Starting phenix.real_space_refine on Fri Jun 13 16:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_14859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_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/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_14859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_14859.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_14859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpo_14859/06_2025/7zpo_14859.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. Time to flip 46 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 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: 10.60, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 2.5 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: 2.20 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: 6.20 Time building geometry restraints manager: 4.92 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: 0.00 - 1.99: 20289 1.99 - 3.99: 336 3.99 - 5.98: 118 5.98 - 7.97: 17 7.97 - 9.97: 14 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 3.040 nonbonded pdb=" OE2 GLU I 393 " pdb=" OG1 THR I 408 " model vdw 2.201 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 137 or resid 1001)) selection = (chain 'D' and (resid 6 through 137 or resid 1001)) selection = (chain 'E' and (resid 6 through 137 or resid 301)) selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = (chain 'L' and (resid 6 through 137 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 7 through 350 or resid 352 through 455 or resid 503)) selection = (chain 'M' and (resid 7 through 16 or resid 21 through 122 or resid 132 through \ 350 or resid 352 through 455 or resid 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 40.770 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.710 ------------------------------------------------------------------------------- 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 15346 Z= 0.179 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 Details of bonding type rmsd hydrogen bonds : bond 0.19693 ( 948) hydrogen bonds : angle 6.60279 ( 2817) covalent geometry : bond 0.00360 (15345) covalent geometry : angle 0.73419 (20774) Misc. bond : bond 0.00581 ( 1) *********************** 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 to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 1.730 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: 0.6602 (t0) REVERT: I 387 PHE cc_start: 0.7432 (t80) cc_final: 0.7191 (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: 0.7710 (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: 0.3025 time to fit residues: 224.7892 Evaluate side-chains 368 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN H 119 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS E 119 HIS ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 M 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106215 restraints weight = 21653.614| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.95 r_work: 0.3027 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15346 Z= 0.195 Angle : 0.716 10.812 20774 Z= 0.345 Chirality : 0.047 0.190 2499 Planarity : 0.005 0.045 2541 Dihedral : 13.552 177.674 2363 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.86 % Allowed : 10.19 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1905 helix: 1.98 (0.14), residues: 1183 sheet: 1.70 (0.29), residues: 280 loop : -0.48 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 100 HIS 0.006 0.001 HIS I 79 PHE 0.041 0.002 PHE I 210 TYR 0.011 0.001 TYR H 70 ARG 0.016 0.001 ARG H 130 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 948) hydrogen bonds : angle 4.42948 ( 2817) covalent geometry : bond 0.00448 (15345) covalent geometry : angle 0.71555 (20774) Misc. bond : bond 0.00468 ( 1) *********************** 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 418 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 389 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7339 (mttp) REVERT: E 74 MET cc_start: 0.8731 (tpp) cc_final: 0.8475 (tpp) REVERT: E 119 HIS cc_start: 0.7630 (m90) cc_final: 0.7354 (m90) REVERT: E 129 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7663 (mp) REVERT: F 7 GLN cc_start: 0.6454 (tt0) cc_final: 0.6232 (pt0) REVERT: F 70 TYR cc_start: 0.7493 (m-80) cc_final: 0.6991 (m-80) REVERT: I 260 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7751 (mm-30) REVERT: I 263 ASN cc_start: 0.7748 (t0) cc_final: 0.7437 (t0) REVERT: I 295 ASP cc_start: 0.8061 (t0) cc_final: 0.7467 (t0) REVERT: I 297 THR cc_start: 0.8385 (m) cc_final: 0.8062 (m) REVERT: I 334 MET cc_start: 0.9122 (mmp) cc_final: 0.8869 (mmm) REVERT: A 126 ASP cc_start: 0.8440 (m-30) cc_final: 0.8019 (t0) REVERT: B 50 GLN cc_start: 0.5645 (tm-30) cc_final: 0.5416 (tm-30) REVERT: B 65 LEU cc_start: 0.7974 (mm) cc_final: 0.7765 (mt) REVERT: L 61 THR cc_start: 0.7418 (m) cc_final: 0.7072 (m) REVERT: L 65 LEU cc_start: 0.7778 (mp) cc_final: 0.7429 (mp) REVERT: M 57 ASP cc_start: 0.7761 (m-30) cc_final: 0.7521 (m-30) REVERT: M 79 HIS cc_start: 0.7641 (t70) cc_final: 0.7280 (t70) REVERT: M 94 ILE cc_start: 0.8762 (mm) cc_final: 0.8551 (mt) REVERT: M 212 PHE cc_start: 0.8061 (m-10) cc_final: 0.7811 (m-80) REVERT: M 225 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7848 (mtp180) REVERT: M 387 PHE cc_start: 0.7877 (t80) cc_final: 0.7530 (t80) REVERT: M 390 VAL cc_start: 0.8596 (t) cc_final: 0.8320 (p) REVERT: M 441 GLU cc_start: 0.8048 (tt0) cc_final: 0.7827 (tt0) outliers start: 29 outliers final: 16 residues processed: 409 average time/residue: 0.2730 time to fit residues: 161.7284 Evaluate side-chains 366 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 349 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 119 HIS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 293 SER 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 82 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 25 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 HIS I 182 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097651 restraints weight = 24057.201| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.13 r_work: 0.2911 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15346 Z= 0.176 Angle : 0.665 9.558 20774 Z= 0.317 Chirality : 0.046 0.277 2499 Planarity : 0.004 0.043 2541 Dihedral : 11.784 171.865 2363 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.12 % Allowed : 13.53 % Favored : 84.36 % 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: 2.16 (0.19), residues: 1905 helix: 2.15 (0.14), residues: 1178 sheet: 1.31 (0.29), residues: 280 loop : -0.44 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 355 HIS 0.004 0.001 HIS I 79 PHE 0.034 0.001 PHE I 210 TYR 0.010 0.001 TYR J 70 ARG 0.022 0.001 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 948) hydrogen bonds : angle 4.24433 ( 2817) covalent geometry : bond 0.00405 (15345) covalent geometry : angle 0.66506 (20774) Misc. bond : bond 0.00141 ( 1) *********************** 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 407 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 374 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7400 (mttp) REVERT: E 74 MET cc_start: 0.8803 (tpp) cc_final: 0.8555 (tpp) REVERT: E 119 HIS cc_start: 0.7841 (m90) cc_final: 0.7592 (m90) REVERT: E 129 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7904 (mt) REVERT: F 7 GLN cc_start: 0.6305 (tt0) cc_final: 0.5999 (pt0) REVERT: F 61 THR cc_start: 0.7483 (m) cc_final: 0.7134 (m) REVERT: I 151 ILE cc_start: 0.9084 (mt) cc_final: 0.8859 (mp) REVERT: I 260 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7891 (mm-30) REVERT: I 295 ASP cc_start: 0.7984 (t0) cc_final: 0.7701 (t0) REVERT: I 380 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8317 (mtt) REVERT: A 126 ASP cc_start: 0.8741 (m-30) cc_final: 0.8172 (t0) REVERT: B 50 GLN cc_start: 0.5637 (tm-30) cc_final: 0.5401 (tm-30) REVERT: B 133 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7076 (mmt-90) REVERT: J 23 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7537 (mm-30) REVERT: J 134 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7811 (mtmt) REVERT: L 65 LEU cc_start: 0.7694 (mp) cc_final: 0.7426 (mp) REVERT: L 113 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8464 (tp40) REVERT: M 79 HIS cc_start: 0.7910 (t70) cc_final: 0.7564 (t70) REVERT: M 295 ASP cc_start: 0.8293 (t0) cc_final: 0.7994 (t0) REVERT: M 341 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7813 (mmm160) REVERT: M 387 PHE cc_start: 0.7625 (t80) cc_final: 0.7418 (t80) REVERT: M 390 VAL cc_start: 0.8630 (t) cc_final: 0.8357 (p) outliers start: 33 outliers final: 22 residues processed: 396 average time/residue: 0.2892 time to fit residues: 163.9700 Evaluate side-chains 359 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 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 F residue 52 ILE 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 A residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU 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 198 ASN Chi-restraints excluded: chain M residue 297 THR 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 85 optimal weight: 0.0980 chunk 175 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 37 optimal weight: 0.0030 chunk 127 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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** F 25 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101864 restraints weight = 33909.794| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.53 r_work: 0.2918 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15346 Z= 0.111 Angle : 0.603 7.456 20774 Z= 0.283 Chirality : 0.042 0.188 2499 Planarity : 0.003 0.042 2541 Dihedral : 10.542 167.780 2363 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.79 % Allowed : 15.06 % Favored : 83.14 % 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: 2.34 (0.19), residues: 1905 helix: 2.35 (0.15), residues: 1175 sheet: 1.40 (0.30), residues: 272 loop : -0.54 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 100 HIS 0.003 0.001 HIS M 176 PHE 0.031 0.001 PHE I 210 TYR 0.005 0.001 TYR I 172 ARG 0.006 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 948) hydrogen bonds : angle 4.04972 ( 2817) covalent geometry : bond 0.00228 (15345) covalent geometry : angle 0.60290 (20774) Misc. bond : bond 0.00244 ( 1) *********************** 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 400 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 372 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6690 (pttt) REVERT: H 97 LYS cc_start: 0.7775 (mmtm) cc_final: 0.7229 (mttp) REVERT: E 74 MET cc_start: 0.8539 (tpp) cc_final: 0.8311 (tpp) REVERT: F 70 TYR cc_start: 0.7611 (m-80) cc_final: 0.7117 (m-80) REVERT: I 170 MET cc_start: 0.8585 (mmm) cc_final: 0.8378 (mtm) REVERT: I 260 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7733 (mm-30) REVERT: I 295 ASP cc_start: 0.7946 (t0) cc_final: 0.7685 (t0) REVERT: A 126 ASP cc_start: 0.8506 (m-30) cc_final: 0.7975 (t0) REVERT: B 39 ASP cc_start: 0.6970 (m-30) cc_final: 0.6553 (m-30) REVERT: B 50 GLN cc_start: 0.5580 (tm-30) cc_final: 0.5361 (tm-30) REVERT: B 133 ARG cc_start: 0.7757 (mmt90) cc_final: 0.6952 (mmt-90) REVERT: J 23 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7370 (mm-30) REVERT: J 114 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8453 (tttt) REVERT: L 64 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7149 (pt0) REVERT: L 113 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8306 (tp40) REVERT: M 79 HIS cc_start: 0.7842 (t70) cc_final: 0.7517 (t70) REVERT: M 109 MET cc_start: 0.8101 (mmm) cc_final: 0.7789 (mtt) REVERT: M 341 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7492 (mmm160) REVERT: M 390 VAL cc_start: 0.8648 (t) cc_final: 0.8390 (p) outliers start: 28 outliers final: 20 residues processed: 389 average time/residue: 0.2862 time to fit residues: 161.5025 Evaluate side-chains 358 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 337 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 114 LYS 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 324 ILE 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 187 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 HIS E 119 HIS F 7 GLN F 25 GLN I 182 ASN B 58 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098656 restraints weight = 28223.711| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.22 r_work: 0.2896 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15346 Z= 0.182 Angle : 0.662 8.098 20774 Z= 0.314 Chirality : 0.045 0.204 2499 Planarity : 0.004 0.044 2541 Dihedral : 10.264 167.825 2363 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.76 % Allowed : 14.87 % Favored : 82.37 % 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: 2.22 (0.19), residues: 1905 helix: 2.30 (0.15), residues: 1176 sheet: 1.14 (0.30), residues: 270 loop : -0.53 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 100 HIS 0.004 0.001 HIS I 79 PHE 0.032 0.002 PHE I 210 TYR 0.010 0.001 TYR L 70 ARG 0.009 0.001 ARG H 130 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 948) hydrogen bonds : angle 4.13619 ( 2817) covalent geometry : bond 0.00423 (15345) covalent geometry : angle 0.66173 (20774) Misc. bond : bond 0.00297 ( 1) *********************** 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 398 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 355 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7107 (ttpt) cc_final: 0.6669 (pttt) REVERT: H 97 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7361 (mttp) REVERT: E 74 MET cc_start: 0.8525 (tpp) cc_final: 0.8299 (tpp) REVERT: E 133 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6403 (mmm160) REVERT: I 136 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.6966 (ttp-170) REVERT: I 151 ILE cc_start: 0.9114 (mt) cc_final: 0.8848 (mp) REVERT: I 292 ASN cc_start: 0.8679 (p0) cc_final: 0.8448 (p0) REVERT: A 126 ASP cc_start: 0.8459 (m-30) cc_final: 0.7953 (t0) REVERT: B 37 ASN cc_start: 0.7457 (t0) cc_final: 0.7020 (t0) REVERT: B 133 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7026 (mmt-90) REVERT: L 65 LEU cc_start: 0.7858 (mp) cc_final: 0.7554 (mp) REVERT: M 79 HIS cc_start: 0.7934 (t70) cc_final: 0.7603 (t70) REVERT: M 151 ILE cc_start: 0.9072 (mt) cc_final: 0.8827 (mp) REVERT: M 295 ASP cc_start: 0.8112 (t0) cc_final: 0.7787 (t0) REVERT: M 341 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7541 (mmm160) REVERT: M 390 VAL cc_start: 0.8610 (t) cc_final: 0.8358 (p) outliers start: 43 outliers final: 30 residues processed: 385 average time/residue: 0.2842 time to fit residues: 158.1777 Evaluate side-chains 356 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 326 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 10 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 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain 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 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 52 ILE 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 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 147 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094900 restraints weight = 30436.766| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.34 r_work: 0.2823 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15346 Z= 0.213 Angle : 0.685 8.249 20774 Z= 0.326 Chirality : 0.046 0.220 2499 Planarity : 0.004 0.050 2541 Dihedral : 10.202 178.120 2363 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.33 % Allowed : 15.77 % Favored : 80.90 % 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: 1.97 (0.19), residues: 1905 helix: 2.18 (0.15), residues: 1172 sheet: 0.82 (0.30), residues: 270 loop : -0.69 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 100 HIS 0.004 0.001 HIS I 79 PHE 0.033 0.002 PHE I 210 TYR 0.010 0.002 TYR A 70 ARG 0.011 0.001 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 948) hydrogen bonds : angle 4.21171 ( 2817) covalent geometry : bond 0.00500 (15345) covalent geometry : angle 0.68548 (20774) Misc. bond : bond 0.00324 ( 1) *********************** 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 417 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 365 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7107 (ttpt) cc_final: 0.6623 (pttt) REVERT: H 23 GLU cc_start: 0.8380 (tp30) cc_final: 0.8142 (tp30) REVERT: H 97 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7551 (mttp) REVERT: D 127 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8636 (tpt) REVERT: E 118 ASP cc_start: 0.7509 (m-30) cc_final: 0.6506 (t0) REVERT: I 57 ASP cc_start: 0.7992 (m-30) cc_final: 0.7666 (m-30) REVERT: I 136 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.6897 (ttp80) REVERT: I 151 ILE cc_start: 0.9116 (mt) cc_final: 0.8880 (mp) REVERT: I 292 ASN cc_start: 0.8716 (p0) cc_final: 0.8482 (p0) REVERT: A 126 ASP cc_start: 0.8524 (m-30) cc_final: 0.8015 (t0) REVERT: B 37 ASN cc_start: 0.7340 (t0) cc_final: 0.6851 (t0) REVERT: J 64 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7273 (tp30) REVERT: L 65 LEU cc_start: 0.7689 (mp) cc_final: 0.7478 (mp) REVERT: M 79 HIS cc_start: 0.8004 (t70) cc_final: 0.7655 (t70) REVERT: M 151 ILE cc_start: 0.9121 (mt) cc_final: 0.8826 (mp) REVERT: M 341 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7724 (mmm160) REVERT: M 391 MET cc_start: 0.7893 (ttt) cc_final: 0.7508 (mtp) outliers start: 52 outliers final: 37 residues processed: 394 average time/residue: 0.2846 time to fit residues: 160.7663 Evaluate side-chains 375 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain E residue 10 VAL 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 E residue 105 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER 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 283 SER Chi-restraints excluded: chain I residue 293 SER 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 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 73 VAL 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 29 SER Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 84 SER 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 251 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 HIS I 93 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098007 restraints weight = 29873.840| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.34 r_work: 0.2875 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15346 Z= 0.128 Angle : 0.625 8.200 20774 Z= 0.293 Chirality : 0.043 0.191 2499 Planarity : 0.003 0.045 2541 Dihedral : 9.350 169.116 2363 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.69 % Allowed : 16.92 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1905 helix: 2.33 (0.15), residues: 1177 sheet: 0.90 (0.30), residues: 270 loop : -0.63 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 355 HIS 0.003 0.001 HIS D 119 PHE 0.030 0.001 PHE I 210 TYR 0.008 0.001 TYR L 70 ARG 0.008 0.001 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 948) hydrogen bonds : angle 4.06766 ( 2817) covalent geometry : bond 0.00281 (15345) covalent geometry : angle 0.62516 (20774) Misc. bond : bond 0.00180 ( 1) *********************** 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 409 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7123 (ttpt) cc_final: 0.6677 (pttt) REVERT: H 22 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7775 (tttp) REVERT: H 97 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7455 (mttp) REVERT: D 127 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (tpt) REVERT: F 26 ASP cc_start: 0.7234 (m-30) cc_final: 0.6909 (m-30) REVERT: I 136 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.6913 (ttp-170) REVERT: I 151 ILE cc_start: 0.9095 (mt) cc_final: 0.8845 (mp) REVERT: I 260 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7731 (mm-30) REVERT: I 292 ASN cc_start: 0.8637 (p0) cc_final: 0.8374 (p0) REVERT: I 295 ASP cc_start: 0.7885 (t0) cc_final: 0.7486 (t0) REVERT: I 299 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: A 126 ASP cc_start: 0.8481 (m-30) cc_final: 0.7928 (t0) REVERT: B 37 ASN cc_start: 0.7436 (t0) cc_final: 0.7020 (t0) REVERT: J 64 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7205 (tp30) REVERT: L 65 LEU cc_start: 0.7731 (mp) cc_final: 0.7530 (mp) REVERT: M 79 HIS cc_start: 0.7946 (t70) cc_final: 0.7636 (t70) REVERT: M 250 LEU cc_start: 0.8320 (tt) cc_final: 0.7784 (mt) REVERT: M 295 ASP cc_start: 0.8082 (t0) cc_final: 0.7772 (t0) REVERT: M 341 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7526 (mmm160) REVERT: M 391 MET cc_start: 0.7858 (ttt) cc_final: 0.7480 (mtp) outliers start: 42 outliers final: 31 residues processed: 394 average time/residue: 0.2805 time to fit residues: 161.1131 Evaluate side-chains 365 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 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 56 THR Chi-restraints excluded: chain I residue 93 GLN Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 29 SER 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 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 112 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 189 optimal weight: 0.0370 chunk 17 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097779 restraints weight = 30048.367| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.35 r_work: 0.2889 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15346 Z= 0.120 Angle : 0.619 8.076 20774 Z= 0.290 Chirality : 0.043 0.226 2499 Planarity : 0.003 0.045 2541 Dihedral : 8.841 156.806 2363 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.24 % Allowed : 17.76 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1905 helix: 2.44 (0.15), residues: 1170 sheet: 0.95 (0.30), residues: 270 loop : -0.76 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 355 HIS 0.003 0.000 HIS I 79 PHE 0.029 0.001 PHE I 210 TYR 0.008 0.001 TYR L 70 ARG 0.007 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 948) hydrogen bonds : angle 4.00296 ( 2817) covalent geometry : bond 0.00259 (15345) covalent geometry : angle 0.61932 (20774) Misc. bond : bond 0.00507 ( 1) *********************** 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 394 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 359 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6693 (pttt) REVERT: H 22 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7829 (tttp) REVERT: H 23 GLU cc_start: 0.8263 (tp30) cc_final: 0.7399 (tp30) REVERT: H 97 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7423 (mttp) REVERT: D 127 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8592 (tpt) REVERT: I 136 ARG cc_start: 0.7645 (ttt-90) cc_final: 0.6909 (ttp-170) REVERT: I 151 ILE cc_start: 0.9108 (mt) cc_final: 0.8846 (mp) REVERT: I 250 LEU cc_start: 0.8286 (tt) cc_final: 0.7803 (mt) REVERT: I 292 ASN cc_start: 0.8633 (p0) cc_final: 0.8388 (p0) REVERT: I 295 ASP cc_start: 0.7870 (t0) cc_final: 0.7458 (t0) REVERT: A 126 ASP cc_start: 0.8486 (m-30) cc_final: 0.7936 (t0) REVERT: B 37 ASN cc_start: 0.7453 (t0) cc_final: 0.7041 (t0) REVERT: B 68 ASP cc_start: 0.7989 (p0) cc_final: 0.7779 (p0) REVERT: J 64 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7171 (tp30) REVERT: M 79 HIS cc_start: 0.7947 (t70) cc_final: 0.7657 (t70) REVERT: M 151 ILE cc_start: 0.9066 (mt) cc_final: 0.8834 (mp) REVERT: M 250 LEU cc_start: 0.8321 (tt) cc_final: 0.7794 (mt) REVERT: M 341 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7538 (mmm160) REVERT: M 391 MET cc_start: 0.7927 (ttt) cc_final: 0.7562 (mtp) outliers start: 35 outliers final: 26 residues processed: 381 average time/residue: 0.3028 time to fit residues: 168.8640 Evaluate side-chains 375 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 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 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 99 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 B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain L residue 13 LEU 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 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 83 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 119 GLN I 345 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097326 restraints weight = 30145.928| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.34 r_work: 0.2874 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15346 Z= 0.156 Angle : 0.656 9.236 20774 Z= 0.308 Chirality : 0.044 0.224 2499 Planarity : 0.004 0.053 2541 Dihedral : 8.631 157.433 2363 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 17.63 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 1905 helix: 2.40 (0.15), residues: 1172 sheet: 0.91 (0.30), residues: 270 loop : -0.78 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 100 HIS 0.003 0.001 HIS M 176 PHE 0.030 0.001 PHE I 210 TYR 0.008 0.001 TYR A 70 ARG 0.011 0.001 ARG J 130 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 948) hydrogen bonds : angle 4.06140 ( 2817) covalent geometry : bond 0.00360 (15345) covalent geometry : angle 0.65550 (20774) Misc. bond : bond 0.00678 ( 1) *********************** 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 394 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7119 (ttpt) cc_final: 0.6697 (pttt) REVERT: H 22 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7840 (tttp) REVERT: H 23 GLU cc_start: 0.7912 (tp30) cc_final: 0.7277 (tp30) REVERT: H 97 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7343 (mttp) REVERT: H 118 ASP cc_start: 0.7530 (m-30) cc_final: 0.7238 (m-30) REVERT: D 127 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8574 (tpt) REVERT: I 136 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.6818 (ttp80) REVERT: I 151 ILE cc_start: 0.9124 (mt) cc_final: 0.8859 (mp) REVERT: I 292 ASN cc_start: 0.8678 (p0) cc_final: 0.8439 (p0) REVERT: A 126 ASP cc_start: 0.8487 (m-30) cc_final: 0.7928 (t0) REVERT: B 37 ASN cc_start: 0.7425 (t0) cc_final: 0.7029 (t0) REVERT: J 64 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7277 (tp30) REVERT: M 79 HIS cc_start: 0.7940 (t70) cc_final: 0.7637 (t70) REVERT: M 151 ILE cc_start: 0.9081 (mt) cc_final: 0.8844 (mp) REVERT: M 250 LEU cc_start: 0.8344 (tt) cc_final: 0.7796 (mt) REVERT: M 295 ASP cc_start: 0.8097 (t0) cc_final: 0.7736 (t0) REVERT: M 341 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7513 (mmm160) REVERT: M 391 MET cc_start: 0.7860 (ttt) cc_final: 0.7502 (mtp) outliers start: 38 outliers final: 33 residues processed: 378 average time/residue: 0.2796 time to fit residues: 152.6632 Evaluate side-chains 377 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 343 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 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 84 SER 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 283 SER 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 B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain L residue 13 LEU 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 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 126 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 119 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098532 restraints weight = 23555.803| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.07 r_work: 0.2918 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15346 Z= 0.134 Angle : 0.657 14.367 20774 Z= 0.304 Chirality : 0.044 0.215 2499 Planarity : 0.003 0.045 2541 Dihedral : 8.300 157.448 2363 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.31 % Allowed : 18.08 % Favored : 79.62 % 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: 2.41 (0.15), residues: 1174 sheet: 0.90 (0.30), residues: 270 loop : -0.85 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 100 HIS 0.003 0.001 HIS I 79 PHE 0.030 0.001 PHE I 210 TYR 0.007 0.001 TYR L 70 ARG 0.008 0.001 ARG J 130 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 948) hydrogen bonds : angle 4.05273 ( 2817) covalent geometry : bond 0.00300 (15345) covalent geometry : angle 0.65657 (20774) Misc. bond : bond 0.00495 ( 1) ********************** 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 389 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 353 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6715 (pttt) REVERT: H 22 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7915 (tttp) REVERT: H 23 GLU cc_start: 0.7949 (tp30) cc_final: 0.7729 (tp30) REVERT: H 97 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7366 (mttp) REVERT: H 118 ASP cc_start: 0.7743 (m-30) cc_final: 0.7426 (m-30) REVERT: D 127 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8697 (tpt) REVERT: F 74 MET cc_start: 0.8786 (tpp) cc_final: 0.8490 (tpt) REVERT: F 113 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8585 (tm-30) REVERT: I 79 HIS cc_start: 0.7896 (t70) cc_final: 0.7653 (t70) REVERT: I 136 ARG cc_start: 0.7687 (ttt-90) cc_final: 0.6831 (ttp80) REVERT: I 151 ILE cc_start: 0.9118 (mt) cc_final: 0.8844 (mp) REVERT: I 250 LEU cc_start: 0.8369 (tt) cc_final: 0.7885 (mt) REVERT: I 292 ASN cc_start: 0.8768 (p0) cc_final: 0.8504 (p0) REVERT: I 295 ASP cc_start: 0.7879 (t0) cc_final: 0.7492 (t0) REVERT: A 126 ASP cc_start: 0.8655 (m-30) cc_final: 0.8005 (t0) REVERT: B 22 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7347 (mmtm) REVERT: B 37 ASN cc_start: 0.7489 (t0) cc_final: 0.7099 (t0) REVERT: J 64 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7339 (tp30) REVERT: J 108 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: M 79 HIS cc_start: 0.8017 (t70) cc_final: 0.7691 (t70) REVERT: M 151 ILE cc_start: 0.9118 (mt) cc_final: 0.8868 (mp) REVERT: M 250 LEU cc_start: 0.8386 (tt) cc_final: 0.7848 (mt) REVERT: M 295 ASP cc_start: 0.8166 (t0) cc_final: 0.7826 (t0) REVERT: M 341 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7648 (mmm160) REVERT: M 391 MET cc_start: 0.8211 (ttt) cc_final: 0.7820 (mtp) outliers start: 36 outliers final: 33 residues processed: 375 average time/residue: 0.3133 time to fit residues: 169.7130 Evaluate side-chains 375 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 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 E residue 108 GLN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER 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 283 SER Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 52 ILE 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 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 124 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 166 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN I 119 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097442 restraints weight = 22950.681| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.03 r_work: 0.2906 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15346 Z= 0.165 Angle : 0.684 14.494 20774 Z= 0.319 Chirality : 0.045 0.210 2499 Planarity : 0.004 0.045 2541 Dihedral : 8.354 158.212 2363 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.50 % Allowed : 18.27 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1905 helix: 2.37 (0.15), residues: 1173 sheet: 0.80 (0.30), residues: 270 loop : -0.83 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 100 HIS 0.004 0.001 HIS I 79 PHE 0.030 0.001 PHE I 210 TYR 0.026 0.001 TYR M 158 ARG 0.007 0.001 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 948) hydrogen bonds : angle 4.09805 ( 2817) covalent geometry : bond 0.00383 (15345) covalent geometry : angle 0.68418 (20774) Misc. bond : bond 0.01036 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9143.05 seconds wall clock time: 158 minutes 21.10 seconds (9501.10 seconds total)