Starting phenix.real_space_refine on Fri Jun 28 10:16:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/06_2024/7zpo_14859_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 16 5.49 5 Mg 2 5.21 5 S 98 5.16 5 C 9659 2.51 5 N 2546 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "I PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 149": "OE1" <-> "OE2" Residue "I PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "I ASP 295": "OD1" <-> "OD2" Residue "I PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 393": "OE1" <-> "OE2" Residue "I ASP 450": "OD1" <-> "OD2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 295": "OD1" <-> "OD2" Residue "M PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15102 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "I" Number of atoms: 3347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 436, 3339 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 420} Chain breaks: 2 bond proxies already assigned to first conformer: 3407 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1003 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "L" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain: "M" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3353 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 2 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' K': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {' K': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.59, per 1000 atoms: 0.64 Number of scatterers: 15102 At special positions: 0 Unit cell: (110.523, 93.903, 122.157, 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 2 19.00 S 98 16.00 P 16 15.00 Mg 2 11.99 O 2779 8.00 N 2546 7.00 C 9659 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 10 sheets defined 57.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'H' and resid 15 through 26 removed outlier: 3.512A pdb=" N ALA H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.983A pdb=" N GLY H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 65 Processing helix chain 'H' and resid 81 through 93 Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 123 through 136 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 123 through 136 Processing helix chain 'F' and resid 15 through 27 Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 81 through 94 Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 123 through 136 Processing helix chain 'I' and resid 24 through 44 Proline residue: I 38 - end of helix removed outlier: 3.618A pdb=" N THR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'I' and resid 76 through 79 No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 82 through 121 Processing helix chain 'I' and resid 134 through 164 removed outlier: 3.964A 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 166 through 181 removed outlier: 3.512A pdb=" N MET I 170 " --> pdb=" O TRP I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 200 through 213 Processing helix chain 'I' and resid 217 through 226 Processing helix chain 'I' and resid 236 through 260 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 272 through 286 Processing helix chain 'I' and resid 301 through 313 Processing helix chain 'I' and resid 326 through 341 Processing helix chain 'I' and resid 355 through 382 Processing helix chain 'I' and resid 387 through 398 Processing helix chain 'I' and resid 413 through 436 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 15 through 26 removed outlier: 3.813A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.702A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.519A pdb=" N GLU B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'J' and resid 15 through 26 Processing helix chain 'J' and resid 38 through 43 Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 59 through 64 Processing helix chain 'J' and resid 81 through 94 Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 123 through 136 removed outlier: 3.551A pdb=" N ALA J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 27 removed outlier: 3.575A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 45 Processing helix chain 'L' and resid 59 through 65 removed outlier: 3.593A pdb=" N ALA L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 Processing helix chain 'L' and resid 106 through 115 Processing helix chain 'L' and resid 123 through 136 removed outlier: 3.631A pdb=" N LYS L 134 " --> pdb=" O ARG L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 44 removed outlier: 3.550A pdb=" N VAL M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Proline residue: M 38 - end of helix removed outlier: 3.567A pdb=" N THR M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 66 Processing helix chain 'M' and resid 76 through 79 No H-bonds generated for 'chain 'M' and resid 76 through 79' Processing helix chain 'M' and resid 82 through 121 Processing helix chain 'M' and resid 134 through 164 removed outlier: 4.008A 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 166 through 181 Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing helix chain 'M' and resid 200 through 215 removed outlier: 3.514A pdb=" N LEU M 215 " --> pdb=" O ILE M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 226 Processing helix chain 'M' and resid 236 through 260 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 272 through 286 removed outlier: 3.536A pdb=" N TRP M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 313 Processing helix chain 'M' and resid 326 through 341 Processing helix chain 'M' and resid 355 through 382 removed outlier: 3.507A pdb=" N LEU M 381 " --> pdb=" O PHE M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 399 Processing helix chain 'M' and resid 413 through 438 Proline residue: M 430 - end of helix removed outlier: 3.529A pdb=" N TYR M 435 " --> pdb=" O LEU M 431 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 119 through 122 removed outlier: 6.771A pdb=" N GLN H 50 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP H 35 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE H 52 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 119 through 121 removed outlier: 4.081A pdb=" N MET D 72 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN D 30 " --> pdb=" O PHE D 8 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 10 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU D 32 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN D 50 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASP D 35 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 52 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 119 through 122 removed outlier: 6.387A pdb=" N VAL E 73 " --> pdb=" O TRP E 100 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LYS E 102 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 75 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET E 72 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 30 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL E 10 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 32 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN E 50 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASP E 35 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 52 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.542A pdb=" N HIS F 119 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN F 30 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL F 10 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 32 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN F 50 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP F 35 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 52 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 346 through 348 removed outlier: 4.436A pdb=" N VAL I 346 " --> pdb=" O VAL I 353 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.642A pdb=" N MET A 72 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN A 30 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL A 10 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU A 32 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A 50 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ASP A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 52 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.214A pdb=" N VAL B 73 " --> pdb=" O TRP B 100 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LYS B 102 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE B 75 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 72 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 30 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 10 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 32 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN B 50 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASP B 35 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 52 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 119 through 121 removed outlier: 6.234A pdb=" N VAL J 73 " --> pdb=" O TRP J 100 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LYS J 102 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE J 75 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET J 72 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN J 30 " --> pdb=" O PHE J 8 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL J 10 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU J 32 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN J 50 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASP J 35 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE J 52 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 119 through 121 removed outlier: 6.478A pdb=" N GLN L 30 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL L 10 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU L 32 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN L 50 " --> pdb=" O ALA L 33 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASP L 35 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE L 52 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 346 through 348 removed outlier: 4.343A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2394 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: 4.74 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4805 1.34 - 1.46: 3414 1.46 - 1.58: 6924 1.58 - 1.70: 24 1.70 - 1.82: 178 Bond restraints: 15345 Sorted by residual: bond pdb=" C2' LMT M 502 " pdb=" C3' LMT M 502 " ideal model delta sigma weight residual 1.524 1.583 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C7 LMT M 503 " pdb=" C8 LMT M 503 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C3' LMT M 503 " pdb=" O3' LMT M 503 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C3' LMT I 503 " pdb=" O3' LMT I 503 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C7 LMT I 501 " pdb=" C8 LMT I 501 " ideal model delta sigma weight residual 1.529 1.488 0.041 2.00e-02 2.50e+03 4.16e+00 ... (remaining 15340 not shown) Histogram of bond angle deviations from ideal: 99.97 - 107.25: 452 107.25 - 114.53: 9466 114.53 - 121.82: 7878 121.82 - 129.10: 2868 129.10 - 136.38: 110 Bond angle restraints: 20774 Sorted by residual: angle pdb=" C ARG I 439 " pdb=" CA ARG I 439 " pdb=" CB ARG I 439 " ideal model delta sigma weight residual 110.81 117.66 -6.85 1.27e+00 6.20e-01 2.91e+01 angle pdb=" C2 LMT I 501 " pdb=" C3 LMT I 501 " pdb=" C4 LMT I 501 " ideal model delta sigma weight residual 117.09 107.12 9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 LMT M 503 " pdb=" C3 LMT M 503 " pdb=" C4 LMT M 503 " ideal model delta sigma weight residual 117.09 107.33 9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT M 502 " pdb=" C3 LMT M 502 " pdb=" C4 LMT M 502 " ideal model delta sigma weight residual 117.09 107.34 9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT I 503 " pdb=" C3 LMT I 503 " pdb=" C4 LMT I 503 " ideal model delta sigma weight residual 117.09 107.37 9.72 3.00e+00 1.11e-01 1.05e+01 ... (remaining 20769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 9085 35.78 - 71.57: 160 71.57 - 107.35: 19 107.35 - 143.14: 18 143.14 - 178.92: 4 Dihedral angle restraints: 9286 sinusoidal: 3786 harmonic: 5500 Sorted by residual: dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 118.92 -178.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP H 301 " pdb=" O5' ADP H 301 " pdb=" PA ADP H 301 " pdb=" O2A ADP H 301 " ideal model delta sinusoidal sigma weight residual 300.00 138.58 161.42 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP F 301 " pdb=" O3A ADP F 301 " pdb=" PA ADP F 301 " pdb=" PB ADP F 301 " ideal model delta sinusoidal sigma weight residual -60.00 91.36 -151.36 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 9283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2004 0.052 - 0.105: 399 0.105 - 0.157: 80 0.157 - 0.209: 10 0.209 - 0.262: 6 Chirality restraints: 2499 Sorted by residual: chirality pdb=" C3B LMT M 502 " pdb=" C2B LMT M 502 " pdb=" C4B LMT M 502 " pdb=" O3B LMT M 502 " both_signs ideal model delta sigma weight residual False 2.50 2.24 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C4' LMT I 503 " pdb=" C3' LMT I 503 " pdb=" C5' LMT I 503 " pdb=" O1B LMT I 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C4' LMT I 501 " pdb=" C3' LMT I 501 " pdb=" C5' LMT I 501 " pdb=" O1B LMT I 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2496 not shown) Planarity restraints: 2541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 94 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ILE I 94 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE I 94 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY I 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET J 122 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.94e+00 pdb=" N PRO J 123 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO J 123 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 123 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 130 " 0.116 9.50e-02 1.11e+02 5.24e-02 2.12e+00 pdb=" NE ARG L 130 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG L 130 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG L 130 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 130 " 0.000 2.00e-02 2.50e+03 ... (remaining 2538 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 206 2.67 - 3.29: 16674 3.29 - 3.91: 30914 3.91 - 4.52: 41225 4.52 - 5.14: 62876 Nonbonded interactions: 151895 Sorted by model distance: nonbonded pdb=" O3A ADP E 301 " pdb="MG MG E 302 " model vdw 2.053 2.170 nonbonded pdb=" O2A ADP E 301 " pdb="MG MG E 302 " model vdw 2.059 2.170 nonbonded pdb=" O3A ADP D1001 " pdb="MG MG D1002 " model vdw 2.084 2.170 nonbonded pdb=" OG SER I 386 " pdb=" OD1 ASP I 388 " model vdw 2.175 2.440 nonbonded pdb=" OE2 GLU I 393 " pdb=" OG1 THR I 408 " model vdw 2.201 2.440 ... (remaining 151890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 137 or resid 1001)) selection = (chain 'D' and (resid 6 through 137 or resid 1001)) selection = (chain 'E' and (resid 6 through 137 or resid 301)) selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = (chain 'L' and (resid 6 through 137 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 7 through 350 or resid 352 through 455 or resid 503)) selection = (chain 'M' and (resid 7 through 16 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.310 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 44.760 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.004 0.059 15345 Z= 0.232 Angle : 0.734 9.967 20774 Z= 0.344 Chirality : 0.046 0.262 2499 Planarity : 0.003 0.052 2541 Dihedral : 16.164 178.923 5728 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.71 (0.19), residues: 1905 helix: 1.68 (0.15), residues: 1166 sheet: 1.89 (0.29), residues: 280 loop : -0.73 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 355 HIS 0.004 0.001 HIS E 58 PHE 0.024 0.001 PHE M 210 TYR 0.011 0.001 TYR I 435 ARG 0.013 0.001 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 ASN cc_start: 0.7120 (t0) cc_final: 0.6452 (t0) REVERT: D 52 ILE cc_start: 0.6500 (mt) cc_final: 0.6250 (tp) REVERT: D 127 MET cc_start: 0.8203 (mmp) cc_final: 0.7971 (mmp) REVERT: F 7 GLN cc_start: 0.6646 (tt0) cc_final: 0.6263 (pt0) REVERT: F 70 TYR cc_start: 0.6985 (m-80) cc_final: 0.6651 (m-80) REVERT: I 295 ASP cc_start: 0.7681 (t0) cc_final: 0.6603 (t0) REVERT: I 387 PHE cc_start: 0.7432 (t80) cc_final: 0.7192 (t80) REVERT: I 449 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 121 ILE cc_start: 0.8290 (mm) cc_final: 0.8081 (mp) REVERT: L 70 TYR cc_start: 0.7303 (m-80) cc_final: 0.7098 (m-80) REVERT: L 81 VAL cc_start: 0.7928 (p) cc_final: 0.7709 (m) REVERT: L 113 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7458 (mt0) REVERT: L 127 MET cc_start: 0.8059 (mmt) cc_final: 0.7811 (mmp) REVERT: M 94 ILE cc_start: 0.8781 (mm) cc_final: 0.8557 (mt) REVERT: M 108 TYR cc_start: 0.8119 (t80) cc_final: 0.7776 (t80) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.2819 time to fit residues: 208.8818 Evaluate side-chains 368 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 172 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS E 108 GLN E 119 HIS F 25 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN I 275 GLN A 58 HIS ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS M 118 GLN M 182 ASN ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15345 Z= 0.217 Angle : 0.656 9.495 20774 Z= 0.308 Chirality : 0.045 0.229 2499 Planarity : 0.004 0.047 2541 Dihedral : 12.880 175.003 2363 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.92 % Allowed : 10.06 % Favored : 88.01 % 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: 2.08 (0.19), residues: 1905 helix: 2.01 (0.15), residues: 1170 sheet: 2.00 (0.30), residues: 280 loop : -0.74 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 100 HIS 0.005 0.001 HIS M 176 PHE 0.040 0.002 PHE I 210 TYR 0.011 0.001 TYR H 70 ARG 0.010 0.001 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 395 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 GLU cc_start: 0.7808 (tp30) cc_final: 0.7598 (tp30) REVERT: D 133 ARG cc_start: 0.7666 (mmm160) cc_final: 0.6762 (ttt180) REVERT: E 129 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7391 (mp) REVERT: L 25 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7148 (pp30) REVERT: L 65 LEU cc_start: 0.7644 (mp) cc_final: 0.7434 (mt) REVERT: M 292 ASN cc_start: 0.8366 (p0) cc_final: 0.7907 (p0) REVERT: M 295 ASP cc_start: 0.7589 (t0) cc_final: 0.7016 (t0) outliers start: 30 outliers final: 23 residues processed: 415 average time/residue: 0.2676 time to fit residues: 160.7810 Evaluate side-chains 369 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 344 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 119 HIS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 388 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 0.0770 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN D 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 119 HIS ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 HIS ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** L 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15345 Z= 0.267 Angle : 0.650 7.798 20774 Z= 0.306 Chirality : 0.045 0.257 2499 Planarity : 0.004 0.041 2541 Dihedral : 10.673 160.385 2363 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.95 % Allowed : 13.46 % Favored : 83.59 % 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: 2.20 (0.19), residues: 1905 helix: 2.17 (0.15), residues: 1163 sheet: 1.90 (0.30), residues: 278 loop : -0.70 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 100 HIS 0.004 0.001 HIS I 79 PHE 0.032 0.001 PHE I 210 TYR 0.009 0.001 TYR J 70 ARG 0.014 0.001 ARG J 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 381 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7296 (mttp) REVERT: D 105 ASP cc_start: 0.7458 (p0) cc_final: 0.7242 (p0) REVERT: E 129 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7736 (mt) REVERT: F 61 THR cc_start: 0.7343 (m) cc_final: 0.7065 (m) REVERT: F 65 LEU cc_start: 0.7635 (mp) cc_final: 0.7106 (mt) REVERT: B 105 ASP cc_start: 0.7620 (p0) cc_final: 0.7220 (p0) REVERT: B 133 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6735 (mmt-90) REVERT: J 134 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7698 (mtmt) REVERT: L 25 GLN cc_start: 0.7391 (pp30) cc_final: 0.7004 (pp30) REVERT: L 80 ASP cc_start: 0.7451 (t0) cc_final: 0.7140 (t70) REVERT: L 113 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8052 (tp40) REVERT: M 250 LEU cc_start: 0.8249 (tt) cc_final: 0.7768 (mt) REVERT: M 295 ASP cc_start: 0.7653 (t0) cc_final: 0.7032 (t0) REVERT: M 298 GLN cc_start: 0.7085 (mt0) cc_final: 0.6794 (mp10) REVERT: M 341 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7035 (mmm160) outliers start: 46 outliers final: 31 residues processed: 404 average time/residue: 0.2802 time to fit residues: 163.1012 Evaluate side-chains 379 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 347 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 293 SER Chi-restraints excluded: chain M residue 297 THR Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15345 Z= 0.167 Angle : 0.596 10.567 20774 Z= 0.276 Chirality : 0.042 0.189 2499 Planarity : 0.003 0.043 2541 Dihedral : 9.600 150.328 2363 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.24 % Allowed : 15.45 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.19), residues: 1905 helix: 2.26 (0.15), residues: 1163 sheet: 2.07 (0.31), residues: 272 loop : -0.78 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 100 HIS 0.003 0.001 HIS M 176 PHE 0.031 0.001 PHE I 210 TYR 0.005 0.001 TYR A 70 ARG 0.006 0.000 ARG F 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 374 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7211 (mttp) REVERT: E 11 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8685 (mp) REVERT: F 26 ASP cc_start: 0.7438 (m-30) cc_final: 0.7088 (m-30) REVERT: F 93 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6392 (mm-30) REVERT: I 295 ASP cc_start: 0.7602 (t0) cc_final: 0.7214 (t0) REVERT: A 88 THR cc_start: 0.9000 (m) cc_final: 0.8781 (m) REVERT: A 105 ASP cc_start: 0.7369 (t70) cc_final: 0.7117 (t70) REVERT: B 7 GLN cc_start: 0.6761 (tt0) cc_final: 0.6451 (tt0) REVERT: B 129 ILE cc_start: 0.8868 (mm) cc_final: 0.8652 (mt) REVERT: J 68 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6970 (p0) REVERT: L 65 LEU cc_start: 0.7828 (mp) cc_final: 0.7593 (mp) REVERT: L 80 ASP cc_start: 0.7543 (t0) cc_final: 0.7236 (t70) REVERT: L 113 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8065 (tp40) REVERT: M 250 LEU cc_start: 0.8232 (tt) cc_final: 0.7766 (mt) REVERT: M 292 ASN cc_start: 0.8514 (p0) cc_final: 0.8043 (p0) REVERT: M 295 ASP cc_start: 0.7692 (t0) cc_final: 0.7209 (t0) REVERT: M 341 ARG cc_start: 0.7410 (mtp85) cc_final: 0.7002 (mmm160) outliers start: 35 outliers final: 26 residues processed: 395 average time/residue: 0.2701 time to fit residues: 153.9917 Evaluate side-chains 377 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 349 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 388 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 GLN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15345 Z= 0.265 Angle : 0.639 10.276 20774 Z= 0.299 Chirality : 0.044 0.198 2499 Planarity : 0.004 0.048 2541 Dihedral : 9.002 128.534 2363 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.01 % Allowed : 15.51 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1905 helix: 2.15 (0.15), residues: 1164 sheet: 1.87 (0.30), residues: 276 loop : -0.77 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 166 HIS 0.004 0.001 HIS I 79 PHE 0.030 0.001 PHE I 210 TYR 0.009 0.001 TYR A 70 ARG 0.010 0.001 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 359 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7200 (mttp) REVERT: H 118 ASP cc_start: 0.7211 (m-30) cc_final: 0.6930 (m-30) REVERT: D 37 ASN cc_start: 0.7731 (t0) cc_final: 0.7367 (t0) REVERT: E 11 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8724 (mp) REVERT: E 74 MET cc_start: 0.7941 (tpp) cc_final: 0.7556 (tpp) REVERT: F 64 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7035 (pt0) REVERT: I 57 ASP cc_start: 0.7320 (m-30) cc_final: 0.7039 (m-30) REVERT: I 136 ARG cc_start: 0.7257 (ttt-90) cc_final: 0.6826 (ttp-170) REVERT: I 151 ILE cc_start: 0.9053 (mt) cc_final: 0.8851 (mp) REVERT: I 292 ASN cc_start: 0.8429 (p0) cc_final: 0.8091 (p0) REVERT: B 37 ASN cc_start: 0.7247 (t0) cc_final: 0.6710 (t0) REVERT: B 105 ASP cc_start: 0.7631 (p0) cc_final: 0.7188 (p0) REVERT: B 133 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7282 (ttt180) REVERT: J 68 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6916 (p0) REVERT: M 151 ILE cc_start: 0.9033 (mt) cc_final: 0.8818 (mp) REVERT: M 295 ASP cc_start: 0.7496 (t0) cc_final: 0.7279 (t0) REVERT: M 341 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7043 (mmm160) outliers start: 47 outliers final: 34 residues processed: 387 average time/residue: 0.2714 time to fit residues: 152.0050 Evaluate side-chains 363 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15345 Z= 0.169 Angle : 0.590 7.347 20774 Z= 0.273 Chirality : 0.042 0.194 2499 Planarity : 0.003 0.047 2541 Dihedral : 8.169 114.725 2363 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.69 % Allowed : 16.09 % Favored : 81.22 % 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: 2.31 (0.19), residues: 1905 helix: 2.30 (0.15), residues: 1164 sheet: 1.98 (0.31), residues: 276 loop : -0.82 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 166 HIS 0.003 0.001 HIS M 176 PHE 0.028 0.001 PHE I 210 TYR 0.024 0.001 TYR I 158 ARG 0.011 0.000 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 358 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7242 (mttp) REVERT: E 11 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 74 MET cc_start: 0.7874 (tpp) cc_final: 0.7492 (tpp) REVERT: F 26 ASP cc_start: 0.7314 (m-30) cc_final: 0.6895 (m-30) REVERT: I 57 ASP cc_start: 0.7335 (m-30) cc_final: 0.7060 (m-30) REVERT: I 136 ARG cc_start: 0.7212 (ttt-90) cc_final: 0.6807 (ttp-170) REVERT: I 250 LEU cc_start: 0.8119 (tt) cc_final: 0.7689 (mt) REVERT: I 292 ASN cc_start: 0.8378 (p0) cc_final: 0.8043 (p0) REVERT: B 37 ASN cc_start: 0.7198 (t0) cc_final: 0.6673 (t0) REVERT: B 105 ASP cc_start: 0.7660 (p0) cc_final: 0.7143 (p0) REVERT: J 68 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6842 (p0) REVERT: L 65 LEU cc_start: 0.7813 (mp) cc_final: 0.7605 (mp) REVERT: M 250 LEU cc_start: 0.8229 (tt) cc_final: 0.7736 (mt) REVERT: M 292 ASN cc_start: 0.8526 (p0) cc_final: 0.8027 (p0) REVERT: M 341 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6856 (mmm160) outliers start: 42 outliers final: 30 residues processed: 385 average time/residue: 0.2663 time to fit residues: 148.9904 Evaluate side-chains 358 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 326 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 chunk 183 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15345 Z= 0.146 Angle : 0.579 10.515 20774 Z= 0.267 Chirality : 0.041 0.202 2499 Planarity : 0.003 0.043 2541 Dihedral : 7.343 100.370 2363 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.63 % Allowed : 16.86 % Favored : 80.51 % 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 (0.19), residues: 1905 helix: 2.38 (0.15), residues: 1164 sheet: 2.08 (0.31), residues: 270 loop : -0.87 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 166 HIS 0.002 0.001 HIS M 176 PHE 0.027 0.001 PHE I 210 TYR 0.023 0.001 TYR I 158 ARG 0.007 0.000 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 354 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 ASN cc_start: 0.7697 (t0) cc_final: 0.7338 (t0) REVERT: E 11 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8661 (mp) REVERT: F 26 ASP cc_start: 0.7240 (m-30) cc_final: 0.6764 (m-30) REVERT: I 57 ASP cc_start: 0.7254 (m-30) cc_final: 0.6984 (m-30) REVERT: I 136 ARG cc_start: 0.7236 (ttt-90) cc_final: 0.6823 (ttp-170) REVERT: I 250 LEU cc_start: 0.8095 (tt) cc_final: 0.7677 (mt) REVERT: B 37 ASN cc_start: 0.7177 (t0) cc_final: 0.6533 (t0) REVERT: L 65 LEU cc_start: 0.7737 (mp) cc_final: 0.7533 (mp) REVERT: M 151 ILE cc_start: 0.8985 (mt) cc_final: 0.8749 (mp) REVERT: M 250 LEU cc_start: 0.8213 (tt) cc_final: 0.7715 (mt) REVERT: M 292 ASN cc_start: 0.8487 (p0) cc_final: 0.8032 (p0) REVERT: M 341 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6829 (mmm160) outliers start: 41 outliers final: 28 residues processed: 381 average time/residue: 0.2591 time to fit residues: 144.6507 Evaluate side-chains 368 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 339 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 293 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 0.0060 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN B 108 GLN B 119 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN M 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15345 Z= 0.156 Angle : 0.584 9.965 20774 Z= 0.271 Chirality : 0.042 0.192 2499 Planarity : 0.003 0.043 2541 Dihedral : 7.010 97.489 2363 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.12 % Allowed : 17.12 % Favored : 80.77 % 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: 2.42 (0.19), residues: 1905 helix: 2.39 (0.15), residues: 1169 sheet: 2.11 (0.31), residues: 270 loop : -0.85 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 166 HIS 0.002 0.001 HIS I 79 PHE 0.027 0.001 PHE I 210 TYR 0.023 0.001 TYR I 158 ARG 0.007 0.000 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 353 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 118 ASP cc_start: 0.7105 (m-30) cc_final: 0.6848 (m-30) REVERT: E 11 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (mp) REVERT: E 86 LEU cc_start: 0.9127 (tp) cc_final: 0.8845 (tp) REVERT: F 26 ASP cc_start: 0.7245 (m-30) cc_final: 0.6801 (m-30) REVERT: I 57 ASP cc_start: 0.7340 (m-30) cc_final: 0.7063 (m-30) REVERT: I 136 ARG cc_start: 0.7226 (ttt-90) cc_final: 0.6720 (ttp80) REVERT: I 250 LEU cc_start: 0.8069 (tt) cc_final: 0.7654 (mt) REVERT: B 37 ASN cc_start: 0.7184 (t0) cc_final: 0.6605 (t0) REVERT: M 250 LEU cc_start: 0.8212 (tt) cc_final: 0.7710 (mt) REVERT: M 292 ASN cc_start: 0.8519 (p0) cc_final: 0.8290 (p0) REVERT: M 341 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6863 (mmm160) outliers start: 33 outliers final: 27 residues processed: 374 average time/residue: 0.2727 time to fit residues: 146.7973 Evaluate side-chains 364 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 336 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 119 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15345 Z= 0.159 Angle : 0.589 7.650 20774 Z= 0.275 Chirality : 0.042 0.194 2499 Planarity : 0.003 0.055 2541 Dihedral : 6.952 95.785 2363 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.18 % Allowed : 17.82 % Favored : 80.00 % 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: 2.42 (0.19), residues: 1905 helix: 2.39 (0.15), residues: 1169 sheet: 2.11 (0.31), residues: 270 loop : -0.87 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 166 HIS 0.003 0.001 HIS M 176 PHE 0.027 0.001 PHE I 210 TYR 0.026 0.001 TYR I 158 ARG 0.016 0.000 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 349 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 118 ASP cc_start: 0.7101 (m-30) cc_final: 0.6842 (m-30) REVERT: E 11 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8679 (mp) REVERT: F 26 ASP cc_start: 0.7217 (m-30) cc_final: 0.6756 (m-30) REVERT: I 136 ARG cc_start: 0.7195 (ttt-90) cc_final: 0.6632 (ttp80) REVERT: I 250 LEU cc_start: 0.8071 (tt) cc_final: 0.7661 (mt) REVERT: B 37 ASN cc_start: 0.7215 (t0) cc_final: 0.6679 (t0) REVERT: M 250 LEU cc_start: 0.8221 (tt) cc_final: 0.7718 (mt) REVERT: M 292 ASN cc_start: 0.8513 (p0) cc_final: 0.8276 (p0) REVERT: M 341 ARG cc_start: 0.7330 (mtp85) cc_final: 0.6889 (mmm160) outliers start: 34 outliers final: 31 residues processed: 369 average time/residue: 0.2853 time to fit residues: 154.2440 Evaluate side-chains 374 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 342 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 285 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5474 > 50: distance: 128 - 145: 6.838 distance: 132 - 153: 11.033 distance: 136 - 161: 36.528 distance: 140 - 145: 3.805 distance: 141 - 168: 8.449 distance: 145 - 146: 5.474 distance: 146 - 149: 5.667 distance: 147 - 148: 6.546 distance: 147 - 153: 5.262 distance: 148 - 175: 16.002 distance: 149 - 150: 16.725 distance: 150 - 151: 14.703 distance: 151 - 152: 17.769 distance: 153 - 154: 3.766 distance: 154 - 155: 10.938 distance: 154 - 157: 4.441 distance: 155 - 156: 10.917 distance: 155 - 161: 31.907 distance: 156 - 183: 10.899 distance: 157 - 158: 8.282 distance: 157 - 159: 6.692 distance: 158 - 160: 5.139 distance: 161 - 162: 44.108 distance: 162 - 163: 8.632 distance: 162 - 165: 14.112 distance: 163 - 164: 10.465 distance: 163 - 168: 14.611 distance: 164 - 191: 16.981 distance: 165 - 166: 27.211 distance: 165 - 167: 25.873 distance: 168 - 169: 7.700 distance: 169 - 170: 4.114 distance: 169 - 172: 4.773 distance: 170 - 175: 6.411 distance: 171 - 199: 7.337 distance: 172 - 173: 7.810 distance: 172 - 174: 9.054 distance: 175 - 176: 3.574 distance: 178 - 203: 3.360 distance: 180 - 181: 4.599 distance: 181 - 182: 5.699 distance: 183 - 184: 4.577 distance: 184 - 185: 6.868 distance: 184 - 187: 3.689 distance: 185 - 186: 7.000 distance: 185 - 191: 4.595 distance: 186 - 214: 10.659 distance: 187 - 188: 6.375 distance: 187 - 189: 11.659 distance: 188 - 190: 6.527 distance: 192 - 193: 6.349 distance: 193 - 194: 8.511 distance: 193 - 199: 4.396 distance: 194 - 222: 12.430 distance: 195 - 196: 3.599 distance: 195 - 197: 4.885 distance: 196 - 198: 5.029 distance: 200 - 201: 3.205 distance: 201 - 202: 3.022 distance: 204 - 207: 5.058 distance: 205 - 206: 5.429 distance: 205 - 214: 3.619 distance: 208 - 209: 5.226 distance: 211 - 212: 4.701 distance: 214 - 215: 6.146 distance: 215 - 216: 4.372 distance: 215 - 218: 4.942 distance: 216 - 217: 9.232 distance: 216 - 222: 3.390 distance: 218 - 219: 7.737 distance: 218 - 220: 5.834 distance: 219 - 221: 6.228