Starting phenix.real_space_refine on Thu Feb 5 09:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5u_63884/02_2026/9u5u_63884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5u_63884/02_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_63884/02_2026/9u5u_63884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5u_63884/02_2026/9u5u_63884.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5u_63884/02_2026/9u5u_63884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5u_63884/02_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-2.0-5952/lib/python3.9/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: 3.76, per 1000 atoms: 0.23 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: 1.36 Conformation dependent library (CDL) restraints added in 403.1 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: 2.20 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: 3.68 Time building geometry restraints manager: 1.80 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=" C GLU L 148 " pdb=" N PRO L 149 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.08e-02 8.57e+03 4.25e+00 bond pdb=" CB ILE N 258 " pdb=" CG2 ILE N 258 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.04e+00 bond pdb=" CA GLU L 54 " pdb=" C GLU L 54 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.34e-02 5.57e+03 1.99e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C3' DT J -39 " pdb=" O3' DT J -39 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 17280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 24076 1.93 - 3.87: 461 3.87 - 5.80: 33 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=" C GLU N 356 " pdb=" N ASP N 357 " pdb=" CA ASP N 357 " ideal model delta sigma weight residual 121.70 127.81 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA GLU O 64 " pdb=" CB GLU O 64 " pdb=" CG GLU O 64 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.46e+00 angle pdb=" N ILE L 53 " pdb=" CA ILE L 53 " pdb=" C ILE L 53 " ideal model delta sigma weight residual 109.34 115.65 -6.31 2.08e+00 2.31e-01 9.21e+00 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.05e+00 ... (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: 2506 0.061 - 0.122: 243 0.122 - 0.183: 18 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: 1.180 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17285 Z= 0.179 Angle : 0.635 9.664 24579 Z= 0.388 Chirality : 0.038 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 covalent geometry : bond 0.00379 (17285) covalent geometry : angle 0.63517 (24579) hydrogen bonds : bond 0.14713 ( 913) hydrogen bonds : angle 4.97474 ( 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 : 0.472 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: 0.1735 time to fit residues: 70.6146 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 : 0.498 ------------------------------------------------------------------------------- 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: 7.9990 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: 2.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 84 GLN D 49 HIS L 89 ASN L 193 HIS L 229 ASN ** L 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085056 restraints weight = 28722.325| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.87 r_work: 0.2842 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 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 = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17285 Z= 0.204 Angle : 0.606 6.866 24579 Z= 0.350 Chirality : 0.039 0.181 2768 Planarity : 0.005 0.044 2117 Dihedral : 28.486 172.747 4650 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.43 % Allowed : 17.34 % 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: 0.60 (0.24), residues: 1265 helix: 1.46 (0.20), residues: 752 sheet: -1.09 (0.53), residues: 73 loop : -1.20 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.017 0.002 TYR L 129 PHE 0.017 0.002 PHE L 678 TRP 0.011 0.002 TRP L 52 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00470 (17285) covalent geometry : angle 0.60551 (24579) hydrogen bonds : bond 0.04420 ( 913) hydrogen bonds : angle 3.61674 ( 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 249 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9040 (mptt) cc_final: 0.8561 (mttt) REVERT: B 91 LYS cc_start: 0.9311 (ttpt) cc_final: 0.8979 (ttpt) REVERT: C 76 THR cc_start: 0.9121 (p) cc_final: 0.8875 (t) REVERT: C 95 LYS cc_start: 0.9349 (tttp) cc_final: 0.8862 (ttpt) REVERT: D 85 LYS cc_start: 0.9106 (mptt) cc_final: 0.8774 (mmtt) REVERT: D 108 LYS cc_start: 0.8729 (pttt) cc_final: 0.8375 (pttt) REVERT: G 13 LYS cc_start: 0.7056 (tptt) cc_final: 0.6629 (ptmm) REVERT: G 36 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8804 (pttp) REVERT: G 56 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: G 104 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8629 (mt0) REVERT: H 51 ASP cc_start: 0.8723 (p0) cc_final: 0.8468 (p0) REVERT: H 108 LYS cc_start: 0.8456 (tttm) cc_final: 0.8227 (mtpt) REVERT: H 120 LYS cc_start: 0.8246 (tptt) cc_final: 0.7763 (mttp) REVERT: L 11 ASP cc_start: 0.8407 (m-30) cc_final: 0.7964 (m-30) REVERT: L 91 CYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7481 (m) REVERT: L 122 PHE cc_start: 0.8181 (t80) cc_final: 0.7924 (t80) REVERT: L 148 GLU cc_start: 0.7655 (tp30) cc_final: 0.7352 (tp30) REVERT: L 661 LYS cc_start: 0.8547 (mmtm) cc_final: 0.7905 (tptm) REVERT: L 705 SER cc_start: 0.7523 (m) cc_final: 0.7208 (t) REVERT: M 1 MET cc_start: 0.3699 (ppp) cc_final: 0.3112 (ppp) REVERT: M 12 THR cc_start: 0.5295 (OUTLIER) cc_final: 0.4779 (p) REVERT: M 67 LEU cc_start: 0.7934 (pt) cc_final: 0.7036 (mt) REVERT: N 283 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7291 (tm-30) REVERT: N 311 GLU cc_start: 0.7821 (pm20) cc_final: 0.6874 (mt-10) REVERT: N 348 GLU cc_start: 0.2381 (OUTLIER) cc_final: 0.1804 (pt0) REVERT: O 67 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5373 (tm) outliers start: 38 outliers final: 15 residues processed: 236 average time/residue: 0.1603 time to fit residues: 53.5472 Evaluate side-chains 219 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU 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 91 CYS 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 709 LEU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 269 ASN 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: 10.0000 chunk 127 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086954 restraints weight = 29024.827| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.87 r_work: 0.2875 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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= 0.156 Angle : 0.558 6.814 24579 Z= 0.326 Chirality : 0.037 0.167 2768 Planarity : 0.004 0.035 2117 Dihedral : 28.453 173.246 4642 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.80 % Allowed : 18.34 % 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: 0.95 (0.24), residues: 1265 helix: 1.76 (0.20), residues: 752 sheet: -0.93 (0.54), residues: 69 loop : -1.08 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 57 TYR 0.014 0.001 TYR D 83 PHE 0.020 0.001 PHE L 170 TRP 0.004 0.001 TRP N 320 HIS 0.007 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00348 (17285) covalent geometry : angle 0.55805 (24579) hydrogen bonds : bond 0.03751 ( 913) hydrogen bonds : angle 3.36895 ( 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 244 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9043 (mptt) cc_final: 0.8561 (mttt) REVERT: B 91 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8944 (ttpt) REVERT: C 76 THR cc_start: 0.9185 (p) cc_final: 0.8953 (t) REVERT: C 95 LYS cc_start: 0.9350 (tttp) cc_final: 0.8865 (ttpt) REVERT: D 85 LYS cc_start: 0.9078 (mptt) cc_final: 0.8736 (mmtt) REVERT: D 108 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8451 (ptpt) REVERT: G 13 LYS cc_start: 0.7026 (tptt) cc_final: 0.6590 (ptmm) REVERT: G 36 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8668 (pttt) REVERT: G 56 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: G 104 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8616 (mt0) REVERT: H 51 ASP cc_start: 0.8706 (p0) cc_final: 0.8418 (p0) REVERT: H 108 LYS cc_start: 0.8423 (tttm) cc_final: 0.8194 (mtpt) REVERT: H 120 LYS cc_start: 0.8148 (tptt) cc_final: 0.7774 (mtpp) REVERT: L 11 ASP cc_start: 0.8607 (m-30) cc_final: 0.8148 (m-30) REVERT: L 28 GLN cc_start: 0.7206 (pt0) cc_final: 0.6791 (pm20) REVERT: L 122 PHE cc_start: 0.8198 (t80) cc_final: 0.7729 (t80) REVERT: L 148 GLU cc_start: 0.7424 (tp30) cc_final: 0.7187 (tp30) REVERT: L 227 ARG cc_start: 0.5267 (pmt170) cc_final: 0.3825 (mpt-90) REVERT: L 661 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7996 (tptt) REVERT: L 705 SER cc_start: 0.7660 (m) cc_final: 0.7281 (t) REVERT: M 1 MET cc_start: 0.3455 (ppp) cc_final: 0.2922 (ppp) REVERT: M 45 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4525 (p90) REVERT: M 67 LEU cc_start: 0.7936 (pt) cc_final: 0.7019 (mt) REVERT: N 283 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7233 (tm-30) REVERT: N 348 GLU cc_start: 0.2651 (OUTLIER) cc_final: 0.2116 (pt0) REVERT: O 43 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6630 (pp) REVERT: O 67 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5329 (tm) outliers start: 31 outliers final: 19 residues processed: 234 average time/residue: 0.1513 time to fit residues: 49.8178 Evaluate side-chains 221 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 108 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 126 SER Chi-restraints excluded: chain L residue 229 ASN 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 710 HIS Chi-restraints excluded: chain M residue 45 PHE Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 258 ILE 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 43 LEU 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: 2.9990 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083811 restraints weight = 28603.698| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.87 r_work: 0.2820 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17285 Z= 0.225 Angle : 0.600 7.566 24579 Z= 0.347 Chirality : 0.039 0.185 2768 Planarity : 0.005 0.042 2117 Dihedral : 28.722 174.723 4639 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.97 % Allowed : 17.16 % 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: 0.81 (0.24), residues: 1265 helix: 1.63 (0.20), residues: 755 sheet: -1.14 (0.52), residues: 81 loop : -1.11 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.015 0.002 TYR D 83 PHE 0.019 0.002 PHE L 170 TRP 0.004 0.001 TRP N 320 HIS 0.006 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00520 (17285) covalent geometry : angle 0.59958 (24579) hydrogen bonds : bond 0.04469 ( 913) hydrogen bonds : angle 3.40266 ( 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 249 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9032 (mptt) cc_final: 0.8680 (mttm) REVERT: B 91 LYS cc_start: 0.9286 (ttpt) cc_final: 0.8972 (ttpt) REVERT: C 95 LYS cc_start: 0.9390 (tttp) cc_final: 0.8908 (ttpt) REVERT: D 85 LYS cc_start: 0.9132 (mptt) cc_final: 0.8776 (mmtt) REVERT: D 108 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8559 (ptpt) REVERT: G 13 LYS cc_start: 0.7083 (tptt) cc_final: 0.6518 (ptmm) REVERT: G 36 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8626 (pttt) REVERT: G 56 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8813 (tt0) REVERT: G 104 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8638 (mt0) REVERT: H 34 LYS cc_start: 0.7317 (ptpt) cc_final: 0.6578 (tptt) REVERT: H 51 ASP cc_start: 0.8748 (p0) cc_final: 0.8460 (p0) REVERT: H 120 LYS cc_start: 0.8171 (tptt) cc_final: 0.7792 (mtpp) REVERT: L 11 ASP cc_start: 0.8498 (m-30) cc_final: 0.8010 (m-30) REVERT: L 21 ASP cc_start: 0.6960 (t0) cc_final: 0.6263 (p0) REVERT: L 44 TYR cc_start: 0.6612 (m-10) cc_final: 0.6405 (m-10) REVERT: L 80 MET cc_start: 0.5853 (ptp) cc_final: 0.5482 (ptp) REVERT: L 122 PHE cc_start: 0.8308 (t80) cc_final: 0.7716 (t80) REVERT: L 227 ARG cc_start: 0.5601 (pmt170) cc_final: 0.4004 (mpt-90) REVERT: L 661 LYS cc_start: 0.8272 (mmtm) cc_final: 0.8055 (tptm) REVERT: L 702 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8508 (mt0) REVERT: M 45 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4251 (p90) REVERT: N 283 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7200 (tm-30) REVERT: N 331 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: O 27 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7628 (ptmm) REVERT: O 43 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6558 (pp) REVERT: O 67 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5399 (tm) outliers start: 44 outliers final: 26 residues processed: 235 average time/residue: 0.1548 time to fit residues: 51.1628 Evaluate side-chains 229 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain C residue 36 LYS 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 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 119 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 180 LEU 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 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 269 ASN Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 331 HIS 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: 0.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085009 restraints weight = 28855.832| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.85 r_work: 0.2842 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17285 Z= 0.183 Angle : 0.576 7.599 24579 Z= 0.333 Chirality : 0.037 0.165 2768 Planarity : 0.004 0.038 2117 Dihedral : 28.640 174.959 4639 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.61 % Allowed : 18.70 % Favored : 77.69 % 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: 0.93 (0.24), residues: 1265 helix: 1.77 (0.20), residues: 752 sheet: -1.12 (0.53), residues: 81 loop : -1.09 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.016 0.001 TYR D 83 PHE 0.016 0.001 PHE L 50 TRP 0.004 0.001 TRP L 52 HIS 0.006 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00418 (17285) covalent geometry : angle 0.57563 (24579) hydrogen bonds : bond 0.03946 ( 913) hydrogen bonds : angle 3.28957 ( 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 246 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9030 (mptt) cc_final: 0.8666 (mttm) REVERT: B 91 LYS cc_start: 0.9284 (ttpt) cc_final: 0.8967 (ttpt) REVERT: C 95 LYS cc_start: 0.9373 (tttp) cc_final: 0.8876 (ttpt) REVERT: D 85 LYS cc_start: 0.9115 (mptt) cc_final: 0.8752 (mmtt) REVERT: G 13 LYS cc_start: 0.7064 (tptt) cc_final: 0.6461 (ptmm) REVERT: G 36 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8660 (pttt) REVERT: G 56 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: G 104 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8633 (mt0) REVERT: H 34 LYS cc_start: 0.7317 (ptpt) cc_final: 0.6602 (tptt) REVERT: H 51 ASP cc_start: 0.8733 (p0) cc_final: 0.8451 (p0) REVERT: H 120 LYS cc_start: 0.8210 (tptt) cc_final: 0.7849 (mtpp) REVERT: L 11 ASP cc_start: 0.8494 (m-30) cc_final: 0.7985 (m-30) REVERT: L 21 ASP cc_start: 0.6950 (t0) cc_final: 0.6703 (p0) REVERT: L 28 GLN cc_start: 0.7247 (pt0) cc_final: 0.6853 (pm20) REVERT: L 44 TYR cc_start: 0.6520 (m-10) cc_final: 0.6310 (m-10) REVERT: L 122 PHE cc_start: 0.8218 (t80) cc_final: 0.7699 (t80) REVERT: L 227 ARG cc_start: 0.5375 (pmt170) cc_final: 0.4324 (mpt-90) REVERT: L 230 LEU cc_start: 0.8671 (pt) cc_final: 0.7530 (mm) REVERT: L 656 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7183 (mmtt) REVERT: L 702 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: M 45 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4122 (p90) REVERT: N 261 ASN cc_start: 0.8095 (m110) cc_final: 0.7719 (m110) REVERT: N 283 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7245 (tm-30) REVERT: N 331 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6952 (p-80) REVERT: O 67 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5408 (tm) outliers start: 40 outliers final: 28 residues processed: 234 average time/residue: 0.1573 time to fit residues: 51.7539 Evaluate side-chains 233 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU 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 656 LYS 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 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 270 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 331 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 63 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085351 restraints weight = 28718.079| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.85 r_work: 0.2848 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17285 Z= 0.170 Angle : 0.561 7.232 24579 Z= 0.327 Chirality : 0.037 0.180 2768 Planarity : 0.004 0.038 2117 Dihedral : 28.607 174.598 4639 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.07 % Allowed : 18.34 % 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: 1.01 (0.24), residues: 1265 helix: 1.86 (0.20), residues: 744 sheet: -1.08 (0.53), residues: 81 loop : -1.05 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.016 0.001 TYR D 83 PHE 0.018 0.001 PHE L 170 TRP 0.004 0.001 TRP L 52 HIS 0.005 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00385 (17285) covalent geometry : angle 0.56132 (24579) hydrogen bonds : bond 0.03807 ( 913) hydrogen bonds : angle 3.22683 ( 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 246 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9066 (mptt) cc_final: 0.8678 (mttm) REVERT: B 91 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9026 (ttmt) REVERT: C 95 LYS cc_start: 0.9371 (tttp) cc_final: 0.8869 (ttpt) REVERT: D 85 LYS cc_start: 0.9120 (mptt) cc_final: 0.8783 (mmtt) REVERT: G 13 LYS cc_start: 0.7105 (tptt) cc_final: 0.6467 (ptmm) REVERT: G 36 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8689 (tttt) REVERT: G 56 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: G 104 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8630 (mt0) REVERT: H 34 LYS cc_start: 0.7348 (ptpt) cc_final: 0.6638 (tptt) REVERT: H 51 ASP cc_start: 0.8725 (p0) cc_final: 0.8437 (p0) REVERT: H 120 LYS cc_start: 0.8204 (tptt) cc_final: 0.7834 (mtpp) REVERT: L 11 ASP cc_start: 0.8358 (m-30) cc_final: 0.7856 (m-30) REVERT: L 21 ASP cc_start: 0.6889 (t0) cc_final: 0.6514 (p0) REVERT: L 44 TYR cc_start: 0.6353 (m-10) cc_final: 0.6147 (m-10) REVERT: L 122 PHE cc_start: 0.8234 (t80) cc_final: 0.7686 (t80) REVERT: L 211 MET cc_start: 0.8142 (mtt) cc_final: 0.7471 (mmm) REVERT: L 227 ARG cc_start: 0.5297 (pmt170) cc_final: 0.4380 (mpt-90) REVERT: L 230 LEU cc_start: 0.8653 (pt) cc_final: 0.7468 (mm) REVERT: L 702 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: M 1 MET cc_start: 0.4439 (tmm) cc_final: 0.4037 (ppp) REVERT: M 73 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6538 (pp) REVERT: N 253 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: N 261 ASN cc_start: 0.8034 (m110) cc_final: 0.7665 (m110) REVERT: N 283 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7106 (tm-30) REVERT: N 331 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6853 (p-80) REVERT: O 67 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5365 (tm) outliers start: 45 outliers final: 30 residues processed: 232 average time/residue: 0.1673 time to fit residues: 54.6612 Evaluate side-chains 236 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 119 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 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 270 SER Chi-restraints excluded: chain N residue 322 GLU Chi-restraints excluded: chain N residue 331 HIS 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: 3.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 63 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.142629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084300 restraints weight = 28643.233| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.82 r_work: 0.2829 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17285 Z= 0.201 Angle : 0.586 6.676 24579 Z= 0.339 Chirality : 0.038 0.181 2768 Planarity : 0.004 0.039 2117 Dihedral : 28.706 175.336 4639 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.07 % Allowed : 18.88 % Favored : 77.06 % 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: 0.90 (0.24), residues: 1265 helix: 1.76 (0.20), residues: 746 sheet: -1.12 (0.53), residues: 82 loop : -1.09 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.019 0.002 TYR D 83 PHE 0.017 0.002 PHE L 50 TRP 0.004 0.001 TRP L 52 HIS 0.005 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00462 (17285) covalent geometry : angle 0.58638 (24579) hydrogen bonds : bond 0.04141 ( 913) hydrogen bonds : angle 3.25953 ( 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 245 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9043 (mptt) cc_final: 0.8685 (mttm) REVERT: B 91 LYS cc_start: 0.9292 (ttpt) cc_final: 0.9026 (ttmt) REVERT: C 95 LYS cc_start: 0.9384 (tttp) cc_final: 0.8910 (ttpt) REVERT: D 85 LYS cc_start: 0.9128 (mptt) cc_final: 0.8779 (mmtt) REVERT: G 13 LYS cc_start: 0.6986 (tptt) cc_final: 0.6479 (ptmm) REVERT: G 56 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8828 (tt0) REVERT: G 104 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8622 (mt0) REVERT: H 34 LYS cc_start: 0.7471 (ptpt) cc_final: 0.6743 (tptt) REVERT: H 51 ASP cc_start: 0.8758 (p0) cc_final: 0.8488 (p0) REVERT: H 120 LYS cc_start: 0.8210 (tptt) cc_final: 0.7835 (mtpp) REVERT: L 11 ASP cc_start: 0.8386 (m-30) cc_final: 0.7871 (m-30) REVERT: L 28 GLN cc_start: 0.7153 (pt0) cc_final: 0.6799 (pm20) REVERT: L 122 PHE cc_start: 0.8217 (t80) cc_final: 0.7667 (t80) REVERT: L 211 MET cc_start: 0.8132 (mtt) cc_final: 0.7442 (mmm) REVERT: L 227 ARG cc_start: 0.5495 (pmt170) cc_final: 0.4456 (mpt-90) REVERT: L 230 LEU cc_start: 0.8651 (pt) cc_final: 0.7418 (mm) REVERT: L 656 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7134 (mmtp) REVERT: L 702 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: M 73 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6856 (pp) REVERT: N 253 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6507 (pt0) REVERT: N 261 ASN cc_start: 0.8033 (m110) cc_final: 0.7783 (m-40) REVERT: N 283 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7083 (tm-30) REVERT: N 331 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6763 (p-80) REVERT: O 67 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5415 (tm) outliers start: 45 outliers final: 31 residues processed: 232 average time/residue: 0.1641 time to fit residues: 53.9932 Evaluate side-chains 232 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 10 SER 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 656 LYS 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 270 SER Chi-restraints excluded: chain N residue 331 HIS 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: 0.9980 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 0.0270 chunk 26 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.143981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086042 restraints weight = 28623.399| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.84 r_work: 0.2863 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17285 Z= 0.143 Angle : 0.560 7.118 24579 Z= 0.326 Chirality : 0.036 0.182 2768 Planarity : 0.004 0.037 2117 Dihedral : 28.639 175.390 4639 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.34 % Allowed : 19.60 % Favored : 77.06 % 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: 1.09 (0.24), residues: 1265 helix: 1.89 (0.20), residues: 744 sheet: -1.04 (0.54), residues: 82 loop : -0.97 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.020 0.001 TYR D 83 PHE 0.017 0.001 PHE L 170 TRP 0.002 0.001 TRP L 52 HIS 0.005 0.001 HIS L 144 Details of bonding type rmsd covalent geometry : bond 0.00312 (17285) covalent geometry : angle 0.55989 (24579) hydrogen bonds : bond 0.03621 ( 913) hydrogen bonds : angle 3.15234 ( 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 238 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9054 (mptt) cc_final: 0.8669 (mttm) REVERT: B 91 LYS cc_start: 0.9273 (ttpt) cc_final: 0.9010 (ttmt) REVERT: C 95 LYS cc_start: 0.9384 (tttp) cc_final: 0.8902 (ttpt) REVERT: D 85 LYS cc_start: 0.9104 (mptt) cc_final: 0.8759 (mmtt) REVERT: G 13 LYS cc_start: 0.6992 (tptt) cc_final: 0.6534 (ptmm) REVERT: G 56 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: G 104 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8652 (mt0) REVERT: H 34 LYS cc_start: 0.7464 (ptpt) cc_final: 0.6684 (tptt) REVERT: H 35 GLU cc_start: 0.7800 (pm20) cc_final: 0.7436 (pm20) REVERT: H 51 ASP cc_start: 0.8730 (p0) cc_final: 0.8447 (p0) REVERT: H 120 LYS cc_start: 0.8187 (tptt) cc_final: 0.7826 (mtpp) REVERT: L 11 ASP cc_start: 0.8374 (m-30) cc_final: 0.7863 (m-30) REVERT: L 96 LEU cc_start: 0.8972 (tt) cc_final: 0.8684 (pp) REVERT: L 122 PHE cc_start: 0.8206 (t80) cc_final: 0.7646 (t80) REVERT: L 211 MET cc_start: 0.8085 (mtt) cc_final: 0.7479 (mmm) REVERT: L 227 ARG cc_start: 0.5493 (pmt170) cc_final: 0.4402 (mpt-90) REVERT: L 230 LEU cc_start: 0.8632 (pt) cc_final: 0.7416 (mm) REVERT: L 702 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: M 73 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6738 (pp) REVERT: N 253 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6358 (pt0) REVERT: N 261 ASN cc_start: 0.8020 (m110) cc_final: 0.7767 (m-40) REVERT: N 283 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6992 (tm-30) REVERT: N 331 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6714 (p-80) REVERT: O 67 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5426 (tm) outliers start: 37 outliers final: 25 residues processed: 227 average time/residue: 0.1512 time to fit residues: 48.5759 Evaluate side-chains 228 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 56 GLU 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 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 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 331 HIS Chi-restraints excluded: chain O residue 9 THR 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: 7.9990 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 HIS ** 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 = 0.3921 r_free = 0.3921 target = 0.140912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082429 restraints weight = 28677.686| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.87 r_work: 0.2789 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17285 Z= 0.275 Angle : 0.638 7.686 24579 Z= 0.366 Chirality : 0.042 0.206 2768 Planarity : 0.005 0.038 2117 Dihedral : 28.939 177.227 4639 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.52 % Allowed : 18.97 % 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: 0.73 (0.24), residues: 1265 helix: 1.57 (0.20), residues: 748 sheet: -0.91 (0.56), residues: 76 loop : -1.14 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.026 0.002 TYR F 88 PHE 0.017 0.002 PHE L 678 TRP 0.004 0.001 TRP N 320 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00640 (17285) covalent geometry : angle 0.63829 (24579) hydrogen bonds : bond 0.04819 ( 913) hydrogen bonds : angle 3.36436 ( 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 236 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9012 (mptt) cc_final: 0.8668 (mttm) REVERT: B 91 LYS cc_start: 0.9291 (ttpt) cc_final: 0.9017 (ttmt) REVERT: C 95 LYS cc_start: 0.9364 (tttp) cc_final: 0.8885 (ttpt) REVERT: D 85 LYS cc_start: 0.9138 (mptt) cc_final: 0.8784 (mmtt) REVERT: G 13 LYS cc_start: 0.6689 (tptt) cc_final: 0.6175 (ptmm) REVERT: G 56 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8835 (tt0) REVERT: G 104 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8642 (mt0) REVERT: H 34 LYS cc_start: 0.7536 (ptpt) cc_final: 0.6808 (tptt) REVERT: H 51 ASP cc_start: 0.8751 (p0) cc_final: 0.8522 (p0) REVERT: H 120 LYS cc_start: 0.8252 (tptt) cc_final: 0.7895 (mtpp) REVERT: L 11 ASP cc_start: 0.8343 (m-30) cc_final: 0.7819 (m-30) REVERT: L 96 LEU cc_start: 0.9076 (tt) cc_final: 0.8726 (pp) REVERT: L 122 PHE cc_start: 0.8459 (t80) cc_final: 0.7862 (t80) REVERT: L 148 GLU cc_start: 0.7656 (tp30) cc_final: 0.7003 (mm-30) REVERT: L 227 ARG cc_start: 0.5751 (pmt170) cc_final: 0.4529 (mpt-90) REVERT: L 702 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: M 68 HIS cc_start: 0.6405 (m170) cc_final: 0.6168 (m170) REVERT: M 73 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6892 (pp) REVERT: N 261 ASN cc_start: 0.7973 (m110) cc_final: 0.7587 (m-40) REVERT: N 331 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6661 (p-80) REVERT: O 27 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7716 (ptmm) REVERT: O 67 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5196 (tm) outliers start: 39 outliers final: 30 residues processed: 228 average time/residue: 0.1502 time to fit residues: 47.8954 Evaluate side-chains 226 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 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 A residue 87 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU 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 24 VAL 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 151 HIS 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 331 HIS 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: 4.9990 chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 110 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086934 restraints weight = 28561.034| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.83 r_work: 0.2880 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17285 Z= 0.144 Angle : 0.570 7.489 24579 Z= 0.330 Chirality : 0.036 0.182 2768 Planarity : 0.004 0.040 2117 Dihedral : 28.593 175.562 4639 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.44 % Allowed : 20.33 % Favored : 77.24 % 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: 1.07 (0.24), residues: 1265 helix: 1.85 (0.20), residues: 746 sheet: -0.73 (0.56), residues: 76 loop : -1.02 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.023 0.001 TYR D 83 PHE 0.021 0.001 PHE L 170 TRP 0.005 0.001 TRP L 52 HIS 0.005 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00316 (17285) covalent geometry : angle 0.56977 (24579) hydrogen bonds : bond 0.03452 ( 913) hydrogen bonds : angle 3.11622 ( 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 229 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9067 (mptt) cc_final: 0.8505 (mmmm) REVERT: B 91 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8953 (ttpt) REVERT: C 95 LYS cc_start: 0.9362 (tttp) cc_final: 0.8874 (ttpt) REVERT: D 85 LYS cc_start: 0.9060 (mptt) cc_final: 0.8707 (mmtt) REVERT: G 13 LYS cc_start: 0.6739 (tptt) cc_final: 0.6285 (ptmm) REVERT: G 56 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: G 104 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8663 (mt0) REVERT: H 34 LYS cc_start: 0.7529 (ptpt) cc_final: 0.6809 (tptt) REVERT: H 51 ASP cc_start: 0.8659 (p0) cc_final: 0.8403 (p0) REVERT: H 120 LYS cc_start: 0.8142 (tptt) cc_final: 0.7801 (mtpp) REVERT: L 11 ASP cc_start: 0.8356 (m-30) cc_final: 0.7833 (m-30) REVERT: L 28 GLN cc_start: 0.7202 (pt0) cc_final: 0.6821 (pm20) REVERT: L 96 LEU cc_start: 0.9017 (tt) cc_final: 0.8707 (pp) REVERT: L 122 PHE cc_start: 0.8134 (t80) cc_final: 0.7617 (t80) REVERT: L 148 GLU cc_start: 0.7486 (tp30) cc_final: 0.6958 (mm-30) REVERT: L 211 MET cc_start: 0.7954 (mtt) cc_final: 0.7457 (mmm) REVERT: L 227 ARG cc_start: 0.5523 (pmt170) cc_final: 0.4614 (mpt-90) REVERT: L 228 PHE cc_start: 0.6809 (m-80) cc_final: 0.6594 (m-80) REVERT: L 230 LEU cc_start: 0.8602 (pt) cc_final: 0.7412 (mm) REVERT: L 702 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: M 73 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6814 (pp) REVERT: N 253 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6359 (pt0) REVERT: N 261 ASN cc_start: 0.8027 (m110) cc_final: 0.7776 (m110) REVERT: N 274 HIS cc_start: 0.7270 (m90) cc_final: 0.6985 (m90) REVERT: N 283 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6936 (tm-30) REVERT: O 6 LYS cc_start: 0.5435 (mtmm) cc_final: 0.5175 (mmmm) REVERT: O 27 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7642 (ptmm) REVERT: O 67 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5479 (tm) outliers start: 27 outliers final: 21 residues processed: 224 average time/residue: 0.1529 time to fit residues: 48.3458 Evaluate side-chains 220 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain L residue 10 SER 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 151 HIS Chi-restraints excluded: chain L residue 654 VAL 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 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: 0.8980 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 110 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086097 restraints weight = 28554.202| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.83 r_work: 0.2869 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3241 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= 0.156 Angle : 0.569 7.272 24579 Z= 0.328 Chirality : 0.037 0.188 2768 Planarity : 0.004 0.039 2117 Dihedral : 28.620 174.944 4639 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.44 % Allowed : 20.23 % 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: 1.10 (0.24), residues: 1265 helix: 1.88 (0.20), residues: 746 sheet: -0.76 (0.56), residues: 76 loop : -1.01 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.024 0.002 TYR D 83 PHE 0.017 0.001 PHE N 313 TRP 0.003 0.001 TRP L 52 HIS 0.004 0.001 HIS L 169 Details of bonding type rmsd covalent geometry : bond 0.00349 (17285) covalent geometry : angle 0.56859 (24579) hydrogen bonds : bond 0.03597 ( 913) hydrogen bonds : angle 3.12267 ( 2328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.06 seconds wall clock time: 98 minutes 45.95 seconds (5925.95 seconds total)