Starting phenix.real_space_refine on Fri Jul 3 22:15:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5u_63884/07_2026/9u5u_63884.cif" } resolution = 3.12 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= 0.003 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 26 5.16 5 C 9393 2.51 5 N 3037 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16392 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2332 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 3 Chain: "M" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "N" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 911 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 106} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU O 73 " occ=0.78 ... (6 atoms not shown) pdb=" CD2 LEU O 73 " occ=0.78 residue: pdb=" N GLY O 75 " occ=0.79 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.79 residue: pdb=" N GLY O 76 " occ=0.70 ... (3 atoms not shown) pdb=" OXT GLY O 76 " occ=0.70 Time building chain proxies: 3.67, per 1000 atoms: 0.22 Number of scatterers: 16392 At special positions: 0 Unit cell: (132.846, 117.475, 139.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 294 15.00 O 3642 8.00 N 3037 7.00 C 9393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 559.4 milliseconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 61.2% alpha, 6.5% beta 133 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.667A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.012A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.705A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.527A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.501A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.556A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.602A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.693A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.695A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.443A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 54 through 60 removed outlier: 3.537A pdb=" N SER L 58 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.858A pdb=" N ALA L 95 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN L 102 " --> pdb=" O SER L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 119 removed outlier: 4.009A pdb=" N ARG L 114 " --> pdb=" O PRO L 110 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET L 115 " --> pdb=" O THR L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 129 through 133 Processing helix chain 'L' and resid 134 through 144 removed outlier: 3.843A pdb=" N ALA L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 236 through 241 Processing helix chain 'L' and resid 649 through 668 removed outlier: 3.547A pdb=" N PHE L 660 " --> pdb=" O LYS L 656 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP L 663 " --> pdb=" O LYS L 659 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN L 665 " --> pdb=" O LYS L 661 " (cutoff:3.500A) Processing helix chain 'L' and resid 671 through 686 Processing helix chain 'L' and resid 687 through 695 removed outlier: 4.153A pdb=" N LEU L 691 " --> pdb=" O MET L 687 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 4.322A pdb=" N LYS M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 269 through 275 Processing helix chain 'N' and resid 277 through 285 Processing helix chain 'N' and resid 286 through 288 No H-bonds generated for 'chain 'N' and resid 286 through 288' Processing helix chain 'N' and resid 304 through 308 removed outlier: 4.233A pdb=" N LEU N 308 " --> pdb=" O SER N 305 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 327 Processing helix chain 'N' and resid 330 through 349 removed outlier: 3.523A pdb=" N VAL N 335 " --> pdb=" O HIS N 331 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG N 336 " --> pdb=" O GLU N 332 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS N 345 " --> pdb=" O MET N 341 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL N 347 " --> pdb=" O LYS N 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.620A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.381A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.933A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.420A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.525A pdb=" N VAL L 171 " --> pdb=" O PHE L 48 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA L 167 " --> pdb=" O TRP L 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 12 through 15 removed outlier: 3.536A pdb=" N PHE M 45 " --> pdb=" O LYS M 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 12 through 16 removed outlier: 4.071A pdb=" N SER O 65 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE O 44 " --> pdb=" O HIS O 68 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3538 1.33 - 1.45: 4904 1.45 - 1.57: 8210 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 17285 Sorted by residual: bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 ... (remaining 17280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 23688 1.93 - 3.87: 848 3.87 - 5.80: 34 5.80 - 7.73: 6 7.73 - 9.66: 3 Bond angle restraints: 24579 Sorted by residual: angle pdb=" N GLU L 54 " pdb=" CA GLU L 54 " pdb=" C GLU L 54 " ideal model delta sigma weight residual 110.80 120.46 -9.66 2.13e+00 2.20e-01 2.06e+01 angle pdb=" N3 DT J 64 " pdb=" C4 DT J 64 " pdb=" O4 DT J 64 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I 66 " pdb=" C4 DT I 66 " pdb=" O4 DT I 66 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 24574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 8175 34.05 - 68.10: 1483 68.10 - 102.16: 18 102.16 - 136.21: 1 136.21 - 170.26: 2 Dihedral angle restraints: 9679 sinusoidal: 5937 harmonic: 3742 Sorted by residual: dihedral pdb=" CA ASP O 39 " pdb=" C ASP O 39 " pdb=" N GLN O 40 " pdb=" CA GLN O 40 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE L 660 " pdb=" C PHE L 660 " pdb=" N LYS L 661 " pdb=" CA LYS L 661 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 9676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2277 0.061 - 0.122: 466 0.122 - 0.183: 24 0.183 - 0.244: 0 0.244 - 0.304: 1 Chirality restraints: 2768 Sorted by residual: chirality pdb=" CA GLU L 54 " pdb=" N GLU L 54 " pdb=" C GLU L 54 " pdb=" CB GLU L 54 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE L 176 " pdb=" CA ILE L 176 " pdb=" CG1 ILE L 176 " pdb=" CG2 ILE L 176 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA PHE N 312 " pdb=" N PHE N 312 " pdb=" C PHE N 312 " pdb=" CB PHE N 312 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 2765 not shown) Planarity restraints: 2117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 41 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO L 42 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP O 58 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP O 58 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP O 58 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR O 59 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 81 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ASP E 81 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP E 81 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 82 " -0.011 2.00e-02 2.50e+03 ... (remaining 2114 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 27 2.37 - 3.00: 7842 3.00 - 3.63: 26091 3.63 - 4.27: 41149 4.27 - 4.90: 61449 Nonbonded interactions: 136558 Sorted by model distance: nonbonded pdb=" OE2 GLU C 61 " pdb=" NH1 ARG L 59 " model vdw 1.735 3.120 nonbonded pdb=" OE2 GLU C 61 " pdb=" CZ ARG L 59 " model vdw 1.846 3.270 nonbonded pdb=" O GLU L 54 " pdb=" N ARG L 56 " model vdw 1.898 3.120 nonbonded pdb=" OH TYR L 129 " pdb=" O LEU O 71 " model vdw 2.091 3.040 nonbonded pdb=" OG SER L 123 " pdb=" OG SER L 126 " model vdw 2.152 3.040 ... (remaining 136553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = (chain 'O' and resid 1 through 75) } 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.790 Find NCS groups from input model: 0.150 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17285 Z= 0.458 Angle : 0.750 9.664 24579 Z= 0.611 Chirality : 0.047 0.304 2768 Planarity : 0.004 0.059 2117 Dihedral : 25.226 170.259 7257 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.76 % Rotamer: Outliers : 1.90 % Allowed : 18.61 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.23 (0.24), residues: 1265 helix: 1.12 (0.20), residues: 744 sheet: -1.17 (0.54), residues: 77 loop : -1.22 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 336 TYR 0.013 0.001 TYR B 51 PHE 0.018 0.002 PHE L 660 TRP 0.012 0.002 TRP L 202 HIS 0.008 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.46 (17285) covalent geometry : angle 0.75035 / 0.61 (24579) hydrogen bonds : bond 0.14713 / 9.61 ( 913) hydrogen bonds : angle 4.97474 / 3.60 ( 2328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 79 LYS cc_start: 0.8994 (mptt) cc_final: 0.8515 (mttt) REVERT: B 91 LYS cc_start: 0.9175 (ttpt) cc_final: 0.8967 (ttpt) REVERT: C 73 ASN cc_start: 0.8982 (t0) cc_final: 0.8757 (t0) REVERT: C 95 LYS cc_start: 0.9361 (tttp) cc_final: 0.8918 (ttpt) REVERT: D 85 LYS cc_start: 0.9045 (mptt) cc_final: 0.8795 (mmtt) REVERT: D 108 LYS cc_start: 0.8677 (pttt) cc_final: 0.8395 (pttt) REVERT: G 13 LYS cc_start: 0.6944 (tptt) cc_final: 0.6648 (ptmm) REVERT: G 36 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8747 (pttp) REVERT: G 104 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8502 (mt0) REVERT: H 108 LYS cc_start: 0.8400 (tttm) cc_final: 0.8196 (mtpt) REVERT: H 120 LYS cc_start: 0.8281 (tptt) cc_final: 0.7909 (mtpp) REVERT: L 44 TYR cc_start: 0.6470 (m-80) cc_final: 0.6184 (m-10) REVERT: L 57 ARG cc_start: 0.5913 (tpp80) cc_final: 0.5518 (tpt90) REVERT: L 142 ASN cc_start: 0.7939 (m-40) cc_final: 0.7650 (m-40) REVERT: L 230 LEU cc_start: 0.7955 (pt) cc_final: 0.7524 (mt) REVERT: M 1 MET cc_start: 0.3412 (ppp) cc_final: 0.1513 (ptm) REVERT: M 12 THR cc_start: 0.4620 (OUTLIER) cc_final: 0.4291 (p) REVERT: N 283 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6969 (pp30) REVERT: N 294 GLN cc_start: 0.5675 (pm20) cc_final: 0.5467 (pp30) REVERT: N 304 SER cc_start: 0.6415 (t) cc_final: 0.6061 (m) REVERT: O 67 LEU cc_start: 0.5224 (OUTLIER) cc_final: 0.4229 (tm) outliers start: 21 outliers final: 7 residues processed: 294 average time/residue: 0.1716 time to fit residues: 69.9299 Evaluate side-chains 224 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 94 HIS Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 84 GLN D 49 HIS L 89 ASN ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS L 229 ASN ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN N 269 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.143608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085770 restraints weight = 28735.445| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.87 r_work: 0.2856 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17285 Z= 0.189 Angle : 0.652 8.020 24579 Z= 0.376 Chirality : 0.046 0.244 2768 Planarity : 0.005 0.054 2117 Dihedral : 28.535 172.074 4650 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.43 % Allowed : 17.25 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.49 (0.24), residues: 1265 helix: 1.36 (0.20), residues: 759 sheet: -1.36 (0.52), residues: 73 loop : -1.20 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 238 TYR 0.022 0.002 TYR L 129 PHE 0.018 0.002 PHE O 4 TRP 0.005 0.002 TRP N 320 HIS 0.007 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (17285) covalent geometry : angle 0.65205 / 0.38 (24579) hydrogen bonds : bond 0.05142 / 3.38 ( 913) hydrogen bonds : angle 3.86120 / 2.79 ( 2328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9049 (mptt) cc_final: 0.8550 (mttt) REVERT: B 91 LYS cc_start: 0.9305 (ttpt) cc_final: 0.9013 (ttmt) REVERT: C 95 LYS cc_start: 0.9362 (tttp) cc_final: 0.8879 (ttpt) REVERT: D 85 LYS cc_start: 0.9127 (mptt) cc_final: 0.8816 (mmtt) REVERT: D 108 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8370 (pttt) REVERT: F 31 LYS cc_start: 0.8846 (tttm) cc_final: 0.8643 (tttm) REVERT: F 35 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8701 (ttm-80) REVERT: G 13 LYS cc_start: 0.7019 (tptt) cc_final: 0.6652 (ptmm) REVERT: G 36 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8696 (pttp) REVERT: G 104 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8550 (mt0) REVERT: H 51 ASP cc_start: 0.8631 (p0) cc_final: 0.8398 (p0) REVERT: H 86 ARG cc_start: 0.8756 (mmt90) cc_final: 0.8548 (mmt-90) REVERT: H 108 LYS cc_start: 0.8444 (tttm) cc_final: 0.8217 (mtpt) REVERT: H 120 LYS cc_start: 0.8301 (tptt) cc_final: 0.7860 (mtpp) REVERT: L 11 ASP cc_start: 0.8242 (m-30) cc_final: 0.7730 (m-30) REVERT: L 53 ILE cc_start: 0.0205 (OUTLIER) cc_final: -0.0330 (mt) REVERT: L 230 LEU cc_start: 0.8726 (pt) cc_final: 0.7796 (mt) REVERT: L 661 LYS cc_start: 0.8386 (mmtm) cc_final: 0.7773 (tptt) REVERT: M 1 MET cc_start: 0.3721 (ppp) cc_final: 0.3161 (ppp) REVERT: N 283 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7286 (tm-30) REVERT: N 304 SER cc_start: 0.6372 (t) cc_final: 0.5909 (m) REVERT: N 311 GLU cc_start: 0.7777 (pm20) cc_final: 0.6919 (mt-10) REVERT: N 348 GLU cc_start: 0.2028 (OUTLIER) cc_final: 0.1768 (pt0) REVERT: O 67 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.4963 (tm) outliers start: 38 outliers final: 21 residues processed: 233 average time/residue: 0.1617 time to fit residues: 53.2424 Evaluate side-chains 222 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 94 HIS Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 660 PHE Chi-restraints excluded: chain L residue 688 LEU Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 269 ASN Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 50 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN H 63 ASN H 95 GLN L 89 ASN ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 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 = 0.3973 r_free = 0.3973 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086880 restraints weight = 29025.550| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.88 r_work: 0.2883 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17285 Z= 0.145 Angle : 0.602 7.787 24579 Z= 0.350 Chirality : 0.043 0.249 2768 Planarity : 0.004 0.038 2117 Dihedral : 28.663 173.092 4643 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 17.89 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.76 (0.24), residues: 1265 helix: 1.63 (0.20), residues: 753 sheet: -1.22 (0.54), residues: 67 loop : -1.18 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 271 TYR 0.022 0.001 TYR L 129 PHE 0.024 0.002 PHE L 170 TRP 0.008 0.001 TRP L 52 HIS 0.006 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (17285) covalent geometry : angle 0.60172 / 0.35 (24579) hydrogen bonds : bond 0.04404 / 2.91 ( 913) hydrogen bonds : angle 3.64946 / 2.64 ( 2328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9057 (mptt) cc_final: 0.8537 (mttt) REVERT: B 91 LYS cc_start: 0.9240 (ttpt) cc_final: 0.8939 (ttpt) REVERT: C 76 THR cc_start: 0.9116 (p) cc_final: 0.8875 (t) REVERT: C 95 LYS cc_start: 0.9354 (tttp) cc_final: 0.8883 (ttpt) REVERT: D 85 LYS cc_start: 0.9095 (mptt) cc_final: 0.8788 (mmtt) REVERT: D 108 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8262 (pttt) REVERT: F 31 LYS cc_start: 0.8775 (tttm) cc_final: 0.8522 (tttm) REVERT: F 35 ARG cc_start: 0.8989 (ttm-80) cc_final: 0.8656 (ttm-80) REVERT: G 13 LYS cc_start: 0.7035 (tptt) cc_final: 0.6649 (ptmm) REVERT: G 36 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8824 (pttp) REVERT: G 104 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8510 (mt0) REVERT: H 108 LYS cc_start: 0.8421 (tttm) cc_final: 0.8195 (mtpt) REVERT: H 120 LYS cc_start: 0.8287 (tptt) cc_final: 0.7858 (mtpp) REVERT: L 11 ASP cc_start: 0.8276 (m-30) cc_final: 0.7780 (m-30) REVERT: L 148 GLU cc_start: 0.7369 (tp30) cc_final: 0.6925 (tp30) REVERT: L 661 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8063 (tptm) REVERT: L 705 SER cc_start: 0.7551 (m) cc_final: 0.7200 (t) REVERT: M 1 MET cc_start: 0.3679 (ppp) cc_final: 0.3211 (ppp) REVERT: M 67 LEU cc_start: 0.7927 (pt) cc_final: 0.7076 (mt) REVERT: N 283 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7254 (tm-30) REVERT: N 348 GLU cc_start: 0.2466 (OUTLIER) cc_final: 0.1915 (pt0) REVERT: O 67 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5014 (tm) outliers start: 35 outliers final: 19 residues processed: 227 average time/residue: 0.1656 time to fit residues: 52.8655 Evaluate side-chains 220 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 94 HIS Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 660 PHE Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 688 LEU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.144283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086417 restraints weight = 28651.363| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.86 r_work: 0.2868 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17285 Z= 0.150 Angle : 0.600 8.514 24579 Z= 0.344 Chirality : 0.043 0.252 2768 Planarity : 0.004 0.037 2117 Dihedral : 28.828 173.521 4643 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.98 % Allowed : 17.80 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.89 (0.24), residues: 1265 helix: 1.73 (0.20), residues: 752 sheet: -1.00 (0.56), residues: 69 loop : -1.15 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 131 TYR 0.018 0.002 TYR L 129 PHE 0.021 0.002 PHE L 170 TRP 0.006 0.001 TRP L 52 HIS 0.006 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (17285) covalent geometry : angle 0.60026 / 0.34 (24579) hydrogen bonds : bond 0.04303 / 2.85 ( 913) hydrogen bonds : angle 3.51821 / 2.55 ( 2328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9023 (mptt) cc_final: 0.8532 (mttt) REVERT: B 91 LYS cc_start: 0.9256 (ttpt) cc_final: 0.8951 (ttpt) REVERT: C 76 THR cc_start: 0.9139 (p) cc_final: 0.8912 (t) REVERT: C 95 LYS cc_start: 0.9362 (tttp) cc_final: 0.8878 (ttpt) REVERT: D 59 MET cc_start: 0.8951 (tpp) cc_final: 0.8708 (tpp) REVERT: D 85 LYS cc_start: 0.9105 (mptt) cc_final: 0.8783 (mmtt) REVERT: D 108 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8360 (pttt) REVERT: F 31 LYS cc_start: 0.8785 (tttm) cc_final: 0.8545 (tttm) REVERT: F 35 ARG cc_start: 0.9011 (ttm-80) cc_final: 0.8691 (ttm-80) REVERT: G 13 LYS cc_start: 0.7056 (tptt) cc_final: 0.6580 (ptmm) REVERT: G 36 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8818 (pttp) REVERT: G 104 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8574 (mt0) REVERT: H 108 LYS cc_start: 0.8441 (tttm) cc_final: 0.8201 (mtpt) REVERT: H 120 LYS cc_start: 0.8197 (tptt) cc_final: 0.7835 (mtpp) REVERT: L 11 ASP cc_start: 0.8274 (m-30) cc_final: 0.7779 (m-30) REVERT: L 148 GLU cc_start: 0.7363 (tp30) cc_final: 0.6999 (tp30) REVERT: L 211 MET cc_start: 0.8065 (mmm) cc_final: 0.7567 (mmm) REVERT: L 661 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8103 (tptt) REVERT: L 702 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: L 705 SER cc_start: 0.7555 (m) cc_final: 0.7191 (t) REVERT: M 1 MET cc_start: 0.3773 (ppp) cc_final: 0.3345 (ppp) REVERT: M 67 LEU cc_start: 0.7998 (pt) cc_final: 0.7080 (mt) REVERT: N 283 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7214 (tm-30) REVERT: N 348 GLU cc_start: 0.2342 (OUTLIER) cc_final: 0.1772 (pt0) REVERT: O 27 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7505 (ptmm) REVERT: O 43 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6629 (pp) REVERT: O 67 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5033 (tm) outliers start: 33 outliers final: 19 residues processed: 226 average time/residue: 0.1515 time to fit residues: 48.3061 Evaluate side-chains 223 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 0.0020 chunk 59 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 118 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087187 restraints weight = 28789.406| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.86 r_work: 0.2884 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17285 Z= 0.134 Angle : 0.586 9.273 24579 Z= 0.336 Chirality : 0.042 0.254 2768 Planarity : 0.004 0.037 2117 Dihedral : 28.863 174.034 4640 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.89 % Allowed : 18.25 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.00 (0.24), residues: 1265 helix: 1.85 (0.20), residues: 751 sheet: -1.00 (0.55), residues: 69 loop : -1.15 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 265 TYR 0.017 0.001 TYR L 129 PHE 0.020 0.001 PHE L 170 TRP 0.009 0.001 TRP N 320 HIS 0.005 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (17285) covalent geometry : angle 0.58565 / 0.34 (24579) hydrogen bonds : bond 0.04010 / 2.66 ( 913) hydrogen bonds : angle 3.42150 / 2.48 ( 2328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9024 (mptt) cc_final: 0.8535 (mttt) REVERT: B 91 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8940 (ttpt) REVERT: C 76 THR cc_start: 0.9148 (p) cc_final: 0.8946 (t) REVERT: C 95 LYS cc_start: 0.9341 (tttp) cc_final: 0.8849 (ttpt) REVERT: D 85 LYS cc_start: 0.9100 (mptt) cc_final: 0.8780 (mmtt) REVERT: D 108 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (ptpt) REVERT: F 31 LYS cc_start: 0.8732 (tttm) cc_final: 0.8485 (tttm) REVERT: F 35 ARG cc_start: 0.8986 (ttm-80) cc_final: 0.8681 (ttm-80) REVERT: G 13 LYS cc_start: 0.7009 (tptt) cc_final: 0.6578 (ptmm) REVERT: G 36 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8635 (pttt) REVERT: G 104 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8517 (mt0) REVERT: H 83 TYR cc_start: 0.8291 (m-10) cc_final: 0.7999 (m-10) REVERT: H 108 LYS cc_start: 0.8415 (tttm) cc_final: 0.8176 (mtpt) REVERT: H 120 LYS cc_start: 0.8144 (tptt) cc_final: 0.7758 (mtpp) REVERT: L 11 ASP cc_start: 0.8573 (m-30) cc_final: 0.8070 (m-30) REVERT: L 32 ILE cc_start: 0.7142 (pp) cc_final: 0.6933 (tp) REVERT: L 44 TYR cc_start: 0.6506 (m-10) cc_final: 0.6282 (m-10) REVERT: L 94 HIS cc_start: 0.7767 (t-90) cc_final: 0.7021 (t-90) REVERT: L 127 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8797 (mttp) REVERT: L 211 MET cc_start: 0.7948 (mmm) cc_final: 0.7449 (mmm) REVERT: L 661 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8078 (tptm) REVERT: L 702 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8647 (mt0) REVERT: L 705 SER cc_start: 0.7692 (m) cc_final: 0.7358 (t) REVERT: M 1 MET cc_start: 0.3466 (ppp) cc_final: 0.3174 (ppp) REVERT: M 45 PHE cc_start: 0.5322 (OUTLIER) cc_final: 0.4632 (p90) REVERT: M 67 LEU cc_start: 0.8002 (pt) cc_final: 0.7041 (mt) REVERT: N 253 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: N 283 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7202 (tm-30) REVERT: N 348 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.2020 (pt0) REVERT: O 67 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5375 (tm) outliers start: 32 outliers final: 19 residues processed: 233 average time/residue: 0.1532 time to fit residues: 50.1647 Evaluate side-chains 225 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 104 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085732 restraints weight = 28677.635| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.86 r_work: 0.2861 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17285 Z= 0.155 Angle : 0.595 7.486 24579 Z= 0.338 Chirality : 0.043 0.255 2768 Planarity : 0.004 0.050 2117 Dihedral : 28.953 174.114 4639 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.98 % Allowed : 19.24 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.99 (0.24), residues: 1265 helix: 1.84 (0.20), residues: 752 sheet: -1.22 (0.55), residues: 76 loop : -1.10 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 54 TYR 0.016 0.002 TYR D 83 PHE 0.019 0.002 PHE L 170 TRP 0.005 0.001 TRP L 52 HIS 0.005 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (17285) covalent geometry : angle 0.59455 / 0.34 (24579) hydrogen bonds : bond 0.04186 / 2.77 ( 913) hydrogen bonds : angle 3.40532 / 2.47 ( 2328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9034 (mptt) cc_final: 0.8557 (mttt) REVERT: B 91 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8947 (ttpt) REVERT: C 76 THR cc_start: 0.9146 (p) cc_final: 0.8939 (t) REVERT: C 95 LYS cc_start: 0.9337 (tttp) cc_final: 0.8857 (ttpt) REVERT: D 85 LYS cc_start: 0.9101 (mptt) cc_final: 0.8777 (mmtt) REVERT: D 108 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (ptpt) REVERT: F 31 LYS cc_start: 0.8766 (tttm) cc_final: 0.8560 (tttm) REVERT: F 35 ARG cc_start: 0.9001 (ttm-80) cc_final: 0.8772 (ttm-80) REVERT: F 85 ASP cc_start: 0.8979 (m-30) cc_final: 0.8670 (m-30) REVERT: G 13 LYS cc_start: 0.6991 (tptt) cc_final: 0.6491 (ptmm) REVERT: G 36 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8585 (pttt) REVERT: G 72 ASP cc_start: 0.8402 (m-30) cc_final: 0.8103 (t0) REVERT: G 104 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8586 (mt0) REVERT: H 34 LYS cc_start: 0.7284 (ptpt) cc_final: 0.6537 (tptt) REVERT: H 108 LYS cc_start: 0.8445 (tttm) cc_final: 0.8196 (mtpt) REVERT: H 120 LYS cc_start: 0.8150 (tptt) cc_final: 0.7773 (mtpp) REVERT: L 11 ASP cc_start: 0.8554 (m-30) cc_final: 0.8039 (m-30) REVERT: L 21 ASP cc_start: 0.6983 (t70) cc_final: 0.6244 (p0) REVERT: L 32 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6909 (tp) REVERT: L 94 HIS cc_start: 0.7841 (t-90) cc_final: 0.7131 (t-90) REVERT: L 661 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8113 (tptm) REVERT: L 702 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8716 (mt0) REVERT: L 705 SER cc_start: 0.7749 (m) cc_final: 0.7402 (t) REVERT: M 1 MET cc_start: 0.3518 (ppp) cc_final: 0.3247 (ppp) REVERT: M 45 PHE cc_start: 0.5273 (OUTLIER) cc_final: 0.4128 (p90) REVERT: N 253 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6564 (pt0) REVERT: N 283 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7171 (tm-30) REVERT: N 348 GLU cc_start: 0.2556 (OUTLIER) cc_final: 0.2023 (pt0) REVERT: O 67 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5306 (tm) outliers start: 33 outliers final: 19 residues processed: 228 average time/residue: 0.1597 time to fit residues: 51.5136 Evaluate side-chains 227 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085585 restraints weight = 28616.844| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.85 r_work: 0.2857 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17285 Z= 0.155 Angle : 0.601 7.800 24579 Z= 0.340 Chirality : 0.043 0.258 2768 Planarity : 0.004 0.055 2117 Dihedral : 29.009 174.535 4639 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.25 % Allowed : 19.15 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.00 (0.24), residues: 1265 helix: 1.83 (0.20), residues: 752 sheet: -1.18 (0.56), residues: 76 loop : -1.07 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.015 0.002 TYR F 88 PHE 0.020 0.002 PHE L 170 TRP 0.006 0.001 TRP L 52 HIS 0.004 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (17285) covalent geometry : angle 0.60064 / 0.34 (24579) hydrogen bonds : bond 0.04178 / 2.77 ( 913) hydrogen bonds : angle 3.39554 / 2.46 ( 2328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9010 (mptt) cc_final: 0.8551 (mttt) REVERT: B 91 LYS cc_start: 0.9261 (ttpt) cc_final: 0.8951 (ttpt) REVERT: C 76 THR cc_start: 0.9173 (p) cc_final: 0.8964 (t) REVERT: C 95 LYS cc_start: 0.9345 (tttp) cc_final: 0.8866 (ttpt) REVERT: D 85 LYS cc_start: 0.9083 (mptt) cc_final: 0.8752 (mmtt) REVERT: D 108 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8491 (ptpt) REVERT: F 31 LYS cc_start: 0.8765 (tttm) cc_final: 0.8558 (tttm) REVERT: F 35 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8761 (ttm-80) REVERT: F 85 ASP cc_start: 0.8966 (m-30) cc_final: 0.8624 (m-30) REVERT: G 13 LYS cc_start: 0.7001 (tptt) cc_final: 0.6500 (ptmm) REVERT: G 36 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8577 (pttt) REVERT: G 72 ASP cc_start: 0.8416 (m-30) cc_final: 0.8108 (t0) REVERT: G 104 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8605 (mt0) REVERT: H 34 LYS cc_start: 0.7290 (ptpt) cc_final: 0.6557 (tptt) REVERT: H 108 LYS cc_start: 0.8441 (tttm) cc_final: 0.8191 (mtpt) REVERT: H 120 LYS cc_start: 0.8151 (tptt) cc_final: 0.7779 (mtpp) REVERT: L 11 ASP cc_start: 0.8555 (m-30) cc_final: 0.8051 (m-30) REVERT: L 21 ASP cc_start: 0.6962 (t70) cc_final: 0.6581 (p0) REVERT: L 32 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6822 (tp) REVERT: L 94 HIS cc_start: 0.7845 (t-90) cc_final: 0.7101 (t-90) REVERT: L 227 ARG cc_start: 0.5631 (pmt170) cc_final: 0.4095 (mtt-85) REVERT: L 230 LEU cc_start: 0.8672 (pt) cc_final: 0.7667 (mm) REVERT: L 702 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: L 705 SER cc_start: 0.7622 (m) cc_final: 0.7289 (t) REVERT: M 1 MET cc_start: 0.3542 (ppp) cc_final: 0.3273 (ppp) REVERT: M 45 PHE cc_start: 0.5255 (OUTLIER) cc_final: 0.4491 (p90) REVERT: M 67 LEU cc_start: 0.7681 (pp) cc_final: 0.6989 (mt) REVERT: N 253 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6512 (pt0) REVERT: N 261 ASN cc_start: 0.8148 (m110) cc_final: 0.7912 (m110) REVERT: N 283 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7046 (tm-30) REVERT: N 331 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6947 (p-80) REVERT: N 348 GLU cc_start: 0.2638 (OUTLIER) cc_final: 0.2056 (pt0) REVERT: O 54 ARG cc_start: 0.6034 (tmm-80) cc_final: 0.5815 (tmm-80) REVERT: O 67 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5314 (tm) outliers start: 36 outliers final: 25 residues processed: 232 average time/residue: 0.1593 time to fit residues: 52.6210 Evaluate side-chains 234 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 331 HIS Chi-restraints excluded: chain N residue 347 VAL Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086834 restraints weight = 28703.738| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.86 r_work: 0.2879 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17285 Z= 0.134 Angle : 0.583 7.866 24579 Z= 0.333 Chirality : 0.042 0.257 2768 Planarity : 0.004 0.052 2117 Dihedral : 28.978 174.661 4639 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.16 % Allowed : 19.87 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.10 (0.24), residues: 1265 helix: 1.92 (0.20), residues: 751 sheet: -1.04 (0.56), residues: 74 loop : -1.08 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.017 0.001 TYR L 129 PHE 0.019 0.001 PHE L 170 TRP 0.006 0.001 TRP L 52 HIS 0.004 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (17285) covalent geometry : angle 0.58285 / 0.33 (24579) hydrogen bonds : bond 0.03931 / 2.61 ( 913) hydrogen bonds : angle 3.31938 / 2.39 ( 2328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9002 (mptt) cc_final: 0.8538 (mttt) REVERT: B 91 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8938 (ttpt) REVERT: C 76 THR cc_start: 0.9160 (p) cc_final: 0.8960 (t) REVERT: C 95 LYS cc_start: 0.9333 (tttp) cc_final: 0.8853 (ttpt) REVERT: D 51 ASP cc_start: 0.8438 (p0) cc_final: 0.8237 (p0) REVERT: D 85 LYS cc_start: 0.9069 (mptt) cc_final: 0.8735 (mmtt) REVERT: D 108 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8436 (ptpt) REVERT: F 31 LYS cc_start: 0.8731 (tttm) cc_final: 0.8522 (tttm) REVERT: F 35 ARG cc_start: 0.8985 (ttm-80) cc_final: 0.8754 (ttm-80) REVERT: F 85 ASP cc_start: 0.8980 (m-30) cc_final: 0.8633 (m-30) REVERT: G 13 LYS cc_start: 0.6990 (tptt) cc_final: 0.6503 (ptmm) REVERT: G 36 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8555 (pttt) REVERT: G 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8093 (t0) REVERT: G 104 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8539 (mt0) REVERT: H 34 LYS cc_start: 0.7316 (ptpt) cc_final: 0.6579 (tptt) REVERT: H 83 TYR cc_start: 0.8264 (m-10) cc_final: 0.8000 (m-10) REVERT: H 108 LYS cc_start: 0.8416 (tttm) cc_final: 0.8165 (mtpt) REVERT: H 120 LYS cc_start: 0.8150 (tptt) cc_final: 0.7770 (mtpp) REVERT: L 11 ASP cc_start: 0.8525 (m-30) cc_final: 0.8008 (m-30) REVERT: L 21 ASP cc_start: 0.6993 (t70) cc_final: 0.6610 (p0) REVERT: L 28 GLN cc_start: 0.7152 (pt0) cc_final: 0.6743 (pm20) REVERT: L 32 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6829 (tp) REVERT: L 94 HIS cc_start: 0.7929 (t-90) cc_final: 0.7106 (t-90) REVERT: L 227 ARG cc_start: 0.5632 (pmt170) cc_final: 0.4196 (mtt-85) REVERT: L 230 LEU cc_start: 0.8671 (pt) cc_final: 0.7653 (mm) REVERT: L 702 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8635 (mt0) REVERT: M 1 MET cc_start: 0.3442 (ppp) cc_final: 0.3208 (ppp) REVERT: M 45 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.4141 (p90) REVERT: M 73 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.5578 (pp) REVERT: N 253 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6503 (pt0) REVERT: N 261 ASN cc_start: 0.8114 (m110) cc_final: 0.7849 (m110) REVERT: N 283 GLN cc_start: 0.7353 (tm-30) cc_final: 0.7038 (tm-30) REVERT: N 348 GLU cc_start: 0.2542 (OUTLIER) cc_final: 0.1944 (pt0) REVERT: O 67 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5328 (tm) outliers start: 35 outliers final: 22 residues processed: 231 average time/residue: 0.1526 time to fit residues: 50.4925 Evaluate side-chains 232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 347 VAL Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085564 restraints weight = 28677.667| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.86 r_work: 0.2854 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17285 Z= 0.162 Angle : 0.609 8.048 24579 Z= 0.344 Chirality : 0.043 0.259 2768 Planarity : 0.004 0.047 2117 Dihedral : 29.046 174.519 4638 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.98 % Allowed : 19.51 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.03 (0.24), residues: 1265 helix: 1.84 (0.20), residues: 754 sheet: -1.08 (0.54), residues: 80 loop : -1.06 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 131 TYR 0.049 0.002 TYR O 59 PHE 0.020 0.002 PHE L 170 TRP 0.007 0.001 TRP L 52 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17285) covalent geometry : angle 0.60901 / 0.34 (24579) hydrogen bonds : bond 0.04217 / 2.80 ( 913) hydrogen bonds : angle 3.35690 / 2.42 ( 2328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9019 (mptt) cc_final: 0.8620 (mttm) REVERT: B 91 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8951 (ttpt) REVERT: C 76 THR cc_start: 0.9174 (p) cc_final: 0.8971 (t) REVERT: C 95 LYS cc_start: 0.9340 (tttp) cc_final: 0.8871 (ttpt) REVERT: D 51 ASP cc_start: 0.8416 (p0) cc_final: 0.8208 (p0) REVERT: D 85 LYS cc_start: 0.9074 (mptt) cc_final: 0.8758 (mmtt) REVERT: D 108 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8531 (ptpt) REVERT: F 31 LYS cc_start: 0.8774 (tttm) cc_final: 0.8558 (tttm) REVERT: F 35 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8770 (ttm-80) REVERT: F 85 ASP cc_start: 0.8977 (m-30) cc_final: 0.8641 (m-30) REVERT: G 13 LYS cc_start: 0.7094 (tptt) cc_final: 0.6555 (ptmm) REVERT: G 36 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8672 (pttt) REVERT: G 72 ASP cc_start: 0.8459 (m-30) cc_final: 0.8191 (t0) REVERT: G 104 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8627 (mt0) REVERT: H 34 LYS cc_start: 0.7356 (ptpt) cc_final: 0.6603 (tptt) REVERT: H 108 LYS cc_start: 0.8453 (tttm) cc_final: 0.8195 (mtpt) REVERT: H 120 LYS cc_start: 0.8155 (tptt) cc_final: 0.7777 (mtpp) REVERT: L 11 ASP cc_start: 0.8522 (m-30) cc_final: 0.8006 (m-30) REVERT: L 21 ASP cc_start: 0.6972 (t70) cc_final: 0.6618 (p0) REVERT: L 28 GLN cc_start: 0.7184 (pt0) cc_final: 0.6764 (pm20) REVERT: L 32 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6834 (tp) REVERT: L 94 HIS cc_start: 0.7977 (t-90) cc_final: 0.7136 (t-90) REVERT: L 227 ARG cc_start: 0.5705 (pmt170) cc_final: 0.4094 (mpt-90) REVERT: L 230 LEU cc_start: 0.8751 (pt) cc_final: 0.7652 (mm) REVERT: L 702 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8659 (mt0) REVERT: M 45 PHE cc_start: 0.5336 (OUTLIER) cc_final: 0.4143 (p90) REVERT: M 73 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6193 (pp) REVERT: N 253 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6533 (pt0) REVERT: N 261 ASN cc_start: 0.8158 (m110) cc_final: 0.7809 (m-40) REVERT: N 283 GLN cc_start: 0.7350 (tm-30) cc_final: 0.7036 (tm-30) REVERT: N 303 LEU cc_start: 0.7369 (mp) cc_final: 0.6622 (tt) REVERT: N 331 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6984 (p-80) REVERT: N 348 GLU cc_start: 0.2519 (OUTLIER) cc_final: 0.1940 (pt0) REVERT: O 67 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5408 (tm) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.1503 time to fit residues: 48.4542 Evaluate side-chains 232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 688 LEU Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 331 HIS Chi-restraints excluded: chain N residue 347 VAL Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086330 restraints weight = 28640.354| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.85 r_work: 0.2869 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17285 Z= 0.143 Angle : 0.598 7.348 24579 Z= 0.338 Chirality : 0.042 0.260 2768 Planarity : 0.004 0.048 2117 Dihedral : 29.041 174.842 4638 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.80 % Allowed : 20.23 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1.10 (0.24), residues: 1265 helix: 1.88 (0.20), residues: 754 sheet: -1.10 (0.54), residues: 80 loop : -1.00 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.021 0.002 TYR L 129 PHE 0.021 0.001 PHE L 170 TRP 0.007 0.001 TRP L 52 HIS 0.004 0.001 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (17285) covalent geometry : angle 0.59821 / 0.34 (24579) hydrogen bonds : bond 0.04001 / 2.66 ( 913) hydrogen bonds : angle 3.30216 / 2.37 ( 2328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9024 (mptt) cc_final: 0.8647 (mttm) REVERT: B 91 LYS cc_start: 0.9252 (ttpt) cc_final: 0.8945 (ttpt) REVERT: C 95 LYS cc_start: 0.9365 (tttp) cc_final: 0.8903 (ttpt) REVERT: D 51 ASP cc_start: 0.8408 (p0) cc_final: 0.8197 (p0) REVERT: D 85 LYS cc_start: 0.9074 (mptt) cc_final: 0.8730 (mmtt) REVERT: D 108 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8463 (ptpt) REVERT: F 31 LYS cc_start: 0.8747 (tttm) cc_final: 0.8538 (tttm) REVERT: F 35 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8758 (ttm-80) REVERT: F 85 ASP cc_start: 0.9001 (m-30) cc_final: 0.8650 (m-30) REVERT: G 13 LYS cc_start: 0.7100 (tptt) cc_final: 0.6601 (ptmm) REVERT: G 23 LEU cc_start: 0.9207 (mt) cc_final: 0.8968 (mt) REVERT: G 36 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8668 (pttt) REVERT: G 72 ASP cc_start: 0.8466 (m-30) cc_final: 0.8194 (t0) REVERT: G 104 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8630 (mt0) REVERT: H 34 LYS cc_start: 0.7355 (ptpt) cc_final: 0.6598 (tptt) REVERT: H 83 TYR cc_start: 0.8284 (m-10) cc_final: 0.8008 (m-10) REVERT: H 108 LYS cc_start: 0.8433 (tttm) cc_final: 0.8180 (mtpt) REVERT: H 120 LYS cc_start: 0.8156 (tptt) cc_final: 0.7791 (mtpp) REVERT: L 11 ASP cc_start: 0.8512 (m-30) cc_final: 0.7989 (m-30) REVERT: L 21 ASP cc_start: 0.6939 (t70) cc_final: 0.6610 (p0) REVERT: L 28 GLN cc_start: 0.7199 (pt0) cc_final: 0.6793 (pm20) REVERT: L 32 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6769 (tp) REVERT: L 94 HIS cc_start: 0.7949 (t-90) cc_final: 0.7122 (t-90) REVERT: L 127 LYS cc_start: 0.8562 (mttt) cc_final: 0.8340 (mttp) REVERT: L 227 ARG cc_start: 0.5622 (pmt170) cc_final: 0.4108 (mpt-90) REVERT: L 230 LEU cc_start: 0.8667 (pt) cc_final: 0.7607 (mm) REVERT: L 702 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8647 (mt0) REVERT: M 45 PHE cc_start: 0.5360 (OUTLIER) cc_final: 0.4148 (p90) REVERT: M 73 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6167 (pp) REVERT: N 253 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6501 (pt0) REVERT: N 261 ASN cc_start: 0.8132 (m110) cc_final: 0.7763 (m-40) REVERT: N 283 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7068 (tm-30) REVERT: N 303 LEU cc_start: 0.7460 (mp) cc_final: 0.6683 (tt) REVERT: N 348 GLU cc_start: 0.2510 (OUTLIER) cc_final: 0.2002 (pt0) REVERT: O 67 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5418 (tm) outliers start: 31 outliers final: 22 residues processed: 227 average time/residue: 0.1498 time to fit residues: 48.5608 Evaluate side-chains 232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 654 VAL Chi-restraints excluded: chain L residue 676 CYS Chi-restraints excluded: chain L residue 688 LEU Chi-restraints excluded: chain L residue 702 GLN Chi-restraints excluded: chain L residue 709 LEU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 ILE Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 150 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.083400 restraints weight = 28595.201| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.89 r_work: 0.2817 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17285 Z= 0.215 Angle : 0.663 6.947 24579 Z= 0.366 Chirality : 0.046 0.272 2768 Planarity : 0.005 0.046 2117 Dihedral : 29.234 174.733 4638 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.98 % Allowed : 19.69 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.84 (0.24), residues: 1265 helix: 1.68 (0.20), residues: 748 sheet: -1.26 (0.54), residues: 82 loop : -1.04 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 238 TYR 0.032 0.002 TYR O 59 PHE 0.017 0.002 PHE L 678 TRP 0.009 0.001 TRP L 52 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (17285) covalent geometry : angle 0.66284 / 0.37 (24579) hydrogen bonds : bond 0.04925 / 3.27 ( 913) hydrogen bonds : angle 3.44644 / 2.49 ( 2328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5615.98 seconds wall clock time: 96 minutes 18.29 seconds (5778.29 seconds total)