Starting phenix.real_space_refine on Wed Mar 4 17:26:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.map" model { file = "/net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wua_21908/03_2026/6wua_21908.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 402 5.49 5 S 20 5.16 5 C 7975 2.51 5 N 2807 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15195 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 8569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 8569 Classifications: {'RNA': 402} Modifications used: {'rna2p_pur': 33, 'rna2p_pyr': 39, 'rna3p_pur': 177, 'rna3p_pyr': 153} Link IDs: {'rna2p': 71, 'rna3p': 330} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "m" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 104} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14249 SG CYS n 24 57.908 83.292 49.350 1.00 17.98 S ATOM 14275 SG CYS n 27 61.128 84.467 48.757 1.00 19.90 S ATOM 14387 SG CYS n 40 60.686 82.934 52.027 1.00 18.14 S ATOM 14412 SG CYS n 43 59.723 86.442 51.550 1.00 17.83 S Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15195 At special positions: 0 Unit cell: (109.7, 132.737, 127.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 402 15.00 O 3990 8.00 N 2807 7.00 C 7975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 258.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 6 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 42.4% alpha, 20.4% beta 123 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 45 through 50 Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 4.201A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.565A pdb=" N ARG c 126 " --> pdb=" O LEU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.662A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 3.635A pdb=" N GLY c 158 " --> pdb=" O ARG c 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.704A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.515A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.082A pdb=" N LYS g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.674A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.556A pdb=" N ILE i 39 " --> pdb=" O VAL i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 73 through 91 removed outlier: 3.741A pdb=" N GLY i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 95 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.601A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.711A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.703A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.557A pdb=" N ASP m 54 " --> pdb=" O ASN m 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 Processing helix chain 'm' and resid 68 through 81 removed outlier: 3.840A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.751A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.796A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 3.985A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 70 through 75 removed outlier: 3.801A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.552A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 74 through 79 removed outlier: 3.580A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 6 through 12 removed outlier: 6.540A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AB1, first strand: chain 's' and resid 32 through 33 removed outlier: 3.684A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 494 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1771 1.32 - 1.44: 6560 1.44 - 1.56: 7140 1.56 - 1.68: 802 1.68 - 1.80: 36 Bond restraints: 16309 Sorted by residual: bond pdb=" CA PRO i 40 " pdb=" C PRO i 40 " ideal model delta sigma weight residual 1.527 1.502 0.025 1.35e-02 5.49e+03 3.36e+00 bond pdb=" N ALA m 106 " pdb=" CA ALA m 106 " ideal model delta sigma weight residual 1.457 1.441 0.017 1.10e-02 8.26e+03 2.27e+00 bond pdb=" C5 G a1237 " pdb=" C6 G a1237 " ideal model delta sigma weight residual 1.419 1.391 0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" O3' G a1237 " pdb=" P C a1238 " ideal model delta sigma weight residual 1.607 1.588 0.019 1.50e-02 4.44e+03 1.65e+00 bond pdb=" P G a1237 " pdb=" O5' G a1237 " ideal model delta sigma weight residual 1.593 1.574 0.019 1.50e-02 4.44e+03 1.60e+00 ... (remaining 16304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22880 1.70 - 3.39: 951 3.39 - 5.09: 102 5.09 - 6.79: 20 6.79 - 8.48: 10 Bond angle restraints: 23963 Sorted by residual: angle pdb=" N PRO j 43 " pdb=" CA PRO j 43 " pdb=" C PRO j 43 " ideal model delta sigma weight residual 112.47 120.95 -8.48 2.06e+00 2.36e-01 1.70e+01 angle pdb=" C PRO i 40 " pdb=" N HIS i 41 " pdb=" CA HIS i 41 " ideal model delta sigma weight residual 121.54 113.84 7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" N VAL c 75 " pdb=" CA VAL c 75 " pdb=" C VAL c 75 " ideal model delta sigma weight residual 113.71 110.15 3.56 9.50e-01 1.11e+00 1.40e+01 angle pdb=" C3' U a1226 " pdb=" O3' U a1226 " pdb=" P U a1227 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C2' G a1019 " pdb=" C1' G a1019 " pdb=" N9 G a1019 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.50e+00 4.44e-01 1.00e+01 ... (remaining 23958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 9264 33.72 - 67.44: 1010 67.44 - 101.17: 132 101.17 - 134.89: 3 134.89 - 168.61: 3 Dihedral angle restraints: 10412 sinusoidal: 8021 harmonic: 2391 Sorted by residual: dihedral pdb=" O4' U a1040 " pdb=" C1' U a1040 " pdb=" N1 U a1040 " pdb=" C2 U a1040 " ideal model delta sinusoidal sigma weight residual 200.00 53.67 146.33 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' C a1173 " pdb=" C1' C a1173 " pdb=" N1 C a1173 " pdb=" C2 C a1173 " ideal model delta sinusoidal sigma weight residual 200.00 65.56 134.44 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' U a1152 " pdb=" C1' U a1152 " pdb=" N1 U a1152 " pdb=" C2 U a1152 " ideal model delta sinusoidal sigma weight residual 200.00 67.00 133.00 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 10409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2274 0.051 - 0.102: 608 0.102 - 0.153: 102 0.153 - 0.203: 17 0.203 - 0.254: 4 Chirality restraints: 3005 Sorted by residual: chirality pdb=" CA PRO j 43 " pdb=" N PRO j 43 " pdb=" C PRO j 43 " pdb=" CB PRO j 43 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' A a 974 " pdb=" C4' A a 974 " pdb=" O3' A a 974 " pdb=" C2' A a 974 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' U a1226 " pdb=" O4' U a1226 " pdb=" C2' U a1226 " pdb=" N1 U a1226 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3002 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO j 43 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G a1019 " -0.038 2.00e-02 2.50e+03 1.59e-02 7.56e+00 pdb=" N9 G a1019 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G a1019 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G a1019 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G a1019 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G a1019 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G a1019 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G a1019 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G a1019 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G a1019 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU j 92 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO j 93 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO j 93 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO j 93 " 0.029 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 114 2.57 - 3.16: 11330 3.16 - 3.74: 25652 3.74 - 4.32: 37749 4.32 - 4.90: 53156 Nonbonded interactions: 128001 Sorted by model distance: nonbonded pdb=" O2 U a 976 " pdb=" O2' G a1237 " model vdw 1.992 3.040 nonbonded pdb=" N2 G a1019 " pdb=" N6 A a1052 " model vdw 2.033 2.560 nonbonded pdb=" O4 U a 966 " pdb=" NZ LYS m 103 " model vdw 2.141 3.120 nonbonded pdb=" N1 G a1181 " pdb=" OP2 A a1184 " model vdw 2.166 3.120 nonbonded pdb=" O2' C a1038 " pdb=" O5' U a1039 " model vdw 2.182 3.040 ... (remaining 127996 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.007 0.100 16313 Z= 0.337 Angle : 0.827 18.892 23969 Z= 0.425 Chirality : 0.047 0.254 3005 Planarity : 0.006 0.070 1570 Dihedral : 22.536 168.610 8874 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.38 % Favored : 84.49 % Rotamer: Outliers : 14.80 % Allowed : 15.80 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.24), residues: 819 helix: -2.49 (0.24), residues: 306 sheet: -2.26 (0.38), residues: 139 loop : -3.57 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG s 78 TYR 0.019 0.002 TYR i 72 PHE 0.019 0.002 PHE i 127 TRP 0.013 0.002 TRP c 200 HIS 0.007 0.002 HIS i 41 Details of bonding type rmsd covalent geometry : bond 0.00674 (16309) covalent geometry : angle 0.81283 (23963) hydrogen bonds : bond 0.16246 ( 569) hydrogen bonds : angle 5.93509 ( 1262) metal coordination : bond 0.07231 ( 4) metal coordination : angle 9.60364 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 153 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7746 (m100) REVERT: g 10 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.4987 (tpm170) REVERT: g 13 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tt) REVERT: i 88 LEU cc_start: 0.8452 (tt) cc_final: 0.8201 (tp) REVERT: j 4 GLN cc_start: 0.5306 (OUTLIER) cc_final: 0.4613 (tm-30) REVERT: m 66 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.4102 (tm-30) REVERT: m 75 LEU cc_start: 0.8030 (pp) cc_final: 0.7696 (mt) REVERT: m 100 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: m 109 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7715 (tpt-90) REVERT: n 6 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: s 6 LYS cc_start: 0.2591 (OUTLIER) cc_final: 0.2246 (pmtt) REVERT: s 7 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.3836 (pttt) REVERT: s 27 LYS cc_start: 0.5394 (OUTLIER) cc_final: 0.4796 (mptt) REVERT: s 36 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7014 (mtm110) outliers start: 103 outliers final: 57 residues processed: 233 average time/residue: 0.1656 time to fit residues: 52.6889 Evaluate side-chains 175 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 41 GLU Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 103 LYS Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 36 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 ASN g 28 ASN g 64 GLN g 86 GLN i 66 ASN i 81 HIS m 50 ASN m 105 ASN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064728 restraints weight = 50429.427| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.24 r_work: 0.3128 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16313 Z= 0.125 Angle : 0.591 9.218 23969 Z= 0.309 Chirality : 0.037 0.187 3005 Planarity : 0.005 0.056 1570 Dihedral : 22.562 175.168 7332 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 9.05 % Allowed : 21.55 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.27), residues: 819 helix: -1.02 (0.28), residues: 313 sheet: -1.26 (0.40), residues: 147 loop : -3.19 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 31 TYR 0.012 0.001 TYR s 52 PHE 0.007 0.001 PHE i 127 TRP 0.014 0.001 TRP c 200 HIS 0.003 0.001 HIS c 68 Details of bonding type rmsd covalent geometry : bond 0.00247 (16309) covalent geometry : angle 0.58737 (23963) hydrogen bonds : bond 0.05419 ( 569) hydrogen bonds : angle 3.75679 ( 1262) metal coordination : bond 0.00633 ( 4) metal coordination : angle 4.44204 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 113 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: c 21 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8550 (ptpt) REVERT: c 45 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6911 (mptt) REVERT: c 55 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: c 192 TYR cc_start: 0.8148 (m-80) cc_final: 0.7806 (m-80) REVERT: c 200 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7710 (m100) REVERT: g 10 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5043 (tpm170) REVERT: g 13 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7672 (tt) REVERT: g 18 TYR cc_start: 0.6976 (m-80) cc_final: 0.6349 (m-80) REVERT: g 79 ARG cc_start: 0.6043 (ptp-170) cc_final: 0.4764 (ptt180) REVERT: i 16 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8887 (t) REVERT: m 61 ASP cc_start: 0.7266 (m-30) cc_final: 0.7054 (m-30) REVERT: m 66 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5638 (tm-30) REVERT: m 68 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: m 74 ASN cc_start: 0.8639 (m-40) cc_final: 0.8038 (m-40) REVERT: m 75 LEU cc_start: 0.8342 (pp) cc_final: 0.8089 (mt) REVERT: m 100 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: m 109 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7580 (tpt-90) outliers start: 63 outliers final: 37 residues processed: 167 average time/residue: 0.1446 time to fit residues: 34.1282 Evaluate side-chains 142 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 10 ARG Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 118 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN c 64 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062943 restraints weight = 50490.858| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.41 r_work: 0.3038 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16313 Z= 0.201 Angle : 0.652 7.669 23969 Z= 0.337 Chirality : 0.041 0.232 3005 Planarity : 0.005 0.072 1570 Dihedral : 22.477 168.947 7272 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 9.91 % Allowed : 21.98 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.28), residues: 819 helix: -0.56 (0.29), residues: 307 sheet: -0.91 (0.41), residues: 145 loop : -2.96 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 20 TYR 0.013 0.002 TYR i 72 PHE 0.014 0.002 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.004 0.001 HIS i 41 Details of bonding type rmsd covalent geometry : bond 0.00407 (16309) covalent geometry : angle 0.64859 (23963) hydrogen bonds : bond 0.06766 ( 569) hydrogen bonds : angle 3.64038 ( 1262) metal coordination : bond 0.00729 ( 4) metal coordination : angle 4.16037 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 96 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7509 (m100) REVERT: g 13 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (tt) REVERT: g 18 TYR cc_start: 0.7103 (m-80) cc_final: 0.6536 (m-80) REVERT: g 79 ARG cc_start: 0.6343 (ptp-170) cc_final: 0.4891 (ptt180) REVERT: i 16 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8956 (t) REVERT: m 56 ILE cc_start: 0.8075 (pt) cc_final: 0.7860 (pt) REVERT: m 66 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6035 (tm-30) REVERT: m 74 ASN cc_start: 0.8761 (m-40) cc_final: 0.8135 (m-40) REVERT: m 75 LEU cc_start: 0.8486 (pp) cc_final: 0.8264 (mt) REVERT: m 100 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: s 27 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.4869 (mptt) outliers start: 69 outliers final: 48 residues processed: 156 average time/residue: 0.1367 time to fit residues: 31.0191 Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3463 r_free = 0.3463 target = 0.075102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063654 restraints weight = 50561.135| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.47 r_work: 0.3046 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16313 Z= 0.206 Angle : 0.659 7.335 23969 Z= 0.340 Chirality : 0.041 0.233 3005 Planarity : 0.005 0.063 1570 Dihedral : 22.407 168.089 7254 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 10.78 % Allowed : 22.13 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.28), residues: 819 helix: -0.29 (0.30), residues: 301 sheet: -0.63 (0.41), residues: 147 loop : -2.91 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 31 TYR 0.013 0.002 TYR i 72 PHE 0.013 0.002 PHE s 74 TRP 0.014 0.002 TRP c 200 HIS 0.007 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00418 (16309) covalent geometry : angle 0.65568 (23963) hydrogen bonds : bond 0.06712 ( 569) hydrogen bonds : angle 3.56425 ( 1262) metal coordination : bond 0.00698 ( 4) metal coordination : angle 4.07318 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 94 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: c 55 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: c 200 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7503 (m100) REVERT: c 205 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: g 13 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7910 (tt) REVERT: g 18 TYR cc_start: 0.7115 (m-80) cc_final: 0.6541 (m-80) REVERT: g 79 ARG cc_start: 0.6474 (ptp-170) cc_final: 0.4974 (ptt180) REVERT: i 16 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8941 (t) REVERT: m 66 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5758 (tm-30) REVERT: m 74 ASN cc_start: 0.8755 (m-40) cc_final: 0.8129 (m-40) REVERT: m 100 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: m 109 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7521 (tpt-90) REVERT: s 6 LYS cc_start: 0.2436 (OUTLIER) cc_final: 0.1963 (pmtt) REVERT: s 7 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.3585 (pttt) REVERT: s 27 LYS cc_start: 0.5707 (OUTLIER) cc_final: 0.4779 (mptt) REVERT: s 37 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7338 (ptp-170) outliers start: 75 outliers final: 49 residues processed: 161 average time/residue: 0.1307 time to fit residues: 30.8814 Evaluate side-chains 154 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 93 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.0270 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3443 r_free = 0.3443 target = 0.074296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061482 restraints weight = 50678.831| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.24 r_work: 0.3042 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16313 Z= 0.245 Angle : 0.708 8.539 23969 Z= 0.364 Chirality : 0.043 0.253 3005 Planarity : 0.006 0.061 1570 Dihedral : 22.445 165.568 7254 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 11.35 % Allowed : 22.99 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.28), residues: 819 helix: -0.24 (0.30), residues: 300 sheet: -0.48 (0.42), residues: 147 loop : -2.81 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG j 31 TYR 0.016 0.002 TYR i 72 PHE 0.015 0.002 PHE s 74 TRP 0.014 0.002 TRP c 200 HIS 0.007 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00500 (16309) covalent geometry : angle 0.70520 (23963) hydrogen bonds : bond 0.07470 ( 569) hydrogen bonds : angle 3.65739 ( 1262) metal coordination : bond 0.00746 ( 4) metal coordination : angle 4.17093 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 92 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7513 (m100) REVERT: c 205 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: g 13 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8001 (tt) REVERT: g 18 TYR cc_start: 0.7149 (m-80) cc_final: 0.6606 (m-80) REVERT: g 79 ARG cc_start: 0.6376 (ptp-170) cc_final: 0.4844 (ptt180) REVERT: i 113 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6889 (ptt90) REVERT: m 66 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: m 74 ASN cc_start: 0.8928 (m-40) cc_final: 0.8205 (m-40) REVERT: m 100 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: m 105 ASN cc_start: 0.6671 (t0) cc_final: 0.6291 (t0) REVERT: m 109 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7651 (tpt-90) REVERT: n 6 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: s 6 LYS cc_start: 0.2484 (OUTLIER) cc_final: 0.2072 (pmtt) REVERT: s 7 LYS cc_start: 0.5244 (OUTLIER) cc_final: 0.3525 (pttt) REVERT: s 27 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5023 (mptt) REVERT: s 37 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7329 (ptp-170) outliers start: 79 outliers final: 59 residues processed: 158 average time/residue: 0.1257 time to fit residues: 29.2409 Evaluate side-chains 161 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 90 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3508 r_free = 0.3508 target = 0.077080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064613 restraints weight = 50613.005| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.33 r_work: 0.3103 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16313 Z= 0.123 Angle : 0.559 7.614 23969 Z= 0.292 Chirality : 0.036 0.189 3005 Planarity : 0.005 0.052 1570 Dihedral : 22.283 171.766 7253 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 9.77 % Allowed : 24.57 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.29), residues: 819 helix: -0.01 (0.30), residues: 316 sheet: -0.07 (0.43), residues: 147 loop : -2.63 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 31 TYR 0.009 0.001 TYR g 154 PHE 0.006 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.006 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00243 (16309) covalent geometry : angle 0.55578 (23963) hydrogen bonds : bond 0.05080 ( 569) hydrogen bonds : angle 3.28899 ( 1262) metal coordination : bond 0.00576 ( 4) metal coordination : angle 3.79013 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 94 time to evaluate : 0.339 Fit side-chains REVERT: c 39 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8277 (mtt90) REVERT: c 199 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (m) REVERT: c 200 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.7637 (m100) REVERT: c 205 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: g 13 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7720 (tt) REVERT: g 18 TYR cc_start: 0.7052 (m-80) cc_final: 0.6593 (m-80) REVERT: g 79 ARG cc_start: 0.6281 (ptp-170) cc_final: 0.4896 (ptt180) REVERT: i 113 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8523 (ttt180) REVERT: j 48 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8753 (tp) REVERT: m 66 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.5814 (tm-30) REVERT: m 74 ASN cc_start: 0.8848 (m-40) cc_final: 0.8203 (m-40) REVERT: m 100 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: m 105 ASN cc_start: 0.6538 (t0) cc_final: 0.6123 (t0) REVERT: m 109 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7542 (tpt-90) REVERT: n 6 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: s 27 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4792 (mptt) REVERT: s 37 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7168 (ptp-170) outliers start: 68 outliers final: 39 residues processed: 155 average time/residue: 0.1263 time to fit residues: 28.5852 Evaluate side-chains 145 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain c residue 40 LYS Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain m residue 89 ILE Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3516 r_free = 0.3516 target = 0.077428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.064736 restraints weight = 50300.525| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.24 r_work: 0.3131 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16313 Z= 0.117 Angle : 0.542 9.502 23969 Z= 0.282 Chirality : 0.035 0.188 3005 Planarity : 0.005 0.068 1570 Dihedral : 22.201 171.568 7236 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 8.33 % Allowed : 25.43 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.30), residues: 819 helix: 0.08 (0.30), residues: 323 sheet: 0.10 (0.43), residues: 147 loop : -2.61 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 31 TYR 0.012 0.001 TYR g 154 PHE 0.007 0.001 PHE s 74 TRP 0.013 0.001 TRP c 200 HIS 0.006 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00233 (16309) covalent geometry : angle 0.53961 (23963) hydrogen bonds : bond 0.04975 ( 569) hydrogen bonds : angle 3.22590 ( 1262) metal coordination : bond 0.00539 ( 4) metal coordination : angle 3.56521 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.318 Fit side-chains REVERT: c 200 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7681 (m100) REVERT: c 205 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6286 (pm20) REVERT: g 13 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7809 (tt) REVERT: g 18 TYR cc_start: 0.7046 (m-80) cc_final: 0.6599 (m-80) REVERT: g 79 ARG cc_start: 0.6138 (ptp-170) cc_final: 0.4687 (ptt180) REVERT: i 113 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.6910 (ptt90) REVERT: j 101 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7773 (tptp) REVERT: m 66 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5471 (tm-30) REVERT: m 74 ASN cc_start: 0.8770 (m-40) cc_final: 0.8093 (m-40) REVERT: m 100 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: m 105 ASN cc_start: 0.6463 (t0) cc_final: 0.6102 (t0) REVERT: m 109 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7466 (tpt-90) REVERT: n 6 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8109 (mmt) REVERT: n 41 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7427 (ttm170) REVERT: s 27 LYS cc_start: 0.5833 (OUTLIER) cc_final: 0.4863 (mptt) REVERT: s 37 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7094 (ptp-170) outliers start: 58 outliers final: 33 residues processed: 143 average time/residue: 0.1190 time to fit residues: 24.9359 Evaluate side-chains 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 99 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3496 r_free = 0.3496 target = 0.076541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064941 restraints weight = 50607.034| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.48 r_work: 0.3085 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16313 Z= 0.148 Angle : 0.576 8.860 23969 Z= 0.298 Chirality : 0.037 0.207 3005 Planarity : 0.005 0.070 1570 Dihedral : 22.167 170.480 7223 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 7.47 % Allowed : 26.44 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.29), residues: 819 helix: 0.09 (0.30), residues: 322 sheet: 0.12 (0.43), residues: 147 loop : -2.58 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 31 TYR 0.011 0.001 TYR i 72 PHE 0.010 0.001 PHE s 74 TRP 0.012 0.001 TRP c 200 HIS 0.006 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00298 (16309) covalent geometry : angle 0.57348 (23963) hydrogen bonds : bond 0.05479 ( 569) hydrogen bonds : angle 3.28010 ( 1262) metal coordination : bond 0.00561 ( 4) metal coordination : angle 3.52456 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.350 Fit side-chains REVERT: c 200 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.7804 (m100) REVERT: c 205 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6364 (pm20) REVERT: g 13 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7881 (tt) REVERT: g 18 TYR cc_start: 0.7052 (m-80) cc_final: 0.6612 (m-80) REVERT: g 70 MET cc_start: 0.7542 (mtp) cc_final: 0.7315 (mtm) REVERT: g 79 ARG cc_start: 0.6214 (ptp-170) cc_final: 0.4704 (ptt180) REVERT: i 113 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.6839 (ptt90) REVERT: j 101 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7759 (tptp) REVERT: m 66 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5623 (tm-30) REVERT: m 74 ASN cc_start: 0.8791 (m-40) cc_final: 0.8102 (m-40) REVERT: m 100 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: m 105 ASN cc_start: 0.6648 (t0) cc_final: 0.6276 (t0) REVERT: m 109 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7459 (tpt-90) REVERT: n 6 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: n 41 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: s 27 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.4973 (mptt) REVERT: s 37 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7236 (ptp-170) outliers start: 52 outliers final: 38 residues processed: 139 average time/residue: 0.1167 time to fit residues: 24.6788 Evaluate side-chains 142 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3509 r_free = 0.3509 target = 0.077079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064368 restraints weight = 50496.150| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.24 r_work: 0.3121 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16313 Z= 0.121 Angle : 0.554 8.589 23969 Z= 0.288 Chirality : 0.036 0.195 3005 Planarity : 0.005 0.068 1570 Dihedral : 22.165 171.181 7223 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 7.33 % Allowed : 26.72 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.30), residues: 819 helix: 0.16 (0.30), residues: 323 sheet: 0.20 (0.43), residues: 147 loop : -2.52 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 31 TYR 0.014 0.001 TYR g 154 PHE 0.010 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.006 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00243 (16309) covalent geometry : angle 0.55094 (23963) hydrogen bonds : bond 0.05096 ( 569) hydrogen bonds : angle 3.24081 ( 1262) metal coordination : bond 0.00515 ( 4) metal coordination : angle 3.43805 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 0.366 Fit side-chains REVERT: c 200 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.7668 (m100) REVERT: c 205 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6311 (pm20) REVERT: g 13 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (tt) REVERT: g 18 TYR cc_start: 0.7071 (m-80) cc_final: 0.6645 (m-80) REVERT: g 70 MET cc_start: 0.7474 (mtp) cc_final: 0.7271 (mtm) REVERT: g 79 ARG cc_start: 0.6169 (ptp-170) cc_final: 0.4699 (ptt180) REVERT: i 113 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.6903 (ptt90) REVERT: j 48 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8710 (tp) REVERT: j 101 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7781 (tptp) REVERT: m 66 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5560 (tm-30) REVERT: m 74 ASN cc_start: 0.8759 (m-40) cc_final: 0.8069 (m-40) REVERT: m 100 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: m 105 ASN cc_start: 0.6518 (t0) cc_final: 0.6126 (t0) REVERT: m 109 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7435 (tpt-90) REVERT: n 6 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7853 (mmt) REVERT: n 41 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7538 (ttm170) REVERT: s 27 LYS cc_start: 0.5758 (OUTLIER) cc_final: 0.4891 (mptt) REVERT: s 37 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7191 (ptp-170) outliers start: 51 outliers final: 38 residues processed: 138 average time/residue: 0.1206 time to fit residues: 25.0703 Evaluate side-chains 143 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3450 r_free = 0.3450 target = 0.074636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061809 restraints weight = 50878.261| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.24 r_work: 0.3051 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16313 Z= 0.242 Angle : 0.693 9.562 23969 Z= 0.355 Chirality : 0.043 0.253 3005 Planarity : 0.005 0.069 1570 Dihedral : 22.250 166.141 7223 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 7.76 % Allowed : 26.72 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.29), residues: 819 helix: -0.01 (0.30), residues: 316 sheet: 0.01 (0.43), residues: 147 loop : -2.73 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 62 TYR 0.017 0.002 TYR i 72 PHE 0.016 0.002 PHE s 74 TRP 0.014 0.002 TRP c 200 HIS 0.008 0.002 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00496 (16309) covalent geometry : angle 0.69059 (23963) hydrogen bonds : bond 0.07289 ( 569) hydrogen bonds : angle 3.48729 ( 1262) metal coordination : bond 0.00642 ( 4) metal coordination : angle 3.88889 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 93 time to evaluate : 0.371 Fit side-chains REVERT: c 200 TRP cc_start: 0.8360 (OUTLIER) cc_final: 0.7613 (m100) REVERT: c 205 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: g 13 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8031 (tt) REVERT: g 18 TYR cc_start: 0.7164 (m-80) cc_final: 0.6681 (m-80) REVERT: g 79 ARG cc_start: 0.6205 (ptp-170) cc_final: 0.4690 (ptt180) REVERT: i 16 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8944 (t) REVERT: i 113 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.6886 (ptt90) REVERT: m 66 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5760 (tm-30) REVERT: m 74 ASN cc_start: 0.8825 (m-40) cc_final: 0.8136 (m-40) REVERT: m 100 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: m 109 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7608 (tpt-90) REVERT: n 6 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: s 6 LYS cc_start: 0.2429 (OUTLIER) cc_final: 0.2039 (pmtt) REVERT: s 27 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4936 (mptt) REVERT: s 37 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7330 (ptp-170) outliers start: 54 outliers final: 40 residues processed: 140 average time/residue: 0.1144 time to fit residues: 24.6061 Evaluate side-chains 145 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 113 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 100 GLN Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 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 = 0.3465 r_free = 0.3465 target = 0.075201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062397 restraints weight = 50051.426| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.23 r_work: 0.3069 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16313 Z= 0.194 Angle : 0.640 9.172 23969 Z= 0.330 Chirality : 0.040 0.233 3005 Planarity : 0.005 0.071 1570 Dihedral : 22.214 167.625 7223 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 7.90 % Allowed : 26.58 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.29), residues: 819 helix: -0.02 (0.30), residues: 318 sheet: 0.04 (0.43), residues: 147 loop : -2.69 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 31 TYR 0.013 0.002 TYR i 72 PHE 0.013 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.008 0.001 HIS g 153 Details of bonding type rmsd covalent geometry : bond 0.00396 (16309) covalent geometry : angle 0.63709 (23963) hydrogen bonds : bond 0.06432 ( 569) hydrogen bonds : angle 3.41603 ( 1262) metal coordination : bond 0.00617 ( 4) metal coordination : angle 3.93547 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3619.68 seconds wall clock time: 62 minutes 44.12 seconds (3764.12 seconds total)