Starting phenix.real_space_refine on Sun Sep 29 13:28:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/09_2024/8du4_27715.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6774 atoms to isotropic. 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 292 5.49 5 S 37 5.16 5 C 10063 2.51 5 N 3181 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17407 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 2382 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} bond proxies already assigned to first conformer: 2366 Chain: "N" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2440 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN L 225 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN L 225 " occ=0.00 residue: pdb=" N LEU O 73 " occ=0.86 ... (6 atoms not shown) pdb=" CD2 LEU O 73 " occ=0.86 residue: pdb=" N ARG O 74 " occ=0.87 ... (9 atoms not shown) pdb=" NH2 ARG O 74 " occ=0.87 residue: pdb=" N GLY O 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.45 Time building chain proxies: 11.00, per 1000 atoms: 0.63 Number of scatterers: 17407 At special positions: 0 Unit cell: (136.482, 128.018, 119.554, 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 37 16.00 P 292 15.00 O 3834 8.00 N 3181 7.00 C 10063 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: 4.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 21 sheets defined 38.5% alpha, 14.9% beta 145 base pairs and 222 stacking pairs defined. Time for finding SS restraints: 7.81 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.025A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.638A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.306A pdb=" N NLE A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.976A pdb=" N ILE A 124 " --> pdb=" O NLE A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.604A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.926A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.003A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 4.015A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 3.902A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.745A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.154A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.705A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.541A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 87 through 114 removed outlier: 3.710A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.732A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.011A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.761A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.673A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.352A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 20 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.267A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.903A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.800A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.819A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 234 removed outlier: 3.750A pdb=" N GLY N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 41 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: 7.500A 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 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.374A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 36 through 37 removed outlier: 4.407A pdb=" N LYS L 328 " --> pdb=" O SER L 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER L 318 " --> pdb=" O LYS L 328 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN L 314 " --> pdb=" O SER L 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 50 removed outlier: 3.672A pdb=" N SER L 50 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER L 64 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU L 68 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE L 69 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR L 82 " --> pdb=" O ILE L 69 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE L 71 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 90 through 95 removed outlier: 4.494A pdb=" N ASP L 92 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.710A pdb=" N ILE L 113 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 132 through 137 removed outlier: 3.599A pdb=" N VAL L 145 " --> pdb=" O ASN L 136 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE L 144 " --> pdb=" O TRP L 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP L 156 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS L 165 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 179 removed outlier: 3.862A pdb=" N HIS L 178 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL L 187 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 196 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS L 195 " --> pdb=" O THR L 208 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE L 197 " --> pdb=" O LEU L 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 228 through 233 removed outlier: 4.085A pdb=" N THR L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 264 through 267 removed outlier: 4.056A pdb=" N GLN L 295 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 16 through 18 removed outlier: 4.260A pdb=" N ILE N 320 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA N 311 " --> pdb=" O VAL N 301 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL N 301 " --> pdb=" O ALA N 311 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE N 313 " --> pdb=" O LEU N 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 38 through 42 removed outlier: 6.559A pdb=" N ILE N 48 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE N 61 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 50 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 69 through 74 removed outlier: 3.811A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER N 83 " --> pdb=" O SER N 91 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N SER N 91 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP N 94 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS N 100 " --> pdb=" O ASP N 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 114 through 116 removed outlier: 3.855A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS N 116 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 133 through 136 Processing sheet with id=AB9, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.519A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 201 through 206 Processing sheet with id=AC2, first strand: chain 'N' and resid 265 through 268 removed outlier: 3.722A pdb=" N ILE N 278 " --> pdb=" O LYS N 288 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 12 through 16 488 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 222 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3899 1.33 - 1.45: 4973 1.45 - 1.57: 8833 1.57 - 1.69: 582 1.69 - 1.81: 48 Bond restraints: 18335 Sorted by residual: bond pdb=" CB THR F 73 " pdb=" CG2 THR F 73 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" C3' DC J 276 " pdb=" O3' DC J 276 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CA HIS F 75 " pdb=" CB HIS F 75 " ideal model delta sigma weight residual 1.525 1.543 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 18330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 25878 2.75 - 5.51: 158 5.51 - 8.26: 12 8.26 - 11.01: 6 11.01 - 13.77: 1 Bond angle restraints: 26055 Sorted by residual: angle pdb=" C ASP N 149 " pdb=" CA ASP N 149 " pdb=" CB ASP N 149 " ideal model delta sigma weight residual 117.23 109.76 7.47 1.36e+00 5.41e-01 3.02e+01 angle pdb=" CA GLN F 27 " pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" N VAL N 249 " pdb=" CA VAL N 249 " pdb=" C VAL N 249 " ideal model delta sigma weight residual 112.96 108.82 4.14 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CA LEU N 185 " pdb=" CB LEU N 185 " pdb=" CG LEU N 185 " ideal model delta sigma weight residual 116.30 130.07 -13.77 3.50e+00 8.16e-02 1.55e+01 angle pdb=" CA ASP N 149 " pdb=" C ASP N 149 " pdb=" N ASP N 150 " ideal model delta sigma weight residual 119.98 116.71 3.27 8.50e-01 1.38e+00 1.48e+01 ... (remaining 26050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 8661 33.05 - 66.10: 1559 66.10 - 99.15: 46 99.15 - 132.20: 2 132.20 - 165.25: 1 Dihedral angle restraints: 10269 sinusoidal: 6058 harmonic: 4211 Sorted by residual: dihedral pdb=" CA ASN H 81 " pdb=" C ASN H 81 " pdb=" N LYS H 82 " pdb=" CA LYS H 82 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C4' DG J 244 " pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " pdb=" P DG J 245 " ideal model delta sinusoidal sigma weight residual 220.00 54.75 165.25 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA LEU G 33 " pdb=" C LEU G 33 " pdb=" N LEU G 34 " pdb=" CA LEU G 34 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 10266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2522 0.053 - 0.106: 392 0.106 - 0.159: 54 0.159 - 0.211: 2 0.211 - 0.264: 2 Chirality restraints: 2972 Sorted by residual: chirality pdb=" CG LEU L 240 " pdb=" CB LEU L 240 " pdb=" CD1 LEU L 240 " pdb=" CD2 LEU L 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA MET H 59 " pdb=" N MET H 59 " pdb=" C MET H 59 " pdb=" CB MET H 59 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU N 178 " pdb=" CB LEU N 178 " pdb=" CD1 LEU N 178 " pdb=" CD2 LEU N 178 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2969 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 27 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C GLN F 27 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 27 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY F 28 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 54 " -0.014 2.00e-02 2.50e+03 1.79e-02 7.21e+00 pdb=" N1 DC I 54 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DC I 54 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC I 54 " 0.027 2.00e-02 2.50e+03 pdb=" N3 DC I 54 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 54 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC I 54 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 54 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 43 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 552 2.67 - 3.23: 15706 3.23 - 3.79: 30493 3.79 - 4.34: 38759 4.34 - 4.90: 57661 Nonbonded interactions: 143171 Sorted by model distance: nonbonded pdb=" OH TYR L 252 " pdb=" O LEU L 288 " model vdw 2.118 3.040 nonbonded pdb=" NE2 GLN G 84 " pdb=" O GLY G 106 " model vdw 2.134 3.120 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR N 217 " pdb=" OD1 ASP N 219 " model vdw 2.143 3.040 nonbonded pdb=" O ALA E 75 " pdb=" N LYS E 79 " model vdw 2.172 3.120 ... (remaining 143166 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.090 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 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 0.048 18335 Z= 0.215 Angle : 0.690 13.768 26055 Z= 0.403 Chirality : 0.040 0.264 2972 Planarity : 0.005 0.066 2279 Dihedral : 25.341 165.255 7551 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.78 % Allowed : 16.22 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1418 helix: -0.14 (0.23), residues: 515 sheet: -1.40 (0.36), residues: 212 loop : -2.19 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 74 HIS 0.025 0.001 HIS F 75 PHE 0.017 0.002 PHE E 67 TYR 0.017 0.002 TYR E 54 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 54 TYR cc_start: 0.8741 (m-80) cc_final: 0.8446 (m-10) REVERT: H 93 THR cc_start: 0.7301 (t) cc_final: 0.4729 (p) REVERT: L 182 ASP cc_start: 0.2575 (m-30) cc_final: 0.1098 (t70) REVERT: N 166 ILE cc_start: -0.1510 (OUTLIER) cc_final: -0.1986 (mm) outliers start: 21 outliers final: 10 residues processed: 114 average time/residue: 0.3518 time to fit residues: 57.6530 Evaluate side-chains 87 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain N residue 166 ILE Chi-restraints excluded: chain N residue 222 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.5980 chunk 126 optimal weight: 40.0000 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 151 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 287 ASN N 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18335 Z= 0.181 Angle : 0.602 10.629 26055 Z= 0.341 Chirality : 0.039 0.165 2972 Planarity : 0.004 0.052 2279 Dihedral : 28.984 167.257 4809 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.07 % Allowed : 15.82 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1418 helix: 0.58 (0.23), residues: 515 sheet: -1.03 (0.39), residues: 202 loop : -2.15 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 286 HIS 0.007 0.001 HIS F 75 PHE 0.014 0.001 PHE E 67 TYR 0.018 0.001 TYR F 98 ARG 0.005 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 86 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5806 (mt-10) REVERT: H 93 THR cc_start: 0.7169 (t) cc_final: 0.5054 (p) REVERT: L 182 ASP cc_start: 0.2600 (m-30) cc_final: 0.1191 (t70) outliers start: 37 outliers final: 19 residues processed: 117 average time/residue: 0.2957 time to fit residues: 52.9419 Evaluate side-chains 99 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 135 optimal weight: 0.0670 chunk 150 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 overall best weight: 2.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 18335 Z= 0.385 Angle : 0.786 11.544 26055 Z= 0.436 Chirality : 0.047 0.280 2972 Planarity : 0.006 0.084 2279 Dihedral : 29.510 173.339 4797 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.92 % Allowed : 16.38 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1418 helix: 0.04 (0.22), residues: 508 sheet: -1.22 (0.37), residues: 215 loop : -2.25 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 286 HIS 0.012 0.002 HIS F 75 PHE 0.024 0.002 PHE H 67 TYR 0.036 0.003 TYR B 98 ARG 0.010 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 93 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7267 (pm20) cc_final: 0.6910 (pm20) REVERT: A 93 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: A 131 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: E 67 PHE cc_start: 0.3980 (OUTLIER) cc_final: 0.3163 (t80) REVERT: E 83 ARG cc_start: 0.1729 (mtp180) cc_final: 0.0484 (mtp85) REVERT: N 65 HIS cc_start: 0.3448 (OUTLIER) cc_final: 0.3237 (m90) REVERT: N 167 TYR cc_start: 0.2657 (OUTLIER) cc_final: 0.1150 (m-10) REVERT: N 259 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.6110 (t80) REVERT: O 15 LEU cc_start: 0.0289 (OUTLIER) cc_final: -0.1570 (tp) REVERT: O 69 LEU cc_start: 0.0727 (OUTLIER) cc_final: 0.0220 (mp) outliers start: 60 outliers final: 33 residues processed: 147 average time/residue: 0.3366 time to fit residues: 71.9589 Evaluate side-chains 119 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 78 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 167 TYR Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS L 130 ASN L 287 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18335 Z= 0.304 Angle : 0.666 8.607 26055 Z= 0.378 Chirality : 0.043 0.263 2972 Planarity : 0.006 0.118 2279 Dihedral : 29.308 173.788 4797 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.68 % Allowed : 18.32 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.22), residues: 1418 helix: 0.18 (0.22), residues: 521 sheet: -0.99 (0.36), residues: 226 loop : -2.26 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.007 0.001 HIS G 82 PHE 0.015 0.002 PHE E 84 TYR 0.032 0.002 TYR B 98 ARG 0.010 0.001 ARG N 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 93 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: D 98 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8252 (mp) REVERT: E 67 PHE cc_start: 0.4536 (OUTLIER) cc_final: 0.3409 (t80) REVERT: E 83 ARG cc_start: 0.0555 (OUTLIER) cc_final: -0.0061 (mtp85) REVERT: L 130 ASN cc_start: 0.3582 (OUTLIER) cc_final: 0.2853 (t0) REVERT: N 65 HIS cc_start: 0.3512 (OUTLIER) cc_final: 0.3208 (m90) REVERT: N 259 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5778 (t80) REVERT: O 69 LEU cc_start: 0.0354 (OUTLIER) cc_final: -0.0191 (mp) outliers start: 57 outliers final: 25 residues processed: 140 average time/residue: 0.3288 time to fit residues: 67.1800 Evaluate side-chains 109 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain L residue 130 ASN Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain O residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** L 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 HIS ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 18335 Z= 0.456 Angle : 0.840 12.382 26055 Z= 0.465 Chirality : 0.050 0.349 2972 Planarity : 0.007 0.055 2279 Dihedral : 29.603 177.146 4795 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.17 % Allowed : 20.02 % Favored : 74.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1418 helix: -0.17 (0.22), residues: 510 sheet: -0.90 (0.38), residues: 213 loop : -2.45 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 286 HIS 0.020 0.002 HIS F 75 PHE 0.019 0.003 PHE H 67 TYR 0.059 0.004 TYR L 131 ARG 0.007 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 85 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9041 (tt0) REVERT: A 131 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8427 (ttp80) REVERT: B 35 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7668 (mmt90) REVERT: C 74 LYS cc_start: 0.8087 (mppt) cc_final: 0.7647 (mmtp) REVERT: C 95 LYS cc_start: 0.8548 (tppt) cc_final: 0.8346 (mmmt) REVERT: D 98 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8551 (mp) REVERT: F 44 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8108 (ttmt) REVERT: H 105 LYS cc_start: 0.6680 (ttpt) cc_final: 0.6409 (mmtp) REVERT: N 65 HIS cc_start: 0.3611 (OUTLIER) cc_final: 0.3246 (m90) REVERT: N 259 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5664 (t80) outliers start: 63 outliers final: 33 residues processed: 137 average time/residue: 0.3088 time to fit residues: 62.3659 Evaluate side-chains 112 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 73 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 TYR Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18335 Z= 0.198 Angle : 0.598 8.673 26055 Z= 0.344 Chirality : 0.040 0.199 2972 Planarity : 0.004 0.055 2279 Dihedral : 29.244 173.987 4791 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.31 % Allowed : 21.71 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1418 helix: 0.47 (0.22), residues: 528 sheet: -0.69 (0.38), residues: 207 loop : -2.25 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 286 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.001 PHE O 4 TYR 0.012 0.001 TYR F 98 ARG 0.003 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 89 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: B 35 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7481 (mmt90) REVERT: C 74 LYS cc_start: 0.7891 (mppt) cc_final: 0.7509 (mttm) REVERT: C 95 LYS cc_start: 0.8560 (tppt) cc_final: 0.8301 (mmmt) REVERT: D 98 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 97 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: L 129 SER cc_start: 0.4803 (p) cc_final: 0.4545 (p) REVERT: N 65 HIS cc_start: 0.3306 (OUTLIER) cc_final: 0.2866 (m90) REVERT: N 259 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5628 (t80) outliers start: 40 outliers final: 21 residues processed: 118 average time/residue: 0.3309 time to fit residues: 57.7593 Evaluate side-chains 110 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 301 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18335 Z= 0.339 Angle : 0.682 8.520 26055 Z= 0.386 Chirality : 0.043 0.217 2972 Planarity : 0.005 0.052 2279 Dihedral : 29.306 174.697 4791 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.63 % Allowed : 22.03 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.22), residues: 1418 helix: 0.23 (0.22), residues: 529 sheet: -0.69 (0.38), residues: 217 loop : -2.23 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.013 0.001 HIS F 75 PHE 0.042 0.002 PHE E 84 TYR 0.022 0.002 TYR F 88 ARG 0.006 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: B 35 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7581 (mmt90) REVERT: C 95 LYS cc_start: 0.8564 (tppt) cc_final: 0.8326 (mmmt) REVERT: D 98 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8429 (mp) REVERT: E 97 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: F 44 LYS cc_start: 0.8395 (ptpt) cc_final: 0.8176 (ttmt) REVERT: H 44 GLN cc_start: 0.2130 (OUTLIER) cc_final: 0.1598 (tm-30) REVERT: N 65 HIS cc_start: 0.3530 (OUTLIER) cc_final: 0.3287 (m90) REVERT: N 242 MET cc_start: 0.4512 (tpt) cc_final: 0.4072 (mmm) REVERT: N 259 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5530 (t80) REVERT: O 1 MET cc_start: 0.1816 (OUTLIER) cc_final: -0.0647 (mtt) outliers start: 44 outliers final: 25 residues processed: 121 average time/residue: 0.3204 time to fit residues: 57.8570 Evaluate side-chains 113 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 0.0370 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18335 Z= 0.262 Angle : 0.628 8.162 26055 Z= 0.358 Chirality : 0.041 0.201 2972 Planarity : 0.005 0.051 2279 Dihedral : 29.160 174.386 4791 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.91 % Allowed : 22.92 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1418 helix: 0.44 (0.22), residues: 532 sheet: -0.53 (0.38), residues: 215 loop : -2.17 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.008 0.001 HIS F 75 PHE 0.028 0.001 PHE E 84 TYR 0.015 0.002 TYR F 88 ARG 0.007 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 82 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7591 (mmt90) REVERT: C 16 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6431 (t) REVERT: C 95 LYS cc_start: 0.8581 (tppt) cc_final: 0.8289 (mmmt) REVERT: F 44 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8084 (ttmt) REVERT: N 65 HIS cc_start: 0.3395 (OUTLIER) cc_final: 0.2881 (m90) REVERT: N 259 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5532 (t80) REVERT: O 1 MET cc_start: 0.1609 (OUTLIER) cc_final: -0.0618 (mtt) outliers start: 35 outliers final: 23 residues processed: 108 average time/residue: 0.3234 time to fit residues: 51.0363 Evaluate side-chains 105 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 92 GLN Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18335 Z= 0.263 Angle : 0.628 7.266 26055 Z= 0.358 Chirality : 0.041 0.185 2972 Planarity : 0.005 0.071 2279 Dihedral : 29.009 176.221 4787 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.23 % Allowed : 22.92 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1418 helix: 0.64 (0.22), residues: 525 sheet: -0.52 (0.36), residues: 229 loop : -2.06 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 286 HIS 0.009 0.001 HIS H 46 PHE 0.019 0.001 PHE H 62 TYR 0.017 0.002 TYR H 39 ARG 0.006 0.001 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7665 (mmt90) REVERT: C 41 GLU cc_start: 0.7489 (tt0) cc_final: 0.7286 (tt0) REVERT: C 76 THR cc_start: 0.8004 (p) cc_final: 0.7668 (p) REVERT: C 95 LYS cc_start: 0.8571 (tppt) cc_final: 0.8287 (mmmt) REVERT: E 97 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: N 259 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5397 (t80) REVERT: O 1 MET cc_start: 0.1848 (OUTLIER) cc_final: -0.0359 (mtt) outliers start: 39 outliers final: 25 residues processed: 131 average time/residue: 0.3590 time to fit residues: 67.4692 Evaluate side-chains 108 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 79 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** L 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18335 Z= 0.312 Angle : 0.666 9.207 26055 Z= 0.377 Chirality : 0.043 0.223 2972 Planarity : 0.005 0.049 2279 Dihedral : 29.153 178.489 4785 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.34 % Allowed : 24.21 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1418 helix: 0.57 (0.22), residues: 523 sheet: -0.55 (0.38), residues: 205 loop : -2.13 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 286 HIS 0.010 0.001 HIS F 75 PHE 0.023 0.002 PHE H 62 TYR 0.019 0.002 TYR F 88 ARG 0.009 0.001 ARG N 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7572 (mmt90) REVERT: C 95 LYS cc_start: 0.8581 (tppt) cc_final: 0.8295 (mmmt) REVERT: E 97 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: H 110 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7695 (mm-30) REVERT: N 259 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5451 (t80) REVERT: O 1 MET cc_start: 0.2002 (OUTLIER) cc_final: -0.0378 (mtt) outliers start: 28 outliers final: 23 residues processed: 109 average time/residue: 0.3397 time to fit residues: 54.2100 Evaluate side-chains 108 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 317 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN N 114 GLN ** N 116 HIS ** 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 = 0.4809 r_free = 0.4809 target = 0.236038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204530 restraints weight = 72103.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.202636 restraints weight = 73963.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.200039 restraints weight = 53009.498| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4418 r_free = 0.4418 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4418 r_free = 0.4418 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.4418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18335 Z= 0.186 Angle : 0.575 8.178 26055 Z= 0.331 Chirality : 0.039 0.182 2972 Planarity : 0.004 0.045 2279 Dihedral : 28.914 179.536 4785 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 24.13 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1418 helix: 1.12 (0.23), residues: 519 sheet: -0.52 (0.36), residues: 238 loop : -2.03 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.007 0.001 HIS F 75 PHE 0.011 0.001 PHE H 62 TYR 0.012 0.001 TYR F 98 ARG 0.005 0.000 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.83 seconds wall clock time: 49 minutes 0.01 seconds (2940.01 seconds total)