Starting phenix.real_space_refine on Sat Dec 9 11:19:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg4_30350/12_2023/7cg4_30350.pdb" } resolution = 3.6 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= 0.002 sd= 0.049 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 7153 2.51 5 N 1775 2.21 5 O 1923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "f ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10943 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "b" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 526 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "d" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "e" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 293 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "r" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1608 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 1 Chain: "s" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1608 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 1 Chain: "t" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1601 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain breaks: 1 Chain: "u" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1583 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 1 Chain: "v" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1559 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 14, 'TRANS': 185} Chain breaks: 2 Time building chain proxies: 6.27, per 1000 atoms: 0.57 Number of scatterers: 10943 At special positions: 0 Unit cell: (105.867, 101.946, 130.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 1923 8.00 N 1775 7.00 C 7153 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 - 3.50 Amino acid : False - 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: 4.44 Conformation dependent library (CDL) restraints added in 2.1 seconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 84.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'a' and resid 34 through 61 removed outlier: 3.864A pdb=" N ASP a 47 " --> pdb=" O ASP a 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 100 Processing helix chain 'b' and resid 37 through 61 removed outlier: 3.924A pdb=" N ALA b 52 " --> pdb=" O ARG b 48 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU b 61 " --> pdb=" O GLU b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 101 Processing helix chain 'c' and resid 34 through 61 removed outlier: 3.727A pdb=" N ARG c 48 " --> pdb=" O ARG c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 102 removed outlier: 4.337A pdb=" N ALA c 73 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET c 102 " --> pdb=" O GLU c 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 34 through 61 Processing helix chain 'd' and resid 70 through 101 removed outlier: 4.465A pdb=" N GLN d 76 " --> pdb=" O MET d 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS d 77 " --> pdb=" O ALA d 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER d 79 " --> pdb=" O MET d 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 61 removed outlier: 3.676A pdb=" N LEU e 38 " --> pdb=" O PHE e 34 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS e 39 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN e 49 " --> pdb=" O ILE e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 100 removed outlier: 3.671A pdb=" N GLN e 76 " --> pdb=" O MET e 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 100 Processing helix chain 'r' and resid 42 through 61 removed outlier: 3.554A pdb=" N THR r 52 " --> pdb=" O ILE r 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE r 53 " --> pdb=" O THR r 49 " (cutoff:3.500A) Proline residue: r 55 - end of helix Processing helix chain 'r' and resid 64 through 78 removed outlier: 3.931A pdb=" N ILE r 68 " --> pdb=" O PHE r 64 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE r 69 " --> pdb=" O THR r 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 101 removed outlier: 4.255A pdb=" N LEU r 94 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR r 97 " --> pdb=" O ALA r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 117 Proline residue: r 115 - end of helix Processing helix chain 'r' and resid 122 through 142 removed outlier: 4.460A pdb=" N ASP r 128 " --> pdb=" O GLN r 124 " (cutoff:3.500A) Proline residue: r 133 - end of helix removed outlier: 3.605A pdb=" N GLN r 141 " --> pdb=" O PHE r 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR r 142 " --> pdb=" O MET r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 155 removed outlier: 3.799A pdb=" N ALA r 148 " --> pdb=" O GLU r 144 " (cutoff:3.500A) Processing helix chain 'r' and resid 166 through 207 removed outlier: 3.679A pdb=" N LEU r 171 " --> pdb=" O MET r 167 " (cutoff:3.500A) Proline residue: r 172 - end of helix removed outlier: 3.696A pdb=" N SER r 177 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR r 181 " --> pdb=" O SER r 177 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE r 183 " --> pdb=" O LEU r 179 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN r 184 " --> pdb=" O LYS r 180 " (cutoff:3.500A) Proline residue: r 192 - end of helix Processing helix chain 'r' and resid 214 through 229 Proline residue: r 220 - end of helix Processing helix chain 'r' and resid 230 through 245 Processing helix chain 's' and resid 39 through 59 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 64 through 78 removed outlier: 3.800A pdb=" N ILE s 68 " --> pdb=" O PHE s 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE s 69 " --> pdb=" O THR s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 85 through 117 removed outlier: 3.618A pdb=" N LEU s 89 " --> pdb=" O PRO s 85 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR s 97 " --> pdb=" O ALA s 93 " (cutoff:3.500A) Proline residue: s 103 - end of helix Proline residue: s 115 - end of helix Processing helix chain 's' and resid 122 through 142 removed outlier: 4.630A pdb=" N ASP s 128 " --> pdb=" O GLN s 124 " (cutoff:3.500A) Proline residue: s 133 - end of helix removed outlier: 4.546A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN s 141 " --> pdb=" O PHE s 137 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR s 142 " --> pdb=" O MET s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 143 through 155 Processing helix chain 's' and resid 170 through 206 removed outlier: 3.780A pdb=" N SER s 177 " --> pdb=" O ALA s 173 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR s 181 " --> pdb=" O SER s 177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE s 183 " --> pdb=" O LEU s 179 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN s 184 " --> pdb=" O LYS s 180 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR s 188 " --> pdb=" O GLN s 184 " (cutoff:3.500A) Proline residue: s 192 - end of helix Processing helix chain 's' and resid 214 through 229 Proline residue: s 220 - end of helix Processing helix chain 's' and resid 230 through 245 Processing helix chain 't' and resid 39 through 61 removed outlier: 3.792A pdb=" N THR t 52 " --> pdb=" O ILE t 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE t 53 " --> pdb=" O THR t 49 " (cutoff:3.500A) Proline residue: t 55 - end of helix Processing helix chain 't' and resid 64 through 78 removed outlier: 3.644A pdb=" N ILE t 68 " --> pdb=" O PHE t 64 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE t 69 " --> pdb=" O THR t 65 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL t 70 " --> pdb=" O ARG t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 85 through 101 removed outlier: 3.600A pdb=" N LEU t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 101 through 114 removed outlier: 3.511A pdb=" N ILE t 105 " --> pdb=" O MET t 101 " (cutoff:3.500A) Processing helix chain 't' and resid 122 through 141 removed outlier: 4.475A pdb=" N ASP t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) Proline residue: t 133 - end of helix Processing helix chain 't' and resid 143 through 155 removed outlier: 4.036A pdb=" N LEU t 147 " --> pdb=" O ARG t 143 " (cutoff:3.500A) Processing helix chain 't' and resid 170 through 207 removed outlier: 3.549A pdb=" N SER t 177 " --> pdb=" O ALA t 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR t 181 " --> pdb=" O SER t 177 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE t 183 " --> pdb=" O LEU t 179 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR t 188 " --> pdb=" O GLN t 184 " (cutoff:3.500A) Proline residue: t 192 - end of helix removed outlier: 3.618A pdb=" N LEU t 207 " --> pdb=" O VAL t 203 " (cutoff:3.500A) Processing helix chain 't' and resid 214 through 229 Proline residue: t 220 - end of helix Processing helix chain 't' and resid 230 through 244 removed outlier: 4.032A pdb=" N GLY t 237 " --> pdb=" O GLN t 233 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 60 removed outlier: 3.661A pdb=" N LEU u 51 " --> pdb=" O PHE u 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR u 52 " --> pdb=" O ILE u 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE u 53 " --> pdb=" O THR u 49 " (cutoff:3.500A) Proline residue: u 55 - end of helix Processing helix chain 'u' and resid 64 through 78 Processing helix chain 'u' and resid 85 through 101 removed outlier: 4.187A pdb=" N GLY u 91 " --> pdb=" O GLN u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 118 Proline residue: u 115 - end of helix removed outlier: 3.914A pdb=" N GLU u 118 " --> pdb=" O GLN u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 142 removed outlier: 4.834A pdb=" N ASP u 128 " --> pdb=" O GLN u 124 " (cutoff:3.500A) Proline residue: u 133 - end of helix removed outlier: 4.017A pdb=" N ARG u 140 " --> pdb=" O ALA u 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN u 141 " --> pdb=" O PHE u 137 " (cutoff:3.500A) Processing helix chain 'u' and resid 145 through 152 removed outlier: 3.780A pdb=" N LEU u 149 " --> pdb=" O ALA u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 166 through 207 removed outlier: 3.601A pdb=" N LEU u 170 " --> pdb=" O PRO u 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU u 171 " --> pdb=" O MET u 167 " (cutoff:3.500A) Proline residue: u 172 - end of helix removed outlier: 4.144A pdb=" N SER u 177 " --> pdb=" O ALA u 173 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR u 181 " --> pdb=" O SER u 177 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN u 184 " --> pdb=" O LYS u 180 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR u 188 " --> pdb=" O GLN u 184 " (cutoff:3.500A) Proline residue: u 192 - end of helix Processing helix chain 'u' and resid 213 through 229 removed outlier: 4.064A pdb=" N ILE u 217 " --> pdb=" O PRO u 213 " (cutoff:3.500A) Proline residue: u 220 - end of helix Processing helix chain 'u' and resid 230 through 245 Processing helix chain 'v' and resid 39 through 53 Processing helix chain 'v' and resid 53 through 60 removed outlier: 3.554A pdb=" N ILE v 57 " --> pdb=" O PHE v 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU v 58 " --> pdb=" O LEU v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 66 through 78 Processing helix chain 'v' and resid 85 through 101 removed outlier: 4.151A pdb=" N GLY v 91 " --> pdb=" O GLN v 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 118 removed outlier: 3.554A pdb=" N ILE v 105 " --> pdb=" O MET v 101 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN v 114 " --> pdb=" O VAL v 110 " (cutoff:3.500A) Proline residue: v 115 - end of helix Processing helix chain 'v' and resid 122 through 141 Proline residue: v 133 - end of helix Processing helix chain 'v' and resid 145 through 155 removed outlier: 4.212A pdb=" N LEU v 149 " --> pdb=" O ALA v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 166 through 202 removed outlier: 3.797A pdb=" N LEU v 170 " --> pdb=" O PRO v 166 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU v 171 " --> pdb=" O MET v 167 " (cutoff:3.500A) Proline residue: v 172 - end of helix removed outlier: 3.649A pdb=" N SER v 177 " --> pdb=" O ALA v 173 " (cutoff:3.500A) Proline residue: v 192 - end of helix Processing helix chain 'v' and resid 213 through 230 removed outlier: 3.785A pdb=" N ILE v 217 " --> pdb=" O PRO v 213 " (cutoff:3.500A) Proline residue: v 220 - end of helix Processing helix chain 'v' and resid 230 through 245 removed outlier: 4.111A pdb=" N LEU v 234 " --> pdb=" O ASP v 230 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1734 1.31 - 1.44: 2730 1.44 - 1.56: 6496 1.56 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 11144 Sorted by residual: bond pdb=" C MET c 75 " pdb=" O MET c 75 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C MET c 75 " pdb=" N GLN c 76 " ideal model delta sigma weight residual 1.335 1.292 0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" C GLN e 83 " pdb=" O GLN e 83 " ideal model delta sigma weight residual 1.237 1.201 0.035 1.16e-02 7.43e+03 9.22e+00 bond pdb=" N VAL v 88 " pdb=" CA VAL v 88 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.92e+00 bond pdb=" C ASP c 74 " pdb=" N MET c 75 " ideal model delta sigma weight residual 1.334 1.297 0.037 1.33e-02 5.65e+03 7.87e+00 ... (remaining 11139 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.33: 324 105.33 - 112.50: 5788 112.50 - 119.66: 3598 119.66 - 126.83: 5279 126.83 - 134.00: 103 Bond angle restraints: 15092 Sorted by residual: angle pdb=" CB MET c 75 " pdb=" CG MET c 75 " pdb=" SD MET c 75 " ideal model delta sigma weight residual 112.70 98.16 14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" N MET c 75 " pdb=" CA MET c 75 " pdb=" C MET c 75 " ideal model delta sigma weight residual 111.14 106.44 4.70 1.08e+00 8.57e-01 1.89e+01 angle pdb=" N GLN e 83 " pdb=" CA GLN e 83 " pdb=" C GLN e 83 " ideal model delta sigma weight residual 111.14 106.83 4.31 1.08e+00 8.57e-01 1.59e+01 angle pdb=" CA GLN e 83 " pdb=" C GLN e 83 " pdb=" O GLN e 83 " ideal model delta sigma weight residual 120.70 117.12 3.58 1.03e+00 9.43e-01 1.21e+01 angle pdb=" CA ASP c 74 " pdb=" C ASP c 74 " pdb=" N MET c 75 " ideal model delta sigma weight residual 117.63 113.41 4.22 1.25e+00 6.40e-01 1.14e+01 ... (remaining 15087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6077 17.89 - 35.77: 570 35.77 - 53.66: 105 53.66 - 71.55: 14 71.55 - 89.43: 18 Dihedral angle restraints: 6784 sinusoidal: 2658 harmonic: 4126 Sorted by residual: dihedral pdb=" CA SER u 177 " pdb=" C SER u 177 " pdb=" N GLU u 178 " pdb=" CA GLU u 178 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU t 58 " pdb=" C LEU t 58 " pdb=" N LEU t 59 " pdb=" CA LEU t 59 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR u 62 " pdb=" C THR u 62 " pdb=" N SER u 63 " pdb=" CA SER u 63 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1511 0.053 - 0.107: 271 0.107 - 0.160: 28 0.160 - 0.213: 3 0.213 - 0.266: 3 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA MET c 75 " pdb=" N MET c 75 " pdb=" C MET c 75 " pdb=" CB MET c 75 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET u 236 " pdb=" N MET u 236 " pdb=" C MET u 236 " pdb=" CB MET u 236 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET t 236 " pdb=" N MET t 236 " pdb=" C MET t 236 " pdb=" CB MET t 236 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1813 not shown) Planarity restraints: 1885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL u 110 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL u 110 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL u 110 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP u 111 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP c 74 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ASP c 74 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP c 74 " -0.016 2.00e-02 2.50e+03 pdb=" N MET c 75 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN t 114 " 0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO t 115 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO t 115 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO t 115 " 0.030 5.00e-02 4.00e+02 ... (remaining 1882 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 792 2.73 - 3.27: 11956 3.27 - 3.82: 17650 3.82 - 4.36: 18716 4.36 - 4.90: 32588 Nonbonded interactions: 81702 Sorted by model distance: nonbonded pdb=" NE2 GLN v 141 " pdb=" O PHE v 243 " model vdw 2.192 2.520 nonbonded pdb=" O ARG t 140 " pdb=" NH1 ARG t 140 " model vdw 2.217 2.520 nonbonded pdb=" NE ARG r 66 " pdb=" OE2 GLU r 178 " model vdw 2.264 2.520 nonbonded pdb=" OH TYR t 174 " pdb=" OE2 GLU t 178 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG s 75 " pdb=" OD1 ASN s 86 " model vdw 2.282 2.520 ... (remaining 81697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 35 through 103) selection = (chain 'b' and resid 35 through 103) selection = (chain 'c' and resid 35 through 103) selection = (chain 'd' and resid 35 through 103) selection = (chain 'e' and resid 35 through 103) } ncs_group { reference = (chain 'r' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 's' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 't' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 'u' and (resid 35 through 204 or resid 212 through 245)) selection = (chain 'v' and (resid 35 through 154 or resid 163 through 245)) } 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=1.00 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: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.500 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 31.570 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.003 0.054 11144 Z= 0.214 Angle : 0.691 14.541 15092 Z= 0.379 Chirality : 0.041 0.266 1816 Planarity : 0.004 0.055 1885 Dihedral : 14.904 89.431 4086 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.34 % Allowed : 5.57 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.20), residues: 1385 helix: -1.37 (0.14), residues: 1117 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.017 0.001 PHE v 64 TYR 0.013 0.001 TYR s 244 ARG 0.002 0.000 ARG r 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 453 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 454 average time/residue: 0.2212 time to fit residues: 140.1512 Evaluate side-chains 403 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1243 time to fit residues: 1.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 0.0470 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN d 49 GLN e 49 GLN f 69 ASN r 141 GLN t 43 GLN u 86 ASN u 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11144 Z= 0.182 Angle : 0.709 9.536 15092 Z= 0.333 Chirality : 0.040 0.181 1816 Planarity : 0.004 0.051 1885 Dihedral : 4.541 20.874 1484 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 3.21 % Allowed : 18.82 % Favored : 77.97 % 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: -0.80 (0.23), residues: 1385 helix: 0.14 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -3.16 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.018 0.001 PHE c 34 TYR 0.012 0.001 TYR t 244 ARG 0.006 0.000 ARG b 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 413 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 421 average time/residue: 0.2128 time to fit residues: 128.2882 Evaluate side-chains 415 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 393 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1170 time to fit residues: 6.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN f 69 ASN s 36 GLN ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11144 Z= 0.193 Angle : 0.700 8.886 15092 Z= 0.329 Chirality : 0.040 0.187 1816 Planarity : 0.004 0.047 1885 Dihedral : 4.487 21.212 1484 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 2.19 % Allowed : 22.36 % Favored : 75.44 % 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: -0.08 (0.24), residues: 1385 helix: 0.63 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.96 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP t 232 HIS 0.006 0.001 HIS e 39 PHE 0.034 0.001 PHE v 190 TYR 0.013 0.001 TYR s 244 ARG 0.005 0.000 ARG b 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 409 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 417 average time/residue: 0.2217 time to fit residues: 131.0945 Evaluate side-chains 408 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 397 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1284 time to fit residues: 4.0707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN e 49 GLN f 76 GLN s 36 GLN ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11144 Z= 0.188 Angle : 0.706 10.065 15092 Z= 0.330 Chirality : 0.040 0.268 1816 Planarity : 0.004 0.048 1885 Dihedral : 4.424 20.838 1484 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.53 % Allowed : 24.73 % Favored : 72.74 % 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: 0.35 (0.24), residues: 1385 helix: 0.89 (0.16), residues: 1129 sheet: None (None), residues: 0 loop : -2.63 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.019 0.001 PHE v 64 TYR 0.014 0.001 TYR c 96 ARG 0.005 0.000 ARG b 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 403 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 411 average time/residue: 0.2222 time to fit residues: 128.5193 Evaluate side-chains 412 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 394 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1087 time to fit residues: 5.2997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN v 76 ASN ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11144 Z= 0.190 Angle : 0.719 12.378 15092 Z= 0.334 Chirality : 0.040 0.229 1816 Planarity : 0.004 0.045 1885 Dihedral : 4.398 20.762 1484 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 1.77 % Allowed : 26.33 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1385 helix: 1.04 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -2.57 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP t 232 HIS 0.006 0.001 HIS e 39 PHE 0.034 0.001 PHE v 190 TYR 0.016 0.001 TYR a 96 ARG 0.007 0.001 ARG d 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 404 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 415 average time/residue: 0.2195 time to fit residues: 128.6994 Evaluate side-chains 401 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 392 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1092 time to fit residues: 3.5967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11144 Z= 0.181 Angle : 0.721 11.717 15092 Z= 0.333 Chirality : 0.040 0.236 1816 Planarity : 0.004 0.044 1885 Dihedral : 4.303 20.456 1484 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 1.77 % Allowed : 28.19 % Favored : 70.04 % 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: 0.80 (0.24), residues: 1385 helix: 1.20 (0.16), residues: 1133 sheet: None (None), residues: 0 loop : -2.46 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.018 0.001 PHE c 34 TYR 0.011 0.001 TYR s 244 ARG 0.007 0.000 ARG t 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 401 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 408 average time/residue: 0.2170 time to fit residues: 125.9602 Evaluate side-chains 398 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 386 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1015 time to fit residues: 3.9939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 55 GLN ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11144 Z= 0.240 Angle : 0.773 12.389 15092 Z= 0.362 Chirality : 0.043 0.318 1816 Planarity : 0.004 0.042 1885 Dihedral : 4.403 21.613 1484 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.94 % Allowed : 29.11 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1385 helix: 1.14 (0.16), residues: 1141 sheet: None (None), residues: 0 loop : -2.43 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP s 232 HIS 0.008 0.001 HIS e 39 PHE 0.022 0.001 PHE v 64 TYR 0.017 0.002 TYR s 244 ARG 0.008 0.001 ARG v 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 405 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 410 average time/residue: 0.2211 time to fit residues: 127.4381 Evaluate side-chains 414 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 397 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1036 time to fit residues: 5.2255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11144 Z= 0.259 Angle : 0.815 12.328 15092 Z= 0.380 Chirality : 0.043 0.308 1816 Planarity : 0.004 0.055 1885 Dihedral : 4.538 22.468 1484 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 1.18 % Allowed : 30.13 % Favored : 68.69 % 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: 0.75 (0.24), residues: 1385 helix: 1.13 (0.16), residues: 1141 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP s 232 HIS 0.008 0.002 HIS e 39 PHE 0.014 0.001 PHE r 190 TYR 0.016 0.002 TYR s 244 ARG 0.010 0.001 ARG v 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 399 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 403 average time/residue: 0.2213 time to fit residues: 126.1157 Evaluate side-chains 399 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 394 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0914 time to fit residues: 2.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11144 Z= 0.207 Angle : 0.808 12.566 15092 Z= 0.371 Chirality : 0.042 0.322 1816 Planarity : 0.004 0.042 1885 Dihedral : 4.454 21.074 1484 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 0.51 % Allowed : 31.39 % Favored : 68.10 % 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: 0.98 (0.24), residues: 1385 helix: 1.31 (0.16), residues: 1127 sheet: None (None), residues: 0 loop : -2.27 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.016 0.001 PHE t 150 TYR 0.013 0.001 TYR s 244 ARG 0.010 0.001 ARG v 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 396 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 398 average time/residue: 0.2231 time to fit residues: 125.9182 Evaluate side-chains 398 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1042 time to fit residues: 2.4301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 overall best weight: 0.5630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11144 Z= 0.206 Angle : 0.849 20.476 15092 Z= 0.384 Chirality : 0.042 0.287 1816 Planarity : 0.004 0.042 1885 Dihedral : 4.450 22.492 1484 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 0.34 % Allowed : 32.07 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.24), residues: 1385 helix: 1.39 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.25 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.014 0.001 PHE r 187 TYR 0.012 0.001 TYR c 96 ARG 0.009 0.000 ARG v 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 400 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 400 average time/residue: 0.2177 time to fit residues: 122.5152 Evaluate side-chains 392 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 388 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2135 time to fit residues: 2.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 83 GLN ** v 86 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.146076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130110 restraints weight = 18761.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133499 restraints weight = 8632.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135590 restraints weight = 4801.290| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11144 Z= 0.220 Angle : 0.851 18.208 15092 Z= 0.386 Chirality : 0.042 0.284 1816 Planarity : 0.004 0.041 1885 Dihedral : 4.422 26.291 1484 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 0.51 % Allowed : 32.15 % Favored : 67.34 % 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: 1.07 (0.24), residues: 1385 helix: 1.36 (0.16), residues: 1133 sheet: None (None), residues: 0 loop : -2.25 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.013 0.001 PHE v 64 TYR 0.015 0.002 TYR c 96 ARG 0.009 0.000 ARG d 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3116.39 seconds wall clock time: 57 minutes 1.63 seconds (3421.63 seconds total)