Starting phenix.real_space_refine on Sun Jul 21 18:09:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/07_2024/7zpo_14859_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/07_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_14859/07_2024/7zpo_14859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/07_2024/7zpo_14859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/07_2024/7zpo_14859_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zpo_14859/07_2024/7zpo_14859_neut.cif" } 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-5388/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: 10.19, per 1000 atoms: 0.67 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: 6.35 Conformation dependent library (CDL) restraints added in 3.4 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... Secondary structure from input PDB file: 83 helices and 10 sheets defined 65.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'H' and resid 14 through 27 removed outlier: 3.512A pdb=" N ALA H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 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 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 removed outlier: 3.572A pdb=" N ASP H 137 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 70 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: 4.308A 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 80 through 95 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: 3.533A pdb=" N VAL F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 4.336A 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 removed outlier: 3.604A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 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 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 54 through 67 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.703A 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: 3.964A 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 165 through 182 removed outlier: 3.512A pdb=" N MET I 170 " --> pdb=" O TRP I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 197 removed outlier: 3.813A pdb=" N VAL I 197 " --> pdb=" O MET I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 214 removed outlier: 3.593A pdb=" N SER I 203 " --> pdb=" O ASP I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 227 Processing helix chain 'I' and resid 235 through 261 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 271 through 287 removed outlier: 3.963A pdb=" N ARG I 287 " --> pdb=" O SER I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 314 Processing helix chain 'I' and resid 325 through 342 Processing helix chain 'I' and resid 354 through 383 Processing helix chain 'I' and resid 386 through 399 Processing helix chain 'I' and resid 412 through 437 Proline residue: I 430 - end of helix Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.813A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 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 58 through 66 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: 3.501A pdb=" N VAL B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) 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 58 through 66 Processing helix chain 'B' and resid 67 through 70 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 Processing helix chain 'J' and resid 37 through 46 removed outlier: 4.441A 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 95 Processing helix chain 'J' and resid 105 through 116 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.551A pdb=" N ALA J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 28 removed outlier: 3.575A pdb=" N SER L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 4.289A pdb=" N GLY L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 removed outlier: 3.593A pdb=" N ALA L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 95 Processing helix chain 'L' and resid 105 through 116 Processing helix chain 'L' and resid 122 through 137 removed outlier: 3.631A pdb=" N LYS L 134 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 45 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) removed outlier: 3.807A 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: 3.815A pdb=" N PHE M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 122 Processing helix chain 'M' and resid 133 through 165 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 165 through 182 Processing helix chain 'M' and resid 193 through 197 removed outlier: 3.879A pdb=" N VAL M 197 " --> pdb=" O MET M 194 " (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 235 through 261 Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 287 removed outlier: 3.536A pdb=" N TRP M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG M 287 " --> pdb=" O SER M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 314 Processing helix chain 'M' and resid 325 through 341 Processing helix chain 'M' and resid 354 through 383 removed outlier: 3.507A pdb=" N LEU M 381 " --> pdb=" O PHE M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 399 Processing helix chain 'M' and resid 412 through 439 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=AA1, first strand: chain 'H' and resid 50 through 53 removed outlier: 6.442A pdb=" N VAL H 31 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE H 52 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA H 33 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL H 99 " --> pdb=" O HIS H 119 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE H 121 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL H 101 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 50 through 53 removed outlier: 3.522A pdb=" N GLN D 50 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 72 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 99 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE D 121 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 101 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 119 through 121 removed outlier: 6.703A pdb=" N VAL E 99 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE E 121 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 101 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN E 7 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET E 74 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA E 9 " --> pdb=" O MET E 74 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE E 8 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL E 34 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL E 10 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 31 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 52 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA E 33 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 54 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP E 35 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 50 through 53 removed outlier: 3.669A pdb=" N ASP F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET F 72 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL F 73 " --> pdb=" O TRP F 100 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LYS F 102 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE F 75 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL F 99 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE F 121 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 101 " --> pdb=" O ILE F 121 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.417A pdb=" N VAL A 31 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 52 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA A 33 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 72 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 73 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS A 102 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 75 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 99 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 121 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.523A 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: 6.405A pdb=" N VAL B 31 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE B 52 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALA B 33 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 72 " --> pdb=" O GLN B 7 " (cutoff:3.500A) 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: 6.607A pdb=" N VAL B 99 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 121 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 101 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 119 through 121 removed outlier: 6.768A pdb=" N VAL J 99 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE J 121 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 101 " --> pdb=" O ILE J 121 " (cutoff:3.500A) 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: 6.535A pdb=" N VAL J 31 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE J 52 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA J 33 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA J 54 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP J 35 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 50 through 53 removed outlier: 6.222A pdb=" N VAL L 31 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE L 52 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA L 33 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL L 99 " --> pdb=" O HIS L 119 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE L 121 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.636A 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 348 removed outlier: 4.343A pdb=" N VAL M 346 " --> pdb=" O VAL M 353 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2817 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: 5.24 Time building geometry restraints manager: 6.74 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: 203 2.67 - 3.29: 16557 3.29 - 3.91: 30740 3.91 - 4.52: 40966 4.52 - 5.14: 62869 Nonbonded interactions: 151335 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 151330 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: 1.840 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.100 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- 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 : 1.685 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: 0.2904 time to fit residues: 215.4968 Evaluate side-chains 368 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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: 0.9980 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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 ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS M 118 GLN M 182 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15345 Z= 0.294 Angle : 0.701 10.486 20774 Z= 0.337 Chirality : 0.047 0.192 2499 Planarity : 0.004 0.042 2541 Dihedral : 13.248 175.361 2363 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.99 % Allowed : 10.45 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1905 helix: 2.07 (0.14), residues: 1184 sheet: 1.80 (0.30), residues: 280 loop : -0.51 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 100 HIS 0.006 0.001 HIS I 79 PHE 0.038 0.002 PHE I 210 TYR 0.011 0.001 TYR J 70 ARG 0.007 0.001 ARG I 439 *********************** 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 421 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 390 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7557 (mmtm) cc_final: 0.7252 (mttp) REVERT: E 74 MET cc_start: 0.8040 (tpp) cc_final: 0.7786 (tpp) REVERT: E 129 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7489 (mp) REVERT: F 70 TYR cc_start: 0.7385 (m-80) cc_final: 0.6980 (m-80) REVERT: I 260 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 65 LEU cc_start: 0.7986 (mm) cc_final: 0.7769 (mt) REVERT: L 25 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: L 61 THR cc_start: 0.7456 (m) cc_final: 0.7168 (m) REVERT: L 65 LEU cc_start: 0.7796 (mp) cc_final: 0.7479 (mp) REVERT: M 212 PHE cc_start: 0.7744 (m-10) cc_final: 0.7495 (m-80) REVERT: M 225 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7097 (mtp180) REVERT: M 292 ASN cc_start: 0.8460 (p0) cc_final: 0.8014 (p0) REVERT: M 387 PHE cc_start: 0.7548 (t80) cc_final: 0.7223 (t80) outliers start: 31 outliers final: 18 residues processed: 410 average time/residue: 0.2834 time to fit residues: 168.5273 Evaluate side-chains 372 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 352 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain E residue 39 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 84 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 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 197 VAL Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 0.1980 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 171 optimal weight: 0.0270 chunk 58 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.9842 ------------------------------------------------------------------------------- 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** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 25 GLN I 93 GLN I 176 HIS I 182 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15345 Z= 0.249 Angle : 0.642 9.514 20774 Z= 0.305 Chirality : 0.044 0.198 2499 Planarity : 0.004 0.041 2541 Dihedral : 10.926 162.079 2363 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.12 % Allowed : 14.42 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1905 helix: 2.23 (0.15), residues: 1179 sheet: 1.53 (0.30), residues: 280 loop : -0.50 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 100 HIS 0.004 0.001 HIS I 79 PHE 0.035 0.001 PHE I 210 TYR 0.011 0.001 TYR J 70 ARG 0.010 0.001 ARG B 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 406 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 373 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7301 (mttp) REVERT: E 74 MET cc_start: 0.7998 (tpp) cc_final: 0.7731 (tpp) REVERT: E 129 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7714 (mt) REVERT: I 260 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 105 ASP cc_start: 0.7514 (t70) cc_final: 0.7285 (t70) REVERT: A 126 ASP cc_start: 0.7895 (m-30) cc_final: 0.7686 (t0) REVERT: B 133 ARG cc_start: 0.7350 (mmt90) cc_final: 0.6785 (mmt-90) REVERT: J 134 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7562 (mtmt) REVERT: L 65 LEU cc_start: 0.7809 (mp) cc_final: 0.7537 (mp) REVERT: L 113 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8079 (tp40) REVERT: M 292 ASN cc_start: 0.8553 (p0) cc_final: 0.8053 (p0) REVERT: M 341 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7027 (mmm160) outliers start: 33 outliers final: 24 residues processed: 394 average time/residue: 0.2911 time to fit residues: 164.3388 Evaluate side-chains 353 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 328 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D 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 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 93 GLN 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 B residue 32 LEU Chi-restraints excluded: chain B residue 69 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 86 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 197 VAL 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: 0.8980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15345 Z= 0.226 Angle : 0.624 8.193 20774 Z= 0.295 Chirality : 0.044 0.199 2499 Planarity : 0.004 0.041 2541 Dihedral : 9.913 148.913 2363 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.95 % Allowed : 14.87 % Favored : 82.18 % 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: 2.27 (0.19), residues: 1905 helix: 2.26 (0.15), residues: 1177 sheet: 1.53 (0.30), residues: 272 loop : -0.56 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 100 HIS 0.003 0.001 HIS I 79 PHE 0.033 0.001 PHE I 210 TYR 0.009 0.001 TYR J 70 ARG 0.007 0.001 ARG I 439 *********************** 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 414 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 368 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7286 (mttp) REVERT: E 11 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8599 (mp) REVERT: E 74 MET cc_start: 0.7984 (tpp) cc_final: 0.7709 (tpp) REVERT: F 64 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7203 (pt0) REVERT: I 136 ARG cc_start: 0.7164 (ttt-90) cc_final: 0.6786 (ttp-170) REVERT: I 151 ILE cc_start: 0.9050 (mp) cc_final: 0.8839 (mp) REVERT: A 88 THR cc_start: 0.9015 (m) cc_final: 0.8783 (m) REVERT: B 133 ARG cc_start: 0.7285 (mmt90) cc_final: 0.6670 (mmt-90) REVERT: J 37 ASN cc_start: 0.8544 (t0) cc_final: 0.8231 (t0) REVERT: J 39 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: J 134 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7578 (mtmt) REVERT: M 250 LEU cc_start: 0.8234 (tt) cc_final: 0.7751 (mt) REVERT: M 292 ASN cc_start: 0.8557 (p0) cc_final: 0.8017 (p0) REVERT: M 341 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7016 (mmm160) outliers start: 46 outliers final: 33 residues processed: 397 average time/residue: 0.2801 time to fit residues: 160.8437 Evaluate side-chains 375 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL 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 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 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 115 ILE 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 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU 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 J residue 39 ASP Chi-restraints excluded: chain J residue 68 ASP Chi-restraints excluded: chain J residue 71 ASP 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 L residue 99 VAL Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15345 Z= 0.166 Angle : 0.597 7.681 20774 Z= 0.279 Chirality : 0.042 0.201 2499 Planarity : 0.003 0.045 2541 Dihedral : 8.917 133.157 2363 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.76 % Allowed : 15.64 % Favored : 81.60 % 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: 2.37 (0.19), residues: 1905 helix: 2.38 (0.15), residues: 1177 sheet: 1.53 (0.30), residues: 272 loop : -0.61 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 355 HIS 0.003 0.001 HIS M 176 PHE 0.031 0.001 PHE I 210 TYR 0.006 0.001 TYR A 70 ARG 0.009 0.000 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 415 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 372 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7680 (mmtm) cc_final: 0.7192 (mttp) REVERT: E 74 MET cc_start: 0.7915 (tpp) cc_final: 0.7681 (tpp) REVERT: E 111 VAL cc_start: 0.9216 (t) cc_final: 0.9002 (t) REVERT: I 136 ARG cc_start: 0.7182 (ttt-90) cc_final: 0.6783 (ttp-170) REVERT: I 170 MET cc_start: 0.8039 (mmm) cc_final: 0.7797 (mtm) REVERT: B 37 ASN cc_start: 0.7314 (t0) cc_final: 0.7068 (t0) REVERT: B 39 ASP cc_start: 0.6971 (m-30) cc_final: 0.6681 (m-30) REVERT: J 37 ASN cc_start: 0.8559 (t0) cc_final: 0.8290 (t0) REVERT: J 114 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8446 (tttt) REVERT: L 65 LEU cc_start: 0.7881 (mp) cc_final: 0.7668 (mp) REVERT: M 151 ILE cc_start: 0.8977 (mt) cc_final: 0.8766 (mp) REVERT: M 250 LEU cc_start: 0.8212 (tt) cc_final: 0.7736 (mt) REVERT: M 292 ASN cc_start: 0.8534 (p0) cc_final: 0.8006 (p0) REVERT: M 341 ARG cc_start: 0.7396 (mtp85) cc_final: 0.6983 (mmm160) outliers start: 43 outliers final: 27 residues processed: 403 average time/residue: 0.2650 time to fit residues: 155.6357 Evaluate side-chains 367 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 339 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 VAL 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 115 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 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 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 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 324 ILE 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: 0.9980 chunk 165 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS D 25 GLN D 58 HIS D 108 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS B 108 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15345 Z= 0.166 Angle : 0.594 7.500 20774 Z= 0.277 Chirality : 0.042 0.205 2499 Planarity : 0.003 0.042 2541 Dihedral : 8.090 115.055 2363 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 16.22 % 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: 2.37 (0.19), residues: 1905 helix: 2.41 (0.15), residues: 1177 sheet: 1.49 (0.30), residues: 272 loop : -0.66 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 355 HIS 0.002 0.001 HIS M 176 PHE 0.031 0.001 PHE I 210 TYR 0.006 0.001 TYR A 70 ARG 0.005 0.000 ARG D 133 *********************** 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: 40 poor density : 360 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7523 (tttp) REVERT: H 97 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7227 (mttp) REVERT: D 127 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8116 (tpt) REVERT: E 74 MET cc_start: 0.7910 (tpp) cc_final: 0.7703 (tpp) REVERT: E 111 VAL cc_start: 0.9254 (t) cc_final: 0.9006 (t) REVERT: I 136 ARG cc_start: 0.7161 (ttt-90) cc_final: 0.6674 (ttp80) REVERT: I 260 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 37 ASN cc_start: 0.7356 (t0) cc_final: 0.6858 (t0) REVERT: J 37 ASN cc_start: 0.8475 (t0) cc_final: 0.8250 (t0) REVERT: J 64 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7039 (tp30) REVERT: J 114 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8472 (tttt) REVERT: M 151 ILE cc_start: 0.8980 (mt) cc_final: 0.8777 (mp) REVERT: M 250 LEU cc_start: 0.8177 (tt) cc_final: 0.7696 (mt) REVERT: M 292 ASN cc_start: 0.8521 (p0) cc_final: 0.8020 (p0) REVERT: M 341 ARG cc_start: 0.7383 (mtp85) cc_final: 0.6912 (mmm160) outliers start: 40 outliers final: 31 residues processed: 388 average time/residue: 0.2828 time to fit residues: 157.8162 Evaluate side-chains 374 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 341 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain D residue 31 VAL 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 115 ILE Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE 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 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 283 SER Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 99 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 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS D 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15345 Z= 0.334 Angle : 0.685 8.424 20774 Z= 0.327 Chirality : 0.046 0.219 2499 Planarity : 0.004 0.044 2541 Dihedral : 8.462 106.460 2363 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.59 % Allowed : 15.96 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.19), residues: 1905 helix: 2.23 (0.15), residues: 1174 sheet: 1.13 (0.29), residues: 278 loop : -0.64 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 355 HIS 0.004 0.001 HIS I 235 PHE 0.032 0.002 PHE I 210 TYR 0.011 0.002 TYR A 70 ARG 0.009 0.001 ARG H 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 407 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 351 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7417 (mttp) REVERT: D 127 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (tpt) REVERT: I 136 ARG cc_start: 0.7209 (ttt-90) cc_final: 0.6746 (ttp80) REVERT: I 247 LEU cc_start: 0.8839 (tp) cc_final: 0.8610 (tt) REVERT: I 260 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 299 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: B 37 ASN cc_start: 0.7324 (t0) cc_final: 0.6831 (t0) REVERT: B 127 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7917 (tpt) REVERT: M 151 ILE cc_start: 0.9094 (mt) cc_final: 0.8835 (mp) REVERT: M 341 ARG cc_start: 0.7504 (mtp85) cc_final: 0.7114 (mmm160) outliers start: 56 outliers final: 42 residues processed: 386 average time/residue: 0.2762 time to fit residues: 152.5543 Evaluate side-chains 381 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 336 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL 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 127 MET Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE 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 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 391 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL 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 127 MET Chi-restraints excluded: chain J residue 71 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 L residue 99 VAL Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 297 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN L 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15345 Z= 0.157 Angle : 0.621 12.922 20774 Z= 0.290 Chirality : 0.042 0.212 2499 Planarity : 0.003 0.042 2541 Dihedral : 7.500 98.485 2363 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 17.24 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1905 helix: 2.37 (0.15), residues: 1179 sheet: 1.37 (0.31), residues: 270 loop : -0.73 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 355 HIS 0.003 0.000 HIS M 176 PHE 0.029 0.001 PHE I 210 TYR 0.008 0.001 TYR I 172 ARG 0.005 0.000 ARG I 439 *********************** 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 399 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 361 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7668 (tttp) REVERT: H 97 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7255 (mttp) REVERT: H 118 ASP cc_start: 0.7166 (m-30) cc_final: 0.6922 (m-30) REVERT: D 127 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (tpt) REVERT: E 27 SER cc_start: 0.7789 (p) cc_final: 0.7435 (p) REVERT: E 111 VAL cc_start: 0.9271 (t) cc_final: 0.9013 (t) REVERT: F 113 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8143 (tm-30) REVERT: I 136 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6658 (ttp80) REVERT: I 250 LEU cc_start: 0.8079 (tt) cc_final: 0.7662 (mt) REVERT: B 37 ASN cc_start: 0.7287 (t0) cc_final: 0.6907 (t0) REVERT: B 43 GLU cc_start: 0.7244 (mp0) cc_final: 0.6828 (mp0) REVERT: M 250 LEU cc_start: 0.8204 (tt) cc_final: 0.7713 (mt) REVERT: M 292 ASN cc_start: 0.8482 (p0) cc_final: 0.7993 (p0) REVERT: M 341 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6918 (mmm160) outliers start: 38 outliers final: 31 residues processed: 381 average time/residue: 0.2813 time to fit residues: 155.1455 Evaluate side-chains 377 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 345 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 10 VAL 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 F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain I residue 391 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 86 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 299 PHE Chi-restraints excluded: chain M residue 324 ILE 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: 6.9990 chunk 170 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN M 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15345 Z= 0.264 Angle : 0.663 14.221 20774 Z= 0.312 Chirality : 0.045 0.222 2499 Planarity : 0.004 0.042 2541 Dihedral : 7.601 100.446 2363 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.76 % Allowed : 17.56 % Favored : 79.68 % 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: 2.19 (0.19), residues: 1905 helix: 2.35 (0.15), residues: 1173 sheet: 1.17 (0.30), residues: 270 loop : -0.81 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 166 HIS 0.003 0.001 HIS M 176 PHE 0.031 0.001 PHE I 210 TYR 0.009 0.001 TYR A 70 ARG 0.011 0.001 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: 43 poor density : 340 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7635 (tttp) REVERT: H 97 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7325 (mttp) REVERT: H 118 ASP cc_start: 0.7229 (m-30) cc_final: 0.6963 (m-30) REVERT: D 22 LYS cc_start: 0.7800 (mmpt) cc_final: 0.7556 (mmmt) REVERT: D 127 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8220 (tpt) REVERT: E 27 SER cc_start: 0.7776 (p) cc_final: 0.7419 (p) REVERT: I 136 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6690 (ttp80) REVERT: B 37 ASN cc_start: 0.7378 (t0) cc_final: 0.6961 (t0) REVERT: B 43 GLU cc_start: 0.7233 (mp0) cc_final: 0.6772 (mp0) REVERT: B 127 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7865 (tpt) REVERT: M 292 ASN cc_start: 0.8528 (p0) cc_final: 0.8059 (p0) REVERT: M 341 ARG cc_start: 0.7420 (mtp85) cc_final: 0.6992 (mmm160) outliers start: 43 outliers final: 37 residues processed: 364 average time/residue: 0.2837 time to fit residues: 148.6244 Evaluate side-chains 371 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 10 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 F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 380 MET Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 MET 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 99 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 272 THR 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 ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 0.3980 chunk 174 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 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** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN M 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15345 Z= 0.236 Angle : 0.654 14.310 20774 Z= 0.308 Chirality : 0.044 0.225 2499 Planarity : 0.003 0.041 2541 Dihedral : 7.560 100.177 2363 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.76 % Allowed : 17.50 % Favored : 79.74 % 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: 2.17 (0.19), residues: 1905 helix: 2.34 (0.15), residues: 1173 sheet: 1.14 (0.30), residues: 270 loop : -0.83 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 166 HIS 0.003 0.001 HIS H 119 PHE 0.031 0.001 PHE I 210 TYR 0.008 0.001 TYR A 70 ARG 0.009 0.001 ARG F 130 ********************** REFINEMENT MACRO_CYCLE 10 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 381 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 338 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7707 (tttp) REVERT: H 97 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7298 (mttp) REVERT: H 118 ASP cc_start: 0.7226 (m-30) cc_final: 0.6953 (m-30) REVERT: D 22 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7417 (mmmt) REVERT: D 127 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (tpt) REVERT: E 27 SER cc_start: 0.7752 (p) cc_final: 0.7382 (p) REVERT: I 136 ARG cc_start: 0.7182 (ttt-90) cc_final: 0.6678 (ttp80) REVERT: B 37 ASN cc_start: 0.7400 (t0) cc_final: 0.6980 (t0) REVERT: B 43 GLU cc_start: 0.7286 (mp0) cc_final: 0.6854 (mp0) REVERT: B 127 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7861 (tpt) REVERT: M 183 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8555 (t0) REVERT: M 292 ASN cc_start: 0.8490 (p0) cc_final: 0.7999 (p0) REVERT: M 341 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7018 (mmm160) outliers start: 43 outliers final: 38 residues processed: 360 average time/residue: 0.2829 time to fit residues: 146.2775 Evaluate side-chains 374 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 333 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL 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 127 MET Chi-restraints excluded: chain E residue 10 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 31 VAL Chi-restraints excluded: chain F residue 34 VAL 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 380 MET Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 391 MET Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 MET 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 99 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 183 ASN Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 272 THR 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 ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.0270 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** 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** L 25 GLN M 176 HIS M 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098372 restraints weight = 28126.420| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.22 r_work: 0.2888 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15345 Z= 0.283 Angle : 0.683 14.408 20774 Z= 0.324 Chirality : 0.045 0.223 2499 Planarity : 0.004 0.041 2541 Dihedral : 7.535 101.639 2363 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.88 % Allowed : 17.69 % Favored : 79.42 % 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: 2.09 (0.19), residues: 1905 helix: 2.29 (0.15), residues: 1171 sheet: 1.04 (0.30), residues: 270 loop : -0.80 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 166 HIS 0.003 0.001 HIS H 119 PHE 0.031 0.002 PHE I 387 TYR 0.009 0.001 TYR A 70 ARG 0.010 0.001 ARG F 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.65 seconds wall clock time: 68 minutes 34.83 seconds (4114.83 seconds total)