014 0.002 TYR F 70 ARG 0.005 0.000 ARG J 130 Details of bonding type rmsd hydrogen bonds : bond 0.18822 ( 1443) hydrogen bonds : angle 6.57781 ( 4242) covalent geometry : bond 0.00548 (21728) covalent geometry : angle 0.80015 (29458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 772 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7987 (tp30) cc_final: 0.7136 (tp30) REVERT: H 127 MET cc_start: 0.8929 (tpt) cc_final: 0.8175 (tpp) REVERT: D 23 GLU cc_start: 0.7866 (tp30) cc_final: 0.7666 (tp30) REVERT: D 110 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8190 (mtm180) REVERT: D 133 ARG cc_start: 0.7368 (mtt90) cc_final: 0.7025 (mtm-85) REVERT: E 29 SER cc_start: 0.7901 (m) cc_final: 0.7690 (p) REVERT: E 96 VAL cc_start: 0.8462 (t) cc_final: 0.8256 (t) REVERT: E 127 MET cc_start: 0.8340 (mmm) cc_final: 0.8095 (mmm) REVERT: I 92 MET cc_start: 0.7593 (ptt) cc_final: 0.7332 (ptt) REVERT: I 387 PHE cc_start: 0.7513 (t80) cc_final: 0.7042 (t80) REVERT: I 389 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7597 (ttmt) REVERT: I 420 ILE cc_start: 0.7474 (mt) cc_final: 0.7060 (mt) REVERT: I 447 TYR cc_start: 0.8776 (m-80) cc_final: 0.8502 (m-80) REVERT: A 23 GLU cc_start: 0.7777 (tp30) cc_final: 0.7219 (tp30) REVERT: A 133 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7215 (mtm180) REVERT: B 23 GLU cc_start: 0.7382 (tp30) cc_final: 0.7021 (tp30) REVERT: B 127 MET cc_start: 0.9040 (tpt) cc_final: 0.8791 (tpp) REVERT: B 133 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7040 (mtm-85) REVERT: J 122 MET cc_start: 0.7679 (mtp) cc_final: 0.6736 (mtm) REVERT: J 126 ASP cc_start: 0.7860 (m-30) cc_final: 0.7548 (m-30) REVERT: L 98 SER cc_start: 0.7307 (p) cc_final: 0.6760 (p) REVERT: L 122 MET cc_start: 0.7622 (mtp) cc_final: 0.6897 (mtm) REVERT: M 76 THR cc_start: 0.7360 (m) cc_final: 0.7095 (m) REVERT: M 93 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6901 (tp-100) REVERT: M 298 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: M 420 ILE cc_start: 0.7844 (mt) cc_final: 0.7505 (mt) REVERT: M 447 TYR cc_start: 0.8739 (m-80) cc_final: 0.8474 (m-80) REVERT: C 92 MET cc_start: 0.7635 (ptt) cc_final: 0.7375 (ptt) REVERT: C 93 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7235 (tp-100) REVERT: C 108 TYR cc_start: 0.7607 (t80) cc_final: 0.7366 (t80) REVERT: C 136 ARG cc_start: 0.5225 (ttt180) cc_final: 0.4998 (tpt170) REVERT: C 387 PHE cc_start: 0.7615 (t80) cc_final: 0.7195 (t80) REVERT: C 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7639 (ttmt) REVERT: C 420 ILE cc_start: 0.7642 (mt) cc_final: 0.7243 (mt) REVERT: C 447 TYR cc_start: 0.8841 (m-80) cc_final: 0.8597 (m-80) REVERT: C 449 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6444 (mt-10) REVERT: G 93 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6857 (tp-100) REVERT: G 277 LEU cc_start: 0.8276 (tp) cc_final: 0.7858 (tt) REVERT: G 298 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: G 400 THR cc_start: 0.8878 (m) cc_final: 0.8576 (m) REVERT: G 420 ILE cc_start: 0.7862 (mt) cc_final: 0.7609 (mt) REVERT: G 447 TYR cc_start: 0.8782 (m-80) cc_final: 0.8549 (m-80) outliers start: 20 outliers final: 2 residues processed: 782 average time/residue: 0.3530 time to fit residues: 412.4076 Evaluate side-chains 481 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 475 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN I 301 GLN A 50 GLN B 50 GLN J 30 GLN J 108 GLN J 113 GLN M 262 HIS C 78 GLN C 282 GLN C 301 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120334 restraints weight = 47320.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126464 restraints weight = 21731.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129085 restraints weight = 10242.102| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21728 Z= 0.185 Angle : 0.677 7.437 29458 Z= 0.337 Chirality : 0.045 0.163 3548 Planarity : 0.004 0.035 3608 Dihedral : 9.799 178.698 3010 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.65 % Favored : 98.28 % Rotamer: Outliers : 2.27 % Allowed : 11.35 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.16), residues: 2736 helix: 2.14 (0.12), residues: 1776 sheet: 1.55 (0.27), residues: 274 loop : -0.16 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 257 HIS 0.008 0.002 HIS G 79 PHE 0.036 0.002 PHE C 210 TYR 0.010 0.002 TYR G 447 ARG 0.008 0.001 ARG G 427 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1443) hydrogen bonds : angle 4.46440 ( 4242) covalent geometry : bond 0.00414 (21728) covalent geometry : angle 0.67675 (29458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 504 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7872 (tp30) cc_final: 0.7032 (tp30) REVERT: H 110 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8475 (mtm180) REVERT: H 134 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8212 (mtpt) REVERT: D 23 GLU cc_start: 0.7708 (tp30) cc_final: 0.7475 (tp30) REVERT: D 107 PHE cc_start: 0.8527 (m-80) cc_final: 0.8266 (m-10) REVERT: D 127 MET cc_start: 0.8789 (mmm) cc_final: 0.8444 (tpp) REVERT: D 133 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6873 (mtm-85) REVERT: E 72 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6277 (mmm) REVERT: F 72 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6575 (mmm) REVERT: I 139 LYS cc_start: 0.7104 (ttpp) cc_final: 0.6793 (ttmt) REVERT: I 241 MET cc_start: 0.8165 (mmt) cc_final: 0.7899 (mmt) REVERT: I 389 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7476 (ttmt) REVERT: I 420 ILE cc_start: 0.8086 (mt) cc_final: 0.7724 (mt) REVERT: I 447 TYR cc_start: 0.8955 (m-80) cc_final: 0.8676 (m-80) REVERT: A 23 GLU cc_start: 0.7653 (tp30) cc_final: 0.7312 (tp30) REVERT: A 93 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 133 ARG cc_start: 0.7373 (mtt90) cc_final: 0.6935 (mtm-85) REVERT: B 23 GLU cc_start: 0.7660 (tp30) cc_final: 0.7355 (tp30) REVERT: B 133 ARG cc_start: 0.7326 (mtt90) cc_final: 0.7042 (mtm-85) REVERT: J 122 MET cc_start: 0.7712 (mtp) cc_final: 0.7477 (mtm) REVERT: L 23 GLU cc_start: 0.7723 (tp30) cc_final: 0.7469 (tp30) REVERT: M 99 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: M 193 MET cc_start: 0.8202 (mmt) cc_final: 0.7973 (mmt) REVERT: M 241 MET cc_start: 0.8022 (mmt) cc_final: 0.7712 (mmt) REVERT: M 420 ILE cc_start: 0.8355 (mt) cc_final: 0.8046 (mt) REVERT: M 446 LYS cc_start: 0.8565 (tttt) cc_final: 0.8034 (tttm) REVERT: M 447 TYR cc_start: 0.8964 (m-80) cc_final: 0.8698 (m-80) REVERT: C 193 MET cc_start: 0.8128 (mmt) cc_final: 0.7901 (mmt) REVERT: C 241 MET cc_start: 0.8126 (mmt) cc_final: 0.7873 (mmt) REVERT: C 389 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7452 (ttmt) REVERT: C 420 ILE cc_start: 0.8176 (mt) cc_final: 0.7839 (mt) REVERT: C 447 TYR cc_start: 0.8967 (m-80) cc_final: 0.8692 (m-80) REVERT: G 75 ASP cc_start: 0.6603 (t70) cc_final: 0.6381 (t0) REVERT: G 228 ARG cc_start: 0.6855 (ptp-110) cc_final: 0.6634 (ptp-110) REVERT: G 241 MET cc_start: 0.8015 (mmt) cc_final: 0.7743 (mmt) REVERT: G 298 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: G 447 TYR cc_start: 0.8972 (m-80) cc_final: 0.8692 (m-80) outliers start: 51 outliers final: 32 residues processed: 541 average time/residue: 0.3451 time to fit residues: 294.0684 Evaluate side-chains 462 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 426 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 298 GLN Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 131 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN M 93 GLN M 265 ASN M 282 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 282 GLN G 345 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116347 restraints weight = 41536.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121049 restraints weight = 19373.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124091 restraints weight = 11390.427| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21728 Z= 0.183 Angle : 0.651 8.232 29458 Z= 0.321 Chirality : 0.045 0.162 3548 Planarity : 0.004 0.089 3608 Dihedral : 9.111 176.758 3004 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.25 % Allowed : 12.96 % Favored : 83.79 % 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: 2.32 (0.16), residues: 2736 helix: 2.23 (0.12), residues: 1772 sheet: 1.29 (0.27), residues: 274 loop : -0.19 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 257 HIS 0.006 0.001 HIS C 176 PHE 0.029 0.002 PHE I 153 TYR 0.012 0.002 TYR C 447 ARG 0.006 0.001 ARG G 427 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 1443) hydrogen bonds : angle 4.30463 ( 4242) covalent geometry : bond 0.00418 (21728) covalent geometry : angle 0.65117 (29458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 500 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7911 (tp30) cc_final: 0.7166 (tp30) REVERT: H 134 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8242 (mtpt) REVERT: D 23 GLU cc_start: 0.7813 (tp30) cc_final: 0.7526 (tp30) REVERT: D 127 MET cc_start: 0.8840 (mmm) cc_final: 0.8535 (tpp) REVERT: D 133 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6809 (mtm-85) REVERT: E 72 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6643 (mmm) REVERT: E 98 SER cc_start: 0.8083 (p) cc_final: 0.7882 (p) REVERT: F 126 ASP cc_start: 0.8297 (m-30) cc_final: 0.7685 (m-30) REVERT: I 139 LYS cc_start: 0.7315 (ttpp) cc_final: 0.6972 (ttmt) REVERT: I 228 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6859 (ptp-110) REVERT: I 292 ASN cc_start: 0.7101 (p0) cc_final: 0.6612 (p0) REVERT: I 389 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7454 (ttmt) REVERT: I 420 ILE cc_start: 0.8471 (mt) cc_final: 0.8163 (mt) REVERT: A 23 GLU cc_start: 0.7775 (tp30) cc_final: 0.7342 (tp30) REVERT: A 133 ARG cc_start: 0.7430 (mtt90) cc_final: 0.7048 (mmm-85) REVERT: B 23 GLU cc_start: 0.7656 (tp30) cc_final: 0.7235 (tp30) REVERT: J 15 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7839 (mtm-85) REVERT: J 122 MET cc_start: 0.7776 (mtp) cc_final: 0.7413 (mtm) REVERT: L 35 ASP cc_start: 0.7866 (t70) cc_final: 0.7633 (t70) REVERT: L 71 ASP cc_start: 0.8121 (m-30) cc_final: 0.7830 (m-30) REVERT: L 72 MET cc_start: 0.6788 (mmm) cc_final: 0.6378 (mmp) REVERT: M 241 MET cc_start: 0.8140 (mmt) cc_final: 0.7774 (mmt) REVERT: M 419 MET cc_start: 0.8667 (tpp) cc_final: 0.8466 (tpp) REVERT: M 446 LYS cc_start: 0.8585 (tttt) cc_final: 0.8070 (tttm) REVERT: C 292 ASN cc_start: 0.7310 (p0) cc_final: 0.6864 (p0) REVERT: C 389 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7466 (ttmt) REVERT: C 420 ILE cc_start: 0.8573 (mt) cc_final: 0.8304 (mt) REVERT: G 75 ASP cc_start: 0.6783 (t70) cc_final: 0.6582 (t0) REVERT: G 228 ARG cc_start: 0.7089 (ptp-110) cc_final: 0.6781 (ptp-110) REVERT: G 241 MET cc_start: 0.8153 (mmt) cc_final: 0.7777 (mmt) REVERT: G 292 ASN cc_start: 0.7480 (p0) cc_final: 0.6819 (p0) REVERT: G 423 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7168 (mtm) REVERT: G 446 LYS cc_start: 0.8697 (tttt) cc_final: 0.8155 (tttm) REVERT: G 447 TYR cc_start: 0.9051 (m-80) cc_final: 0.8833 (m-80) outliers start: 73 outliers final: 47 residues processed: 552 average time/residue: 0.3158 time to fit residues: 274.1272 Evaluate side-chains 517 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 467 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 30 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 262 optimal weight: 0.0050 chunk 212 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 ASN M 282 GLN M 298 GLN M 345 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105122 restraints weight = 50690.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109658 restraints weight = 22900.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112891 restraints weight = 13384.943| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21728 Z= 0.149 Angle : 0.611 7.350 29458 Z= 0.298 Chirality : 0.043 0.162 3548 Planarity : 0.004 0.080 3608 Dihedral : 8.313 173.722 3001 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.54 % Allowed : 15.41 % Favored : 82.06 % 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: 2.47 (0.16), residues: 2736 helix: 2.40 (0.12), residues: 1770 sheet: 1.27 (0.28), residues: 274 loop : -0.24 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 257 HIS 0.004 0.001 HIS I 176 PHE 0.032 0.002 PHE G 153 TYR 0.010 0.001 TYR G 447 ARG 0.005 0.000 ARG M 427 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1443) hydrogen bonds : angle 4.18320 ( 4242) covalent geometry : bond 0.00339 (21728) covalent geometry : angle 0.61121 (29458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 493 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7941 (tp30) cc_final: 0.7248 (tp30) REVERT: H 110 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8626 (mtm110) REVERT: H 134 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8315 (mtpt) REVERT: D 23 GLU cc_start: 0.7924 (tp30) cc_final: 0.7593 (tp30) REVERT: D 71 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7350 (p0) REVERT: D 127 MET cc_start: 0.8821 (mmm) cc_final: 0.8505 (tpp) REVERT: D 133 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6797 (mtm-85) REVERT: E 72 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6602 (mmt) REVERT: E 98 SER cc_start: 0.8166 (p) cc_final: 0.7066 (p) REVERT: E 126 ASP cc_start: 0.7981 (m-30) cc_final: 0.7715 (m-30) REVERT: F 113 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7293 (tm-30) REVERT: F 114 LYS cc_start: 0.8527 (mttm) cc_final: 0.8248 (mtpt) REVERT: F 126 ASP cc_start: 0.8198 (m-30) cc_final: 0.7508 (m-30) REVERT: I 139 LYS cc_start: 0.7407 (ttpp) cc_final: 0.7020 (ttmt) REVERT: I 241 MET cc_start: 0.8305 (tpp) cc_final: 0.8010 (mmt) REVERT: I 292 ASN cc_start: 0.7148 (p0) cc_final: 0.6769 (p0) REVERT: I 389 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7593 (ttmt) REVERT: I 419 MET cc_start: 0.8693 (tpp) cc_final: 0.8477 (tpt) REVERT: A 23 GLU cc_start: 0.7688 (tp30) cc_final: 0.7226 (tp30) REVERT: A 40 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7663 (mtt180) REVERT: A 42 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8204 (mtpt) REVERT: A 110 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8416 (mtm180) REVERT: A 133 ARG cc_start: 0.7377 (mtt90) cc_final: 0.6957 (mmm-85) REVERT: L 35 ASP cc_start: 0.7842 (t70) cc_final: 0.7604 (t70) REVERT: L 50 GLN cc_start: 0.7836 (tt0) cc_final: 0.7605 (tt0) REVERT: L 72 MET cc_start: 0.6776 (mmm) cc_final: 0.6186 (mmt) REVERT: L 98 SER cc_start: 0.8281 (p) cc_final: 0.7258 (p) REVERT: M 99 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: M 199 ASP cc_start: 0.7283 (t0) cc_final: 0.7073 (t0) REVERT: M 241 MET cc_start: 0.7925 (mmt) cc_final: 0.7655 (mmt) REVERT: M 292 ASN cc_start: 0.7087 (p0) cc_final: 0.6653 (p0) REVERT: M 298 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: M 427 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7132 (tpp-160) REVERT: M 446 LYS cc_start: 0.8593 (tttt) cc_final: 0.8089 (tttm) REVERT: C 241 MET cc_start: 0.8337 (tpp) cc_final: 0.8056 (mmt) REVERT: C 292 ASN cc_start: 0.7229 (p0) cc_final: 0.6823 (p0) REVERT: C 388 ASP cc_start: 0.7392 (p0) cc_final: 0.7030 (p0) REVERT: C 389 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7542 (ttmt) REVERT: C 419 MET cc_start: 0.8690 (tpp) cc_final: 0.8470 (tpt) REVERT: G 241 MET cc_start: 0.7990 (mmt) cc_final: 0.7721 (mmt) REVERT: G 292 ASN cc_start: 0.7374 (p0) cc_final: 0.6802 (p0) REVERT: G 423 MET cc_start: 0.7430 (mtp) cc_final: 0.7143 (mtm) REVERT: G 446 LYS cc_start: 0.8560 (tttt) cc_final: 0.8038 (tttm) outliers start: 57 outliers final: 44 residues processed: 534 average time/residue: 0.3147 time to fit residues: 261.9145 Evaluate side-chains 514 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 465 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 427 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 52 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 101 optimal weight: 0.0670 chunk 35 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN ** G 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.109126 restraints weight = 38908.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113222 restraints weight = 19540.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116029 restraints weight = 12061.859| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21728 Z= 0.133 Angle : 0.598 7.160 29458 Z= 0.290 Chirality : 0.043 0.173 3548 Planarity : 0.003 0.076 3608 Dihedral : 7.876 173.171 3001 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.45 % Allowed : 15.85 % Favored : 81.70 % 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: 2.55 (0.16), residues: 2736 helix: 2.45 (0.12), residues: 1776 sheet: 1.30 (0.28), residues: 274 loop : -0.22 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 257 HIS 0.003 0.001 HIS I 262 PHE 0.029 0.001 PHE C 153 TYR 0.008 0.001 TYR J 70 ARG 0.005 0.000 ARG G 427 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1443) hydrogen bonds : angle 4.13071 ( 4242) covalent geometry : bond 0.00302 (21728) covalent geometry : angle 0.59790 (29458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 494 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7914 (tp30) cc_final: 0.7256 (tp30) REVERT: H 134 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8356 (mtpt) REVERT: D 23 GLU cc_start: 0.7750 (tp30) cc_final: 0.7503 (tp30) REVERT: D 71 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7314 (p0) REVERT: D 127 MET cc_start: 0.8827 (mmm) cc_final: 0.8572 (tpp) REVERT: D 133 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6891 (mtm-85) REVERT: E 72 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6587 (mmt) REVERT: E 98 SER cc_start: 0.8191 (p) cc_final: 0.7085 (p) REVERT: E 113 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7190 (tm-30) REVERT: E 126 ASP cc_start: 0.7917 (m-30) cc_final: 0.7637 (m-30) REVERT: F 72 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6638 (mmm) REVERT: I 241 MET cc_start: 0.8259 (tpp) cc_final: 0.7994 (mmt) REVERT: I 292 ASN cc_start: 0.7045 (p0) cc_final: 0.6589 (p0) REVERT: I 389 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7574 (ttmt) REVERT: I 446 LYS cc_start: 0.8539 (tttt) cc_final: 0.7992 (tttm) REVERT: A 23 GLU cc_start: 0.7647 (tp30) cc_final: 0.7185 (tp30) REVERT: A 110 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8425 (mtm180) REVERT: A 133 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7112 (mmm-85) REVERT: B 127 MET cc_start: 0.8627 (tpp) cc_final: 0.8416 (tpp) REVERT: J 122 MET cc_start: 0.7603 (mtm) cc_final: 0.7372 (mtm) REVERT: L 35 ASP cc_start: 0.7832 (t70) cc_final: 0.7609 (t70) REVERT: L 50 GLN cc_start: 0.7795 (tt0) cc_final: 0.7559 (tt0) REVERT: L 72 MET cc_start: 0.6829 (mmm) cc_final: 0.6305 (mmt) REVERT: L 98 SER cc_start: 0.8294 (p) cc_final: 0.7195 (p) REVERT: M 199 ASP cc_start: 0.6933 (t0) cc_final: 0.6710 (t0) REVERT: M 227 TRP cc_start: 0.7657 (p-90) cc_final: 0.7424 (p-90) REVERT: M 241 MET cc_start: 0.7893 (mmt) cc_final: 0.7612 (mmt) REVERT: M 292 ASN cc_start: 0.7090 (p0) cc_final: 0.6543 (p0) REVERT: M 427 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6960 (tpp-160) REVERT: M 446 LYS cc_start: 0.8527 (tttt) cc_final: 0.8045 (tttm) REVERT: C 292 ASN cc_start: 0.7287 (p0) cc_final: 0.6926 (p0) REVERT: C 295 ASP cc_start: 0.6774 (m-30) cc_final: 0.6526 (p0) REVERT: C 419 MET cc_start: 0.8689 (tpp) cc_final: 0.8479 (tpt) REVERT: G 241 MET cc_start: 0.7973 (mmt) cc_final: 0.7704 (mmt) REVERT: G 292 ASN cc_start: 0.7330 (p0) cc_final: 0.6951 (p0) REVERT: G 388 ASP cc_start: 0.7399 (p0) cc_final: 0.7171 (p0) REVERT: G 423 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7118 (mtm) REVERT: G 446 LYS cc_start: 0.8491 (tttt) cc_final: 0.7931 (tttm) outliers start: 55 outliers final: 38 residues processed: 533 average time/residue: 0.3121 time to fit residues: 260.8312 Evaluate side-chains 507 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 464 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 58 HIS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 427 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 265 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS L 7 GLN M 282 GLN C 78 GLN G 262 HIS G 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104993 restraints weight = 40268.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109083 restraints weight = 20117.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111943 restraints weight = 12377.985| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21728 Z= 0.180 Angle : 0.633 7.151 29458 Z= 0.309 Chirality : 0.044 0.209 3548 Planarity : 0.004 0.078 3608 Dihedral : 7.749 170.550 2998 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.07 % Allowed : 17.10 % Favored : 79.83 % 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: 2.39 (0.16), residues: 2736 helix: 2.36 (0.12), residues: 1776 sheet: 1.11 (0.29), residues: 270 loop : -0.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 166 HIS 0.016 0.001 HIS I 79 PHE 0.028 0.002 PHE M 210 TYR 0.007 0.001 TYR G 447 ARG 0.005 0.000 ARG G 427 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1443) hydrogen bonds : angle 4.17708 ( 4242) covalent geometry : bond 0.00422 (21728) covalent geometry : angle 0.63258 (29458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 472 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7940 (tp30) cc_final: 0.7296 (tp30) REVERT: H 40 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7562 (mtt180) REVERT: H 134 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8338 (mtpt) REVERT: D 23 GLU cc_start: 0.7731 (tp30) cc_final: 0.7522 (tp30) REVERT: D 27 SER cc_start: 0.8354 (t) cc_final: 0.8046 (t) REVERT: D 71 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7346 (p0) REVERT: D 127 MET cc_start: 0.8901 (mmm) cc_final: 0.8579 (tpp) REVERT: D 133 ARG cc_start: 0.7272 (mtt90) cc_final: 0.6895 (mtm-85) REVERT: E 50 GLN cc_start: 0.8004 (tt0) cc_final: 0.7724 (tt0) REVERT: E 72 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6454 (mmp) REVERT: E 98 SER cc_start: 0.8324 (p) cc_final: 0.7360 (p) REVERT: E 126 ASP cc_start: 0.7959 (m-30) cc_final: 0.7637 (m-30) REVERT: F 43 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7096 (mt-10) REVERT: F 72 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6671 (mmm) REVERT: I 241 MET cc_start: 0.8345 (tpp) cc_final: 0.7996 (mmt) REVERT: I 292 ASN cc_start: 0.7134 (p0) cc_final: 0.6745 (p0) REVERT: I 389 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7537 (ptpt) REVERT: I 436 MET cc_start: 0.8144 (mtt) cc_final: 0.7879 (mtt) REVERT: A 23 GLU cc_start: 0.7648 (tp30) cc_final: 0.7240 (tp30) REVERT: A 110 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8442 (mtm180) REVERT: B 23 GLU cc_start: 0.7639 (tp30) cc_final: 0.7331 (tp30) REVERT: J 122 MET cc_start: 0.7659 (mtm) cc_final: 0.7380 (mtm) REVERT: L 35 ASP cc_start: 0.7844 (t70) cc_final: 0.7627 (t0) REVERT: L 72 MET cc_start: 0.6845 (mmm) cc_final: 0.6345 (mmt) REVERT: L 98 SER cc_start: 0.8354 (p) cc_final: 0.7298 (p) REVERT: M 241 MET cc_start: 0.7985 (mmt) cc_final: 0.7669 (mmt) REVERT: M 292 ASN cc_start: 0.7207 (p0) cc_final: 0.6926 (p0) REVERT: M 427 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6912 (tpp-160) REVERT: M 446 LYS cc_start: 0.8667 (tttt) cc_final: 0.8149 (tttm) REVERT: C 292 ASN cc_start: 0.7620 (p0) cc_final: 0.7111 (p0) REVERT: G 35 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7722 (p) REVERT: G 144 PHE cc_start: 0.8230 (t80) cc_final: 0.7967 (t80) REVERT: G 241 MET cc_start: 0.8127 (mmt) cc_final: 0.7782 (mmt) REVERT: G 292 ASN cc_start: 0.7496 (p0) cc_final: 0.7096 (p0) REVERT: G 446 LYS cc_start: 0.8606 (tttt) cc_final: 0.8037 (tttm) outliers start: 69 outliers final: 55 residues processed: 524 average time/residue: 0.3233 time to fit residues: 266.8635 Evaluate side-chains 515 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 455 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 109 MET Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 427 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 27 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115677 restraints weight = 31880.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119416 restraints weight = 16619.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122032 restraints weight = 10531.518| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21728 Z= 0.181 Angle : 0.639 8.903 29458 Z= 0.312 Chirality : 0.045 0.191 3548 Planarity : 0.004 0.079 3608 Dihedral : 7.659 165.910 2998 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.89 % Allowed : 18.17 % Favored : 78.94 % 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: 2.29 (0.16), residues: 2736 helix: 2.32 (0.12), residues: 1766 sheet: 0.98 (0.30), residues: 270 loop : -0.38 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 227 HIS 0.017 0.001 HIS C 79 PHE 0.027 0.002 PHE M 210 TYR 0.026 0.002 TYR C 158 ARG 0.006 0.000 ARG J 130 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1443) hydrogen bonds : angle 4.19604 ( 4242) covalent geometry : bond 0.00426 (21728) covalent geometry : angle 0.63944 (29458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 472 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7904 (tp30) cc_final: 0.7466 (tp30) REVERT: H 40 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7698 (mtt180) REVERT: H 134 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8394 (mtpt) REVERT: D 27 SER cc_start: 0.8638 (t) cc_final: 0.8240 (t) REVERT: D 71 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7301 (p0) REVERT: D 127 MET cc_start: 0.8915 (mmm) cc_final: 0.8611 (tpp) REVERT: D 133 ARG cc_start: 0.7300 (mtt90) cc_final: 0.6928 (mtm-85) REVERT: E 72 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6437 (mmp) REVERT: E 98 SER cc_start: 0.8318 (p) cc_final: 0.7509 (p) REVERT: E 113 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7162 (tm-30) REVERT: E 126 ASP cc_start: 0.7881 (m-30) cc_final: 0.7555 (m-30) REVERT: F 50 GLN cc_start: 0.7815 (tt0) cc_final: 0.7557 (tt0) REVERT: F 72 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6674 (mmm) REVERT: F 82 ASN cc_start: 0.8473 (t0) cc_final: 0.8183 (t0) REVERT: I 241 MET cc_start: 0.8319 (tpp) cc_final: 0.7903 (mmt) REVERT: I 311 MET cc_start: 0.8815 (ptp) cc_final: 0.8511 (ptm) REVERT: I 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7673 (ptpt) REVERT: J 113 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7199 (tm-30) REVERT: J 114 LYS cc_start: 0.8518 (mttm) cc_final: 0.8225 (mtpp) REVERT: J 122 MET cc_start: 0.7636 (mtm) cc_final: 0.7403 (mtm) REVERT: L 23 GLU cc_start: 0.7769 (tp30) cc_final: 0.7450 (tp30) REVERT: L 35 ASP cc_start: 0.7803 (t70) cc_final: 0.7590 (t70) REVERT: L 50 GLN cc_start: 0.7990 (tt0) cc_final: 0.7526 (tt0) REVERT: L 72 MET cc_start: 0.6772 (mmm) cc_final: 0.6322 (mmt) REVERT: L 98 SER cc_start: 0.8429 (p) cc_final: 0.7346 (p) REVERT: M 241 MET cc_start: 0.8027 (mmt) cc_final: 0.7662 (mmt) REVERT: M 292 ASN cc_start: 0.6959 (p0) cc_final: 0.6728 (p0) REVERT: M 298 GLN cc_start: 0.8437 (mm110) cc_final: 0.8048 (mm-40) REVERT: M 388 ASP cc_start: 0.7376 (p0) cc_final: 0.7027 (p0) REVERT: M 427 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6935 (tpp-160) REVERT: M 446 LYS cc_start: 0.8667 (tttt) cc_final: 0.8171 (tttm) REVERT: C 292 ASN cc_start: 0.7653 (p0) cc_final: 0.7188 (p0) REVERT: G 35 VAL cc_start: 0.7999 (m) cc_final: 0.7760 (p) REVERT: G 241 MET cc_start: 0.8093 (mmt) cc_final: 0.7800 (mmt) REVERT: G 292 ASN cc_start: 0.7322 (p0) cc_final: 0.7010 (p0) REVERT: G 446 LYS cc_start: 0.8629 (tttt) cc_final: 0.8102 (tttm) outliers start: 65 outliers final: 55 residues processed: 524 average time/residue: 0.3140 time to fit residues: 256.0628 Evaluate side-chains 515 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 456 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 177 SER Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 427 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 381 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 191 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 GLN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112085 restraints weight = 32292.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116015 restraints weight = 16270.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118634 restraints weight = 10122.834| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 21728 Z= 0.232 Angle : 0.699 7.896 29458 Z= 0.343 Chirality : 0.047 0.212 3548 Planarity : 0.004 0.079 3608 Dihedral : 7.698 155.529 2998 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.21 % Allowed : 18.57 % Favored : 78.23 % 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: 1.99 (0.16), residues: 2736 helix: 2.14 (0.12), residues: 1766 sheet: 0.63 (0.30), residues: 270 loop : -0.51 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 276 HIS 0.004 0.001 HIS I 79 PHE 0.029 0.002 PHE G 210 TYR 0.011 0.001 TYR M 447 ARG 0.008 0.001 ARG J 130 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 1443) hydrogen bonds : angle 4.30844 ( 4242) covalent geometry : bond 0.00553 (21728) covalent geometry : angle 0.69925 (29458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 466 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7968 (tp30) cc_final: 0.7530 (tp30) REVERT: H 40 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7589 (mtt180) REVERT: H 134 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8372 (mtpt) REVERT: D 71 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7257 (p0) REVERT: D 133 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6933 (mtm-85) REVERT: E 50 GLN cc_start: 0.8121 (tt0) cc_final: 0.7686 (tt0) REVERT: E 72 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6595 (mmt) REVERT: E 98 SER cc_start: 0.8389 (p) cc_final: 0.7834 (p) REVERT: F 50 GLN cc_start: 0.7912 (tt0) cc_final: 0.7648 (tt0) REVERT: F 72 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6814 (mmp) REVERT: F 82 ASN cc_start: 0.8396 (t0) cc_final: 0.8140 (t0) REVERT: F 97 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7340 (mmtt) REVERT: I 292 ASN cc_start: 0.7779 (p0) cc_final: 0.7463 (p0) REVERT: I 389 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7836 (ptpt) REVERT: I 404 THR cc_start: 0.7980 (m) cc_final: 0.7733 (m) REVERT: A 23 GLU cc_start: 0.7675 (tp30) cc_final: 0.7416 (tp30) REVERT: L 23 GLU cc_start: 0.7727 (tp30) cc_final: 0.7462 (tp30) REVERT: L 35 ASP cc_start: 0.7856 (t70) cc_final: 0.7635 (t70) REVERT: L 50 GLN cc_start: 0.7910 (tt0) cc_final: 0.7473 (tt0) REVERT: L 72 MET cc_start: 0.6854 (mmm) cc_final: 0.6419 (mmt) REVERT: L 98 SER cc_start: 0.8520 (p) cc_final: 0.7524 (p) REVERT: M 174 LEU cc_start: 0.8814 (tt) cc_final: 0.8569 (tp) REVERT: M 241 MET cc_start: 0.8159 (mmt) cc_final: 0.7803 (mmt) REVERT: M 298 GLN cc_start: 0.8460 (mm110) cc_final: 0.7954 (mm-40) REVERT: M 388 ASP cc_start: 0.7442 (p0) cc_final: 0.7203 (p0) REVERT: M 427 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6911 (tpp-160) REVERT: M 446 LYS cc_start: 0.8724 (tttt) cc_final: 0.8197 (tttm) REVERT: C 292 ASN cc_start: 0.7776 (p0) cc_final: 0.7393 (p0) REVERT: C 410 GLU cc_start: 0.6322 (pt0) cc_final: 0.6023 (pt0) REVERT: G 35 VAL cc_start: 0.7896 (m) cc_final: 0.7684 (p) REVERT: G 241 MET cc_start: 0.8148 (mmt) cc_final: 0.7857 (mmt) REVERT: G 292 ASN cc_start: 0.7441 (p0) cc_final: 0.7126 (p0) REVERT: G 446 LYS cc_start: 0.8705 (tttt) cc_final: 0.8167 (tttm) outliers start: 72 outliers final: 61 residues processed: 523 average time/residue: 0.3450 time to fit residues: 279.9818 Evaluate side-chains 509 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 444 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 92 MET Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 272 THR Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 427 ARG Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 320 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9359 > 50: distance: 37 - 53: 5.484 distance: 41 - 64: 13.530 distance: 45 - 71: 23.741 distance: 48 - 53: 3.612 distance: 49 - 76: 17.168 distance: 53 - 54: 8.255 distance: 54 - 55: 6.411 distance: 54 - 57: 6.169 distance: 55 - 56: 7.641 distance: 55 - 64: 11.616 distance: 56 - 83: 7.266 distance: 57 - 58: 5.655 distance: 58 - 59: 6.547 distance: 58 - 60: 3.247 distance: 59 - 61: 4.260 distance: 60 - 62: 4.088 distance: 61 - 63: 4.198 distance: 62 - 63: 4.060 distance: 64 - 65: 12.002 distance: 65 - 66: 11.997 distance: 65 - 68: 12.381 distance: 66 - 67: 21.698 distance: 66 - 71: 13.367 distance: 67 - 89: 14.695 distance: 68 - 70: 9.159 distance: 71 - 72: 15.845 distance: 72 - 73: 8.378 distance: 72 - 75: 21.280 distance: 73 - 74: 3.351 distance: 73 - 76: 5.814 distance: 74 - 94: 15.494 distance: 76 - 77: 6.342 distance: 77 - 78: 6.257 distance: 77 - 80: 14.781 distance: 78 - 79: 5.378 distance: 78 - 83: 5.955 distance: 79 - 102: 20.554 distance: 80 - 81: 12.811 distance: 80 - 82: 14.011 distance: 83 - 84: 5.665 distance: 84 - 87: 7.363 distance: 85 - 86: 11.120 distance: 85 - 89: 5.881 distance: 87 - 88: 8.095 distance: 89 - 90: 9.650 distance: 90 - 91: 12.044 distance: 90 - 93: 7.501 distance: 91 - 94: 7.427 distance: 94 - 95: 5.788 distance: 95 - 96: 7.848 distance: 95 - 98: 5.706 distance: 98 - 100: 9.345 distance: 99 - 101: 6.436 distance: 102 - 103: 15.653 distance: 104 - 108: 17.019 distance: 108 - 109: 31.594 distance: 109 - 110: 8.159 distance: 109 - 112: 29.095 distance: 110 - 111: 13.274 distance: 110 - 115: 15.496 distance: 112 - 113: 14.002 distance: 115 - 116: 5.711 distance: 116 - 117: 3.682 distance: 116 - 119: 10.287 distance: 117 - 118: 10.673 distance: 117 - 122: 8.680 distance: 119 - 120: 7.250 distance: 119 - 121: 7.985