Starting phenix.real_space_refine on Sun Aug 24 16:13:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpr_14862/08_2025/7zpr_14862.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpr_14862/08_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_14862/08_2025/7zpr_14862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpr_14862/08_2025/7zpr_14862.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpr_14862/08_2025/7zpr_14862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpr_14862/08_2025/7zpr_14862.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 16 5.49 5 Mg 8 5.21 5 S 140 5.16 5 C 13782 2.51 5 N 3576 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21350 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 426, 3259 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 1 bond proxies already assigned to first conformer: 3325 Chain: "G" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3273 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.25 Number of scatterers: 21350 At special positions: 0 Unit cell: (95.9651, 110.921, 173.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 140 16.00 P 16 15.00 Mg 8 11.99 O 3824 8.00 N 3576 7.00 C 13782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 12 sheets defined 69.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 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: 2.65 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4195 1.33 - 1.45: 4835 1.45 - 1.57: 12413 1.57 - 1.69: 24 1.69 - 1.82: 261 Bond restraints: 21728 Sorted by residual: bond pdb=" N PRO H 123 " pdb=" CD PRO H 123 " ideal model delta sigma weight residual 1.473 1.729 -0.256 1.40e-02 5.10e+03 3.35e+02 bond pdb=" C4 ADP J 301 " pdb=" C5 ADP J 301 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5 ADP A1002 " pdb=" C6 ADP A1002 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 21723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 28501 2.16 - 4.32: 817 4.32 - 6.48: 113 6.48 - 8.64: 16 8.64 - 10.80: 11 Bond angle restraints: 29458 Sorted by residual: angle pdb=" C THR G 288 " pdb=" CA THR G 288 " pdb=" CB THR G 288 " ideal model delta sigma weight residual 110.42 119.31 -8.89 1.99e+00 2.53e-01 2.00e+01 angle pdb=" C THR M 288 " pdb=" CA THR M 288 " pdb=" CB THR M 288 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" C LEU G 296 " ideal model delta sigma weight residual 112.89 107.50 5.39 1.24e+00 6.50e-01 1.89e+01 angle pdb=" N LEU M 296 " pdb=" CA LEU M 296 " pdb=" C LEU M 296 " ideal model delta sigma weight residual 112.89 107.58 5.31 1.24e+00 6.50e-01 1.84e+01 angle pdb=" N LEU C 296 " pdb=" CA LEU C 296 " pdb=" C LEU C 296 " ideal model delta sigma weight residual 112.89 107.71 5.18 1.24e+00 6.50e-01 1.75e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 12514 33.64 - 67.28: 281 67.28 - 100.92: 16 100.92 - 134.56: 5 134.56 - 168.20: 6 Dihedral angle restraints: 12822 sinusoidal: 4956 harmonic: 7866 Sorted by residual: dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 131.80 168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 100.80 -160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP L 301 " pdb=" O5' ADP L 301 " pdb=" PA ADP L 301 " pdb=" O2A ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 100.02 -160.01 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3354 0.108 - 0.215: 188 0.215 - 0.322: 2 0.322 - 0.430: 0 0.430 - 0.537: 4 Chirality restraints: 3548 Sorted by residual: chirality pdb=" CA THR G 288 " pdb=" N THR G 288 " pdb=" C THR G 288 " pdb=" CB THR G 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.22e+00 chirality pdb=" CA THR M 288 " pdb=" N THR M 288 " pdb=" C THR M 288 " pdb=" CB THR M 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA THR C 288 " pdb=" N THR C 288 " pdb=" C THR C 288 " pdb=" CB THR C 288 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 ... (remaining 3545 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 92 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C MET M 92 " 0.041 2.00e-02 2.50e+03 pdb=" O MET M 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN M 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET G 92 " -0.041 2.00e-02 2.50e+03 pdb=" O MET G 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN G 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 122 " 0.032 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 123 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.026 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 141 2.56 - 3.21: 19848 3.21 - 3.85: 43220 3.85 - 4.50: 61039 4.50 - 5.14: 95532 Nonbonded interactions: 219780 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O3B ADP A1002 " model vdw 1.919 2.170 nonbonded pdb=" OD1 ASN H 82 " pdb=" ND2 ASN B 82 " model vdw 1.954 3.120 nonbonded pdb=" O2B ADP L 301 " pdb="MG MG L 302 " model vdw 1.977 2.170 nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 301 " pdb="MG MG E 302 " model vdw 1.988 2.170 ... (remaining 219775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 137) selection = (chain 'B' and resid 6 through 137) selection = (chain 'D' and resid 6 through 137) selection = (chain 'E' and resid 6 through 137) selection = (chain 'F' and resid 6 through 137) selection = (chain 'H' and resid 6 through 137) selection = (chain 'J' and resid 6 through 137) selection = (chain 'L' and resid 6 through 137) } ncs_group { reference = (chain 'C' and (resid 21 through 350 or resid 352 through 601)) selection = (chain 'G' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 501)) selection = (chain 'I' and (resid 21 through 350 or resid 352 through 601)) selection = (chain 'M' and (resid 21 through 122 or resid 132 through 350 or resid 352 throu \ gh 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.700 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- 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 : 9.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 1.16 % Favored : 97.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.15), residues: 2736 helix: 1.46 (0.12), residues: 1760 sheet: 1.61 (0.28), residues: 282 loop : -0.34 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 130 TYR 0.014 0.002 TYR F 70 PHE 0.026 0.001 PHE I 210 TRP 0.011 0.001 TRP M 337 HIS 0.005 0.001 HIS G 345 Details of bonding type rmsd covalent geometry : bond 0.00548 (21728) covalent geometry : angle 0.80015 (29458) hydrogen bonds : bond 0.18822 ( 1443) hydrogen bonds : angle 6.57781 ( 4242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 772 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7987 (tp30) cc_final: 0.7137 (tp30) REVERT: H 127 MET cc_start: 0.8929 (tpt) cc_final: 0.8175 (tpp) REVERT: D 110 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8189 (mtm180) REVERT: D 133 ARG cc_start: 0.7368 (mtt90) cc_final: 0.7027 (mtm-85) REVERT: E 29 SER cc_start: 0.7901 (m) cc_final: 0.7693 (p) REVERT: E 96 VAL cc_start: 0.8462 (t) cc_final: 0.8255 (t) REVERT: E 127 MET cc_start: 0.8340 (mmm) cc_final: 0.8094 (mmm) REVERT: I 92 MET cc_start: 0.7593 (ptt) cc_final: 0.7338 (ptt) REVERT: I 387 PHE cc_start: 0.7513 (t80) cc_final: 0.7042 (t80) REVERT: I 389 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7597 (ttmt) REVERT: I 420 ILE cc_start: 0.7474 (mt) cc_final: 0.7061 (mt) REVERT: I 447 TYR cc_start: 0.8776 (m-80) cc_final: 0.8502 (m-80) REVERT: A 23 GLU cc_start: 0.7777 (tp30) cc_final: 0.7219 (tp30) REVERT: A 133 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7215 (mtm180) REVERT: B 23 GLU cc_start: 0.7382 (tp30) cc_final: 0.7021 (tp30) REVERT: B 127 MET cc_start: 0.9040 (tpt) cc_final: 0.8792 (tpp) REVERT: B 133 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7041 (mtm-85) REVERT: J 122 MET cc_start: 0.7679 (mtp) cc_final: 0.6735 (mtm) REVERT: J 126 ASP cc_start: 0.7860 (m-30) cc_final: 0.7547 (m-30) REVERT: L 98 SER cc_start: 0.7307 (p) cc_final: 0.6758 (p) REVERT: L 122 MET cc_start: 0.7622 (mtp) cc_final: 0.6897 (mtm) REVERT: M 76 THR cc_start: 0.7360 (m) cc_final: 0.7106 (m) REVERT: M 93 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6898 (tp-100) REVERT: M 298 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: M 420 ILE cc_start: 0.7844 (mt) cc_final: 0.7506 (mt) REVERT: M 447 TYR cc_start: 0.8739 (m-80) cc_final: 0.8473 (m-80) REVERT: C 92 MET cc_start: 0.7635 (ptt) cc_final: 0.7376 (ptt) REVERT: C 93 GLN cc_start: 0.7529 (tp-100) cc_final: 0.7236 (tp-100) REVERT: C 108 TYR cc_start: 0.7607 (t80) cc_final: 0.7367 (t80) REVERT: C 136 ARG cc_start: 0.5225 (ttt180) cc_final: 0.4998 (tpt170) REVERT: C 387 PHE cc_start: 0.7615 (t80) cc_final: 0.7199 (t80) REVERT: C 389 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7642 (ttmt) REVERT: C 420 ILE cc_start: 0.7642 (mt) cc_final: 0.7245 (mt) REVERT: C 447 TYR cc_start: 0.8841 (m-80) cc_final: 0.8597 (m-80) REVERT: C 449 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6444 (mt-10) REVERT: G 93 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6853 (tp-100) REVERT: G 277 LEU cc_start: 0.8276 (tp) cc_final: 0.7862 (tt) REVERT: G 298 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: G 400 THR cc_start: 0.8878 (m) cc_final: 0.8573 (m) REVERT: G 420 ILE cc_start: 0.7862 (mt) cc_final: 0.7613 (mt) REVERT: G 447 TYR cc_start: 0.8782 (m-80) cc_final: 0.8549 (m-80) outliers start: 20 outliers final: 2 residues processed: 782 average time/residue: 0.1573 time to fit residues: 184.9330 Evaluate side-chains 479 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 473 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 93 GLN M 262 HIS C 78 GLN C 282 GLN C 301 GLN G 345 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119498 restraints weight = 30160.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123255 restraints weight = 16140.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125757 restraints weight = 10295.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127312 restraints weight = 7438.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128480 restraints weight = 5964.808| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21728 Z= 0.233 Angle : 0.734 8.381 29458 Z= 0.367 Chirality : 0.048 0.169 3548 Planarity : 0.005 0.048 3608 Dihedral : 9.752 179.729 3010 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.98 % Favored : 97.95 % Rotamer: Outliers : 3.16 % Allowed : 11.53 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.16), residues: 2736 helix: 1.89 (0.12), residues: 1782 sheet: 1.31 (0.27), residues: 274 loop : -0.14 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 427 TYR 0.012 0.002 TYR G 447 PHE 0.040 0.003 PHE I 210 TRP 0.019 0.002 TRP G 257 HIS 0.008 0.002 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00534 (21728) covalent geometry : angle 0.73393 (29458) hydrogen bonds : bond 0.04663 ( 1443) hydrogen bonds : angle 4.48726 ( 4242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 513 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7910 (tp30) cc_final: 0.7131 (tp30) REVERT: H 40 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7503 (mtt180) REVERT: H 134 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8285 (mtpt) REVERT: D 40 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7931 (mtt180) REVERT: D 107 PHE cc_start: 0.8499 (m-80) cc_final: 0.8258 (m-10) REVERT: D 133 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6931 (mtm-85) REVERT: E 72 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6289 (mmm) REVERT: F 122 MET cc_start: 0.7550 (mtm) cc_final: 0.6772 (mtm) REVERT: F 126 ASP cc_start: 0.8049 (m-30) cc_final: 0.7729 (m-30) REVERT: I 139 LYS cc_start: 0.7292 (ttpp) cc_final: 0.6740 (ttmt) REVERT: I 217 PHE cc_start: 0.8136 (t80) cc_final: 0.7931 (t80) REVERT: I 389 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7517 (ttmt) REVERT: I 420 ILE cc_start: 0.8497 (mt) cc_final: 0.8182 (mt) REVERT: A 23 GLU cc_start: 0.7711 (tp30) cc_final: 0.7355 (tp30) REVERT: A 133 ARG cc_start: 0.7439 (mtt90) cc_final: 0.7037 (mtm-85) REVERT: B 23 GLU cc_start: 0.7629 (tp30) cc_final: 0.7349 (tp30) REVERT: B 127 MET cc_start: 0.8877 (tpt) cc_final: 0.8675 (tpp) REVERT: B 133 ARG cc_start: 0.7360 (mtt90) cc_final: 0.7122 (mtm-85) REVERT: L 23 GLU cc_start: 0.7702 (tp30) cc_final: 0.7498 (tp30) REVERT: L 35 ASP cc_start: 0.7821 (t70) cc_final: 0.7557 (t70) REVERT: L 122 MET cc_start: 0.7569 (mtp) cc_final: 0.6893 (mtm) REVERT: L 126 ASP cc_start: 0.7528 (m-30) cc_final: 0.7295 (m-30) REVERT: M 193 MET cc_start: 0.8140 (mmt) cc_final: 0.7927 (mmt) REVERT: M 241 MET cc_start: 0.8145 (mmt) cc_final: 0.7818 (mmt) REVERT: C 139 LYS cc_start: 0.7334 (ttpp) cc_final: 0.7008 (ttmt) REVERT: C 292 ASN cc_start: 0.7471 (p0) cc_final: 0.7150 (p0) REVERT: C 295 ASP cc_start: 0.6220 (m-30) cc_final: 0.5815 (m-30) REVERT: C 299 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: C 388 ASP cc_start: 0.7154 (p0) cc_final: 0.6846 (p0) REVERT: C 389 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7501 (ttmt) REVERT: C 420 ILE cc_start: 0.8550 (mt) cc_final: 0.8264 (mt) REVERT: G 228 ARG cc_start: 0.6840 (ptp-110) cc_final: 0.6605 (ptp-110) REVERT: G 241 MET cc_start: 0.8059 (mmt) cc_final: 0.7771 (mmt) REVERT: G 298 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7478 (mt0) outliers start: 71 outliers final: 52 residues processed: 561 average time/residue: 0.1438 time to fit residues: 125.9077 Evaluate side-chains 496 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 441 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 228 ARG Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 298 GLN Chi-restraints excluded: chain M residue 320 THR Chi-restraints excluded: chain M residue 344 LYS Chi-restraints excluded: chain M residue 347 VAL Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 298 GLN Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 344 LYS Chi-restraints excluded: chain G residue 428 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8282 > 50: distance: 77 - 103: 8.014 distance: 85 - 110: 10.970 distance: 91 - 96: 5.665 distance: 92 - 117: 5.546 distance: 98 - 99: 4.930 distance: 99 - 126: 6.669 distance: 100 - 102: 9.273 distance: 103 - 104: 4.132 distance: 104 - 105: 3.241 distance: 104 - 107: 3.410 distance: 105 - 110: 3.630 distance: 107 - 108: 7.748 distance: 107 - 109: 16.062 distance: 111 - 112: 4.732 distance: 111 - 114: 6.695 distance: 112 - 113: 5.626 distance: 112 - 117: 6.994 distance: 113 - 140: 3.550 distance: 114 - 115: 5.924 distance: 114 - 116: 11.815 distance: 117 - 118: 4.287 distance: 118 - 119: 3.341 distance: 118 - 121: 3.585 distance: 120 - 145: 13.544 distance: 121 - 122: 11.996 distance: 122 - 123: 10.742 distance: 123 - 124: 5.919 distance: 124 - 125: 10.263 distance: 127 - 128: 3.285 distance: 127 - 130: 3.792 distance: 128 - 129: 8.445 distance: 129 - 153: 20.687 distance: 130 - 131: 9.671 distance: 132 - 133: 4.085 distance: 133 - 136: 5.976 distance: 134 - 135: 3.408 distance: 135 - 161: 34.310 distance: 136 - 137: 5.877 distance: 137 - 138: 11.744 distance: 137 - 139: 6.177 distance: 140 - 141: 9.083 distance: 141 - 142: 11.381 distance: 141 - 144: 8.035 distance: 142 - 143: 12.166 distance: 142 - 145: 4.183 distance: 143 - 168: 26.131 distance: 145 - 146: 6.237 distance: 146 - 147: 6.631 distance: 146 - 149: 5.867 distance: 147 - 148: 3.989 distance: 147 - 153: 5.767 distance: 148 - 175: 10.234 distance: 149 - 150: 8.060 distance: 149 - 151: 7.370 distance: 150 - 152: 11.164 distance: 153 - 154: 9.957 distance: 154 - 155: 12.191 distance: 155 - 156: 15.747 distance: 155 - 161: 34.488 distance: 156 - 181: 18.774 distance: 157 - 158: 6.780 distance: 157 - 159: 5.851 distance: 158 - 160: 12.786 distance: 161 - 162: 35.245 distance: 162 - 163: 3.643 distance: 162 - 165: 17.156 distance: 163 - 164: 8.768 distance: 163 - 168: 8.891 distance: 164 - 185: 16.209 distance: 165 - 166: 17.083 distance: 165 - 167: 17.377