Starting phenix.real_space_refine on Wed Mar 4 17:35:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpo_14859/03_2026/7zpo_14859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpo_14859/03_2026/7zpo_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_14859/03_2026/7zpo_14859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpo_14859/03_2026/7zpo_14859.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpo_14859/03_2026/7zpo_14859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpo_14859/03_2026/7zpo_14859.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 4.23, per 1000 atoms: 0.28 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: 1.44 Conformation dependent library (CDL) restraints added in 841.7 milliseconds 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: 0.45 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: 2.63 Time building geometry restraints manager: 1.90 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 1001) selection = (chain 'E' and resid 6 through 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.180 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- 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 : 10.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.001 ARG I 26 TYR 0.011 0.001 TYR I 435 PHE 0.024 0.001 PHE M 210 TRP 0.011 0.001 TRP I 355 HIS 0.004 0.001 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00360 (15345) covalent geometry : angle 0.73419 (20774) hydrogen bonds : bond 0.19693 ( 948) hydrogen bonds : angle 6.60279 ( 2817) 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 : 0.626 Fit side-chains revert: symmetry clash 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: 0.6454 (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: 0.7969 (mmp) REVERT: F 7 GLN cc_start: 0.6646 (tt0) cc_final: 0.6266 (pt0) REVERT: F 70 TYR cc_start: 0.6985 (m-80) cc_final: 0.6648 (m-80) REVERT: I 387 PHE cc_start: 0.7432 (t80) cc_final: 0.7192 (t80) REVERT: I 449 GLU cc_start: 0.7231 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 121 ILE cc_start: 0.8290 (mm) cc_final: 0.8082 (mp) REVERT: L 70 TYR cc_start: 0.7303 (m-80) cc_final: 0.7100 (m-80) REVERT: L 81 VAL cc_start: 0.7928 (p) cc_final: 0.7708 (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: 0.7810 (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: 0.7777 (t80) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.1279 time to fit residues: 95.8341 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 : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN I 275 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS M 118 GLN M 182 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110431 restraints weight = 28780.911| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.27 r_work: 0.3071 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15346 Z= 0.149 Angle : 0.672 10.539 20774 Z= 0.321 Chirality : 0.045 0.183 2499 Planarity : 0.004 0.039 2541 Dihedral : 13.571 177.263 2363 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.35 % Allowed : 10.06 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 1905 helix: 2.14 (0.14), residues: 1183 sheet: 1.85 (0.30), residues: 280 loop : -0.53 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 110 TYR 0.009 0.001 TYR H 70 PHE 0.040 0.002 PHE I 210 TRP 0.015 0.001 TRP L 100 HIS 0.007 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00322 (15345) covalent geometry : angle 0.67223 (20774) hydrogen bonds : bond 0.04509 ( 948) hydrogen bonds : angle 4.40480 ( 2817) Misc. bond : bond 0.00369 ( 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 411 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 390 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7579 (mmm160) REVERT: E 74 MET cc_start: 0.8463 (tpp) cc_final: 0.8177 (tpp) REVERT: E 119 HIS cc_start: 0.7397 (m90) cc_final: 0.7132 (m90) REVERT: E 129 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7385 (mp) REVERT: F 70 TYR cc_start: 0.7307 (m-80) cc_final: 0.6785 (m-80) REVERT: F 136 LEU cc_start: 0.7261 (mt) cc_final: 0.6977 (mp) REVERT: I 260 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7385 (mm-30) REVERT: I 263 ASN cc_start: 0.7524 (t0) cc_final: 0.7294 (t0) REVERT: I 295 ASP cc_start: 0.7942 (t0) cc_final: 0.7571 (t0) REVERT: A 15 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8251 (mtm110) REVERT: A 121 ILE cc_start: 0.8613 (mm) cc_final: 0.8381 (mp) REVERT: A 126 ASP cc_start: 0.8047 (m-30) cc_final: 0.7756 (t0) REVERT: B 110 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: L 61 THR cc_start: 0.7443 (m) cc_final: 0.7188 (m) REVERT: L 65 LEU cc_start: 0.7696 (mp) cc_final: 0.7402 (mp) REVERT: L 127 MET cc_start: 0.8531 (mmp) cc_final: 0.8313 (tpp) REVERT: M 94 ILE cc_start: 0.8695 (mm) cc_final: 0.8472 (mt) REVERT: M 108 TYR cc_start: 0.8541 (t80) cc_final: 0.8340 (t80) REVERT: M 212 PHE cc_start: 0.7904 (m-10) cc_final: 0.7649 (m-80) REVERT: M 225 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7562 (mtp180) REVERT: M 295 ASP cc_start: 0.7978 (t0) cc_final: 0.7639 (t0) REVERT: M 390 VAL cc_start: 0.8468 (t) cc_final: 0.8202 (p) REVERT: M 441 GLU cc_start: 0.7908 (tt0) cc_final: 0.7619 (tt0) outliers start: 21 outliers final: 13 residues processed: 405 average time/residue: 0.1169 time to fit residues: 69.5621 Evaluate side-chains 365 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 351 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 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 J residue 114 LYS Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN I 176 HIS I 182 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.125595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098649 restraints weight = 23930.322| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.08 r_work: 0.2891 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15346 Z= 0.222 Angle : 0.711 9.856 20774 Z= 0.341 Chirality : 0.047 0.243 2499 Planarity : 0.004 0.042 2541 Dihedral : 11.947 171.111 2363 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 12.95 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1905 helix: 2.04 (0.14), residues: 1179 sheet: 1.30 (0.29), residues: 280 loop : -0.39 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG J 130 TYR 0.013 0.002 TYR J 70 PHE 0.035 0.002 PHE I 210 TRP 0.009 0.001 TRP M 227 HIS 0.005 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00521 (15345) covalent geometry : angle 0.71052 (20774) hydrogen bonds : bond 0.04732 ( 948) hydrogen bonds : angle 4.33145 ( 2817) Misc. bond : bond 0.00437 ( 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 425 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7451 (mttp) REVERT: E 129 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8003 (mt) REVERT: F 61 THR cc_start: 0.7427 (m) cc_final: 0.7084 (m) REVERT: I 136 ARG cc_start: 0.7742 (ttt-90) cc_final: 0.7018 (ttp-170) REVERT: I 271 THR cc_start: 0.7993 (p) cc_final: 0.7688 (m) REVERT: I 292 ASN cc_start: 0.8730 (p0) cc_final: 0.8454 (p0) REVERT: I 295 ASP cc_start: 0.8015 (t0) cc_final: 0.7695 (t0) REVERT: I 334 MET cc_start: 0.9150 (mmp) cc_final: 0.8896 (mmm) REVERT: A 126 ASP cc_start: 0.8703 (m-30) cc_final: 0.8216 (t0) REVERT: B 22 LYS cc_start: 0.7773 (mmpt) cc_final: 0.7555 (mmtm) REVERT: B 133 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7058 (mmt-90) REVERT: J 23 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7645 (mm-30) REVERT: J 134 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7863 (mtmt) REVERT: L 65 LEU cc_start: 0.7731 (mp) cc_final: 0.7482 (mp) REVERT: M 151 ILE cc_start: 0.9024 (mt) cc_final: 0.8820 (mt) REVERT: M 267 MET cc_start: 0.7633 (ttm) cc_final: 0.7391 (ttm) REVERT: M 292 ASN cc_start: 0.8710 (p0) cc_final: 0.8206 (p0) REVERT: M 341 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7863 (mmm160) outliers start: 38 outliers final: 27 residues processed: 411 average time/residue: 0.1267 time to fit residues: 74.7113 Evaluate side-chains 369 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 341 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 90 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 89 MET Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 297 THR Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** D 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 25 GLN I 93 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099695 restraints weight = 27785.973| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.34 r_work: 0.2915 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15346 Z= 0.121 Angle : 0.615 7.631 20774 Z= 0.289 Chirality : 0.043 0.196 2499 Planarity : 0.003 0.042 2541 Dihedral : 10.658 169.930 2363 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.86 % Allowed : 14.87 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1905 helix: 2.31 (0.14), residues: 1175 sheet: 1.34 (0.30), residues: 272 loop : -0.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 130 TYR 0.012 0.001 TYR L 70 PHE 0.032 0.001 PHE I 210 TRP 0.012 0.001 TRP I 355 HIS 0.003 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00256 (15345) covalent geometry : angle 0.61505 (20774) hydrogen bonds : bond 0.03737 ( 948) hydrogen bonds : angle 4.09272 ( 2817) Misc. bond : bond 0.00310 ( 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 404 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 375 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7086 (ttpt) cc_final: 0.6630 (pttt) REVERT: H 97 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7311 (mttp) REVERT: F 64 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7265 (pt0) REVERT: F 93 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6703 (mm-30) REVERT: I 334 MET cc_start: 0.8878 (mmp) cc_final: 0.8646 (mmm) REVERT: A 126 ASP cc_start: 0.8462 (m-30) cc_final: 0.7954 (t0) REVERT: B 22 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7319 (mmtm) REVERT: B 39 ASP cc_start: 0.6974 (m-30) cc_final: 0.6669 (m-30) REVERT: B 133 ARG cc_start: 0.7696 (mmt90) cc_final: 0.6970 (mmt-90) REVERT: J 133 ARG cc_start: 0.7001 (mmm160) cc_final: 0.6663 (mmm160) REVERT: L 65 LEU cc_start: 0.7758 (mp) cc_final: 0.7550 (mp) REVERT: M 109 MET cc_start: 0.8100 (mmm) cc_final: 0.7751 (mtt) REVERT: M 267 MET cc_start: 0.7680 (ttm) cc_final: 0.7455 (ttm) REVERT: M 295 ASP cc_start: 0.8134 (t0) cc_final: 0.7814 (t0) REVERT: M 341 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7448 (mmm160) REVERT: M 390 VAL cc_start: 0.8612 (t) cc_final: 0.8351 (p) REVERT: M 441 GLU cc_start: 0.7793 (tt0) cc_final: 0.7581 (tt0) outliers start: 29 outliers final: 19 residues processed: 393 average time/residue: 0.1176 time to fit residues: 67.7264 Evaluate side-chains 361 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 93 GLN Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 324 ILE 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 172 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS D 58 HIS F 25 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097152 restraints weight = 29756.258| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.33 r_work: 0.2857 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15346 Z= 0.174 Angle : 0.652 8.001 20774 Z= 0.308 Chirality : 0.044 0.199 2499 Planarity : 0.004 0.044 2541 Dihedral : 10.350 162.403 2363 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.88 % Allowed : 15.38 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1905 helix: 2.28 (0.15), residues: 1178 sheet: 1.10 (0.30), residues: 272 loop : -0.49 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 130 TYR 0.014 0.002 TYR L 70 PHE 0.032 0.001 PHE I 210 TRP 0.009 0.001 TRP M 355 HIS 0.003 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00405 (15345) covalent geometry : angle 0.65242 (20774) hydrogen bonds : bond 0.04103 ( 948) hydrogen bonds : angle 4.12103 ( 2817) Misc. bond : bond 0.00340 ( 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 397 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6664 (pttt) REVERT: H 97 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7397 (mttp) REVERT: F 80 ASP cc_start: 0.7719 (t0) cc_final: 0.7481 (t0) REVERT: I 136 ARG cc_start: 0.7736 (ttt-90) cc_final: 0.6987 (ttp-170) REVERT: I 151 ILE cc_start: 0.9102 (mt) cc_final: 0.8835 (mp) REVERT: I 292 ASN cc_start: 0.8689 (p0) cc_final: 0.8463 (p0) REVERT: I 334 MET cc_start: 0.8984 (mmp) cc_final: 0.8749 (mmm) REVERT: A 126 ASP cc_start: 0.8522 (m-30) cc_final: 0.7988 (t0) REVERT: B 22 LYS cc_start: 0.7596 (mmpt) cc_final: 0.7355 (mmtm) REVERT: B 129 ILE cc_start: 0.9049 (mm) cc_final: 0.8815 (mt) REVERT: B 133 ARG cc_start: 0.7808 (mmt90) cc_final: 0.7605 (mmm160) REVERT: L 40 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7413 (mtt180) REVERT: L 65 LEU cc_start: 0.7729 (mp) cc_final: 0.7479 (mp) REVERT: M 341 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7592 (mmm160) REVERT: M 441 GLU cc_start: 0.7855 (tt0) cc_final: 0.7653 (tt0) outliers start: 45 outliers final: 31 residues processed: 379 average time/residue: 0.1137 time to fit residues: 63.3515 Evaluate side-chains 360 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 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 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain 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 40 ARG Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 297 THR 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 142 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100659 restraints weight = 29385.201| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.31 r_work: 0.2923 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15346 Z= 0.119 Angle : 0.613 7.346 20774 Z= 0.286 Chirality : 0.042 0.218 2499 Planarity : 0.003 0.045 2541 Dihedral : 9.741 161.147 2363 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.37 % Allowed : 16.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1905 helix: 2.42 (0.15), residues: 1176 sheet: 1.21 (0.30), residues: 270 loop : -0.53 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 130 TYR 0.012 0.001 TYR L 70 PHE 0.030 0.001 PHE I 210 TRP 0.012 0.001 TRP I 355 HIS 0.002 0.001 HIS M 176 Details of bonding type rmsd covalent geometry : bond 0.00257 (15345) covalent geometry : angle 0.61279 (20774) hydrogen bonds : bond 0.03603 ( 948) hydrogen bonds : angle 4.02515 ( 2817) Misc. bond : bond 0.00240 ( 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 410 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7098 (ttpt) cc_final: 0.6710 (pttt) REVERT: H 97 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7372 (mttp) REVERT: F 93 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6791 (mm-30) REVERT: I 136 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.6942 (ttp-170) REVERT: I 151 ILE cc_start: 0.9079 (mt) cc_final: 0.8785 (mp) REVERT: I 292 ASN cc_start: 0.8641 (p0) cc_final: 0.8386 (p0) REVERT: I 334 MET cc_start: 0.8955 (mmp) cc_final: 0.8727 (mmm) REVERT: A 126 ASP cc_start: 0.8463 (m-30) cc_final: 0.7972 (t0) REVERT: B 22 LYS cc_start: 0.7534 (mmpt) cc_final: 0.7297 (mmtm) REVERT: B 37 ASN cc_start: 0.7145 (t0) cc_final: 0.6816 (t0) REVERT: B 133 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7654 (mmm160) REVERT: J 114 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (tttt) REVERT: M 109 MET cc_start: 0.8102 (mmm) cc_final: 0.7821 (mtt) REVERT: M 151 ILE cc_start: 0.9060 (mt) cc_final: 0.8845 (mp) REVERT: M 295 ASP cc_start: 0.8075 (t0) cc_final: 0.7823 (t0) REVERT: M 341 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7513 (mmm160) outliers start: 37 outliers final: 26 residues processed: 399 average time/residue: 0.1172 time to fit residues: 68.4088 Evaluate side-chains 367 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 340 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 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 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 I residue 56 THR Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 388 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 283 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 133 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS D 25 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 119 HIS ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098853 restraints weight = 27998.554| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.23 r_work: 0.2889 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15346 Z= 0.154 Angle : 0.646 11.398 20774 Z= 0.300 Chirality : 0.044 0.220 2499 Planarity : 0.004 0.045 2541 Dihedral : 9.544 159.930 2363 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.76 % Allowed : 16.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.19), residues: 1905 helix: 2.36 (0.15), residues: 1184 sheet: 1.07 (0.30), residues: 272 loop : -0.49 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 439 TYR 0.025 0.001 TYR I 158 PHE 0.031 0.001 PHE I 210 TRP 0.010 0.001 TRP F 100 HIS 0.003 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00355 (15345) covalent geometry : angle 0.64556 (20774) hydrogen bonds : bond 0.03801 ( 948) hydrogen bonds : angle 4.05734 ( 2817) Misc. bond : bond 0.00466 ( 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 397 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 354 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6700 (pttt) REVERT: H 93 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7428 (mt-10) REVERT: H 97 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7379 (mttp) REVERT: F 93 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6806 (mm-30) REVERT: I 57 ASP cc_start: 0.7964 (m-30) cc_final: 0.7640 (m-30) REVERT: I 136 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.6864 (ttp80) REVERT: I 292 ASN cc_start: 0.8674 (p0) cc_final: 0.8413 (p0) REVERT: I 334 MET cc_start: 0.8945 (mmp) cc_final: 0.8724 (mmm) REVERT: A 126 ASP cc_start: 0.8447 (m-30) cc_final: 0.7992 (t0) REVERT: B 22 LYS cc_start: 0.7644 (mmpt) cc_final: 0.7382 (mmtm) REVERT: B 37 ASN cc_start: 0.7182 (t0) cc_final: 0.6778 (t0) REVERT: L 40 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7379 (mtt180) REVERT: L 65 LEU cc_start: 0.7823 (mp) cc_final: 0.7622 (mp) REVERT: M 151 ILE cc_start: 0.9095 (mt) cc_final: 0.8836 (mp) REVERT: M 250 LEU cc_start: 0.8335 (tt) cc_final: 0.7813 (mt) REVERT: M 341 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7508 (mmm160) outliers start: 43 outliers final: 32 residues processed: 377 average time/residue: 0.1156 time to fit residues: 63.4723 Evaluate side-chains 371 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 338 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 89 LEU 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 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 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 40 ARG 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 283 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 388 ASP Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS D 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099922 restraints weight = 29576.814| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.32 r_work: 0.2924 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4630 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= 0.125 Angle : 0.624 12.695 20774 Z= 0.290 Chirality : 0.043 0.226 2499 Planarity : 0.003 0.044 2541 Dihedral : 9.169 159.038 2363 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.31 % Allowed : 17.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1905 helix: 2.43 (0.15), residues: 1183 sheet: 1.16 (0.30), residues: 270 loop : -0.59 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 133 TYR 0.024 0.001 TYR I 158 PHE 0.030 0.001 PHE I 210 TRP 0.006 0.001 TRP M 224 HIS 0.003 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00277 (15345) covalent geometry : angle 0.62413 (20774) hydrogen bonds : bond 0.03593 ( 948) hydrogen bonds : angle 4.02886 ( 2817) Misc. bond : bond 0.00395 ( 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 396 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 360 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6728 (pttt) REVERT: H 22 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7707 (tttp) REVERT: H 97 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7348 (mttp) REVERT: I 57 ASP cc_start: 0.7971 (m-30) cc_final: 0.7658 (m-30) REVERT: I 136 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.6831 (ttp80) REVERT: I 151 ILE cc_start: 0.9089 (mt) cc_final: 0.8845 (mp) REVERT: I 250 LEU cc_start: 0.8268 (tt) cc_final: 0.7784 (mt) REVERT: I 292 ASN cc_start: 0.8651 (p0) cc_final: 0.8393 (p0) REVERT: I 334 MET cc_start: 0.8938 (mmp) cc_final: 0.8720 (mmm) REVERT: A 126 ASP cc_start: 0.8400 (m-30) cc_final: 0.7867 (t0) REVERT: B 22 LYS cc_start: 0.7643 (mmpt) cc_final: 0.7392 (mmtm) REVERT: B 127 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8448 (tpt) REVERT: M 151 ILE cc_start: 0.9098 (mt) cc_final: 0.8832 (mp) REVERT: M 250 LEU cc_start: 0.8308 (tt) cc_final: 0.7788 (mt) REVERT: M 272 THR cc_start: 0.8050 (m) cc_final: 0.7764 (t) REVERT: M 295 ASP cc_start: 0.8059 (t0) cc_final: 0.7749 (t0) REVERT: M 341 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7490 (mmm160) outliers start: 36 outliers final: 28 residues processed: 383 average time/residue: 0.1189 time to fit residues: 66.7196 Evaluate side-chains 374 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 345 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 E residue 10 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 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 127 MET Chi-restraints excluded: chain J residue 114 LYS 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 283 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 174 optimal weight: 0.0000 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 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 = 0.3503 r_free = 0.3503 target = 0.129080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101887 restraints weight = 29591.236| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.34 r_work: 0.2943 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15346 Z= 0.114 Angle : 0.617 12.981 20774 Z= 0.286 Chirality : 0.043 0.219 2499 Planarity : 0.003 0.044 2541 Dihedral : 8.758 155.557 2363 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.19), residues: 1905 helix: 2.47 (0.15), residues: 1183 sheet: 1.21 (0.30), residues: 270 loop : -0.61 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 130 TYR 0.024 0.001 TYR I 158 PHE 0.029 0.001 PHE I 210 TRP 0.010 0.001 TRP F 100 HIS 0.003 0.000 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00243 (15345) covalent geometry : angle 0.61692 (20774) hydrogen bonds : bond 0.03437 ( 948) hydrogen bonds : angle 3.98227 ( 2817) Misc. bond : bond 0.00379 ( 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 396 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 363 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 LYS cc_start: 0.7128 (ttpt) cc_final: 0.6741 (pttt) REVERT: H 22 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7752 (tttp) REVERT: H 97 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7282 (mttp) REVERT: H 118 ASP cc_start: 0.7515 (m-30) cc_final: 0.7219 (m-30) REVERT: F 26 ASP cc_start: 0.7349 (m-30) cc_final: 0.6990 (m-30) REVERT: F 48 VAL cc_start: 0.8625 (m) cc_final: 0.8397 (p) REVERT: F 122 MET cc_start: 0.8380 (mtp) cc_final: 0.8091 (mtp) REVERT: I 57 ASP cc_start: 0.7949 (m-30) cc_final: 0.7655 (m-30) REVERT: I 136 ARG cc_start: 0.7642 (ttt-90) cc_final: 0.6820 (ttp80) REVERT: I 151 ILE cc_start: 0.9076 (mt) cc_final: 0.8824 (mp) REVERT: I 292 ASN cc_start: 0.8630 (p0) cc_final: 0.8367 (p0) REVERT: A 126 ASP cc_start: 0.8373 (m-30) cc_final: 0.7877 (t0) REVERT: B 22 LYS cc_start: 0.7662 (mmpt) cc_final: 0.7423 (mmtm) REVERT: B 68 ASP cc_start: 0.7927 (p0) cc_final: 0.7725 (p0) REVERT: B 133 ARG cc_start: 0.8254 (mmm160) cc_final: 0.8029 (mmm160) REVERT: J 64 GLU cc_start: 0.7848 (tp30) cc_final: 0.7131 (tp30) REVERT: J 108 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: M 151 ILE cc_start: 0.9086 (mt) cc_final: 0.8803 (mp) REVERT: M 272 THR cc_start: 0.8001 (m) cc_final: 0.7738 (t) REVERT: M 295 ASP cc_start: 0.8042 (t0) cc_final: 0.7764 (t0) REVERT: M 341 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7455 (mmm160) outliers start: 33 outliers final: 27 residues processed: 382 average time/residue: 0.1249 time to fit residues: 69.4742 Evaluate side-chains 373 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 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 34 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain J residue 108 GLN 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 283 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN I 119 GLN B 104 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103126 restraints weight = 19625.237| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.87 r_work: 0.2961 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4781 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= 0.138 Angle : 0.644 14.023 20774 Z= 0.299 Chirality : 0.044 0.216 2499 Planarity : 0.004 0.048 2541 Dihedral : 8.660 156.435 2363 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.24 % Allowed : 17.56 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1905 helix: 2.44 (0.15), residues: 1183 sheet: 1.17 (0.30), residues: 270 loop : -0.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 130 TYR 0.025 0.001 TYR I 158 PHE 0.030 0.001 PHE I 210 TRP 0.008 0.001 TRP M 166 HIS 0.003 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00314 (15345) covalent geometry : angle 0.64410 (20774) hydrogen bonds : bond 0.03641 ( 948) hydrogen bonds : angle 4.02210 ( 2817) Misc. bond : bond 0.00579 ( 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 382 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 347 time to evaluate : 0.581 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: 0.6673 (pttt) REVERT: H 22 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7735 (tttp) REVERT: H 97 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7311 (mttp) REVERT: H 118 ASP cc_start: 0.7703 (m-30) cc_final: 0.7347 (m-30) REVERT: D 133 ARG cc_start: 0.8367 (mmt90) cc_final: 0.7854 (mmt90) REVERT: E 130 ARG cc_start: 0.8448 (mtp180) cc_final: 0.8103 (mtt-85) REVERT: F 122 MET cc_start: 0.8511 (mtp) cc_final: 0.8231 (mtp) REVERT: I 57 ASP cc_start: 0.8072 (m-30) cc_final: 0.7768 (m-30) REVERT: I 136 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.6835 (ttp80) REVERT: I 151 ILE cc_start: 0.9089 (mt) cc_final: 0.8831 (mp) REVERT: I 250 LEU cc_start: 0.8329 (tt) cc_final: 0.7837 (mt) REVERT: I 292 ASN cc_start: 0.8736 (p0) cc_final: 0.8460 (p0) REVERT: I 334 MET cc_start: 0.9046 (mmp) cc_final: 0.8831 (mmm) REVERT: A 126 ASP cc_start: 0.8589 (m-30) cc_final: 0.7967 (t0) REVERT: B 22 LYS cc_start: 0.7664 (mmpt) cc_final: 0.7403 (mmtm) REVERT: B 110 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8539 (mtm-85) REVERT: J 108 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: M 151 ILE cc_start: 0.9133 (mt) cc_final: 0.8831 (mp) REVERT: M 250 LEU cc_start: 0.8390 (tt) cc_final: 0.7861 (mt) REVERT: M 341 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7649 (mmm160) outliers start: 35 outliers final: 31 residues processed: 370 average time/residue: 0.1201 time to fit residues: 65.0646 Evaluate side-chains 373 residues out of total 1558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 341 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 99 VAL 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 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 299 PHE Chi-restraints excluded: chain I residue 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 34 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 108 GLN 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 283 SER Chi-restraints excluded: chain M residue 299 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain M residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 185 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 119 HIS F 25 GLN I 119 GLN I 345 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096899 restraints weight = 29666.590| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.28 r_work: 0.2859 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4850 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= 0.177 Angle : 0.680 14.069 20774 Z= 0.318 Chirality : 0.045 0.208 2499 Planarity : 0.004 0.047 2541 Dihedral : 8.841 159.630 2363 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1905 helix: 2.35 (0.15), residues: 1185 sheet: 0.97 (0.30), residues: 270 loop : -0.63 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 130 TYR 0.025 0.002 TYR I 158 PHE 0.031 0.001 PHE I 210 TRP 0.013 0.001 TRP F 100 HIS 0.005 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00415 (15345) covalent geometry : angle 0.68002 (20774) hydrogen bonds : bond 0.03934 ( 948) hydrogen bonds : angle 4.11216 ( 2817) Misc. bond : bond 0.00618 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3747.71 seconds wall clock time: 64 minutes 56.06 seconds (3896.06 seconds total)