Starting phenix.real_space_refine on Sat Sep 12 10:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wua_21908/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_2026/6wua_21908.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wua_21908/09_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.78, per 1000 atoms: 0.18 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: 0.99 Conformation dependent library (CDL) restraints added in 438.7 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: 2.06 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: 3.17 Time building geometry restraints manager: 1.45 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=" O3' G a1237 " pdb=" P C a1238 " ideal model delta sigma weight residual 1.607 1.588 0.019 1.20e-02 6.94e+03 2.57e+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=" O5' G a1237 " pdb=" C5' G a1237 " ideal model delta sigma weight residual 1.427 1.401 0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 16304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21746 1.70 - 3.39: 1659 3.39 - 5.09: 489 5.09 - 6.79: 57 6.79 - 8.48: 12 Bond angle restraints: 23963 Sorted by residual: angle pdb=" C3' U a1226 " pdb=" O3' U a1226 " pdb=" P U a1227 " ideal model delta sigma weight residual 119.70 124.97 -5.27 1.20e+00 6.94e-01 1.93e+01 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 a1198 " pdb=" O3' U a1198 " pdb=" P G a1199 " ideal model delta sigma weight residual 119.70 123.89 -4.19 1.20e+00 6.94e-01 1.22e+01 ... (remaining 23958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.51: 7772 28.51 - 57.03: 959 57.03 - 85.54: 254 85.54 - 114.06: 4 114.06 - 142.57: 1 Dihedral angle restraints: 8990 sinusoidal: 6599 harmonic: 2391 Sorted by residual: dihedral pdb=" C4' U a 976 " pdb=" C3' U a 976 " pdb=" C2' U a 976 " pdb=" C1' U a 976 " ideal model delta sinusoidal sigma weight residual 36.35 -39.93 76.27 1 3.10e+00 1.04e-01 7.62e+02 dihedral pdb=" C4' G a1069 " pdb=" C3' G a1069 " pdb=" C2' G a1069 " pdb=" C1' G a1069 " ideal model delta sinusoidal sigma weight residual 36.34 -39.73 76.07 1 3.10e+00 1.04e-01 7.59e+02 dihedral pdb=" C4' U a1317 " pdb=" C3' U a1317 " pdb=" C2' U a1317 " pdb=" C1' U a1317 " ideal model delta sinusoidal sigma weight residual 36.35 -39.57 75.92 1 3.10e+00 1.04e-01 7.56e+02 ... (remaining 8987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2163 0.075 - 0.150: 290 0.150 - 0.225: 304 0.225 - 0.300: 229 0.300 - 0.375: 19 Chirality restraints: 3005 Sorted by residual: chirality pdb=" C2' G a1371 " pdb=" C3' G a1371 " pdb=" O2' G a1371 " pdb=" C1' G a1371 " both_signs ideal model delta sigma weight residual False -2.79 -2.41 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" P C a1042 " pdb=" OP1 C a1042 " pdb=" OP2 C a1042 " pdb=" O5' C a1042 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' G a1362 " pdb=" C4' G a1362 " pdb=" O3' G a1362 " pdb=" C2' G a1362 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.73e+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: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.790 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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= 0.340 Angle : 1.097 18.892 23969 Z= 0.468 Chirality : 0.109 0.375 3005 Planarity : 0.006 0.070 1570 Dihedral : 21.708 142.573 7452 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/Z covalent geometry : bond 0.00703 / 0.34 (16309) covalent geometry : angle 1.08678 / 0.47 (23963) hydrogen bonds : bond 0.16246 / 8.42 ( 569) hydrogen bonds : angle 5.93509 / 2.42 ( 1262) metal coordination : bond 0.07231 / 3.62 ( 4) metal coordination : angle 9.60364 / 3.20 ( 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 : 0.268 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: 0.1448 time to fit residues: 46.8924 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 : 0.322 ------------------------------------------------------------------------------- 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: 2.9990 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: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3576 r_free = 0.3576 target = 0.080067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067963 restraints weight = 50471.231| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.47 r_work: 0.3170 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16313 Z= 0.187 Angle : 1.324 17.995 23969 Z= 0.525 Chirality : 0.116 1.062 3005 Planarity : 0.005 0.057 1570 Dihedral : 18.550 172.125 5910 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 9.48 % Allowed : 20.83 % Favored : 69.68 % 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: -2.95 (0.27), residues: 819 helix: -1.03 (0.28), residues: 308 sheet: -1.27 (0.40), residues: 147 loop : -3.11 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 31 TYR 0.011 0.001 TYR s 52 PHE 0.008 0.001 PHE s 74 TRP 0.015 0.001 TRP c 200 HIS 0.002 0.001 HIS c 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (16309) covalent geometry : angle 1.32265 / 0.53 (23963) hydrogen bonds : bond 0.06989 / 3.52 ( 569) hydrogen bonds : angle 3.85657 / 1.56 ( 1262) metal coordination : bond 0.00595 / 0.30 ( 4) metal coordination : angle 4.51371 / 1.50 ( 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 180 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 114 time to evaluate : 0.316 Fit side-chains REVERT: c 39 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (ttm170) REVERT: c 55 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: c 61 ASN cc_start: 0.7840 (t0) cc_final: 0.7632 (t0) REVERT: c 192 TYR cc_start: 0.8236 (m-80) cc_final: 0.7905 (m-80) REVERT: c 200 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7742 (m100) REVERT: g 10 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.5214 (tpm170) REVERT: g 13 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7683 (tt) REVERT: g 18 TYR cc_start: 0.7034 (m-80) cc_final: 0.6452 (m-80) REVERT: g 79 ARG cc_start: 0.6009 (ptp-170) cc_final: 0.4763 (ptt180) REVERT: g 125 MET cc_start: 0.8596 (mtm) cc_final: 0.8391 (mtt) REVERT: i 16 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8925 (t) REVERT: i 88 LEU cc_start: 0.8684 (tt) cc_final: 0.8481 (tp) REVERT: m 14 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.5784 (mtm-85) REVERT: m 61 ASP cc_start: 0.7275 (m-30) cc_final: 0.7006 (m-30) REVERT: m 66 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5560 (tm-30) REVERT: m 68 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: m 74 ASN cc_start: 0.8664 (m-40) cc_final: 0.8107 (m-40) REVERT: m 75 LEU cc_start: 0.8393 (pp) cc_final: 0.8079 (mt) REVERT: m 100 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: m 109 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7628 (tpt-90) REVERT: s 27 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5498 (mptt) outliers start: 66 outliers final: 41 residues processed: 171 average time/residue: 0.1337 time to fit residues: 32.7454 Evaluate side-chains 149 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 56 ASN 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 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 41 GLU 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 overall best weight: 1.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 86 GLN m 105 ASN ** 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 = 0.3596 r_free = 0.3596 target = 0.081127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070086 restraints weight = 50824.092| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.42 r_work: 0.3211 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16313 Z= 0.162 Angle : 1.090 12.293 23969 Z= 0.437 Chirality : 0.093 0.932 3005 Planarity : 0.005 0.065 1570 Dihedral : 18.438 174.717 5863 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 8.76 % Allowed : 22.99 % Favored : 68.25 % 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: -2.29 (0.28), residues: 819 helix: -0.35 (0.30), residues: 312 sheet: -0.76 (0.41), residues: 145 loop : -2.96 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 10 TYR 0.008 0.001 TYR i 72 PHE 0.009 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.003 0.001 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (16309) covalent geometry : angle 1.08794 / 0.44 (23963) hydrogen bonds : bond 0.06660 / 3.36 ( 569) hydrogen bonds : angle 3.45483 / 1.41 ( 1262) metal coordination : bond 0.00630 / 0.31 ( 4) metal coordination : angle 3.92931 / 1.31 ( 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 164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 103 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: c 55 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: c 200 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7760 (m100) REVERT: g 13 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7773 (tt) REVERT: g 18 TYR cc_start: 0.7004 (m-80) cc_final: 0.6474 (m-80) REVERT: g 79 ARG cc_start: 0.6137 (ptp-170) cc_final: 0.4730 (ptt180) REVERT: i 9 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8492 (p) REVERT: j 91 ASP cc_start: 0.6090 (p0) cc_final: 0.5792 (p0) REVERT: m 56 ILE cc_start: 0.7959 (pt) cc_final: 0.7724 (pt) REVERT: m 74 ASN cc_start: 0.8771 (m-40) cc_final: 0.8185 (m-40) REVERT: m 100 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: m 105 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6230 (t0) REVERT: m 109 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7566 (tpt-90) REVERT: s 7 LYS cc_start: 0.5330 (OUTLIER) cc_final: 0.3659 (pttt) REVERT: s 22 GLN cc_start: 0.7438 (mt0) cc_final: 0.7195 (tt0) REVERT: s 27 LYS cc_start: 0.5708 (OUTLIER) cc_final: 0.5069 (mptt) REVERT: s 36 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7025 (ptm160) outliers start: 61 outliers final: 36 residues processed: 156 average time/residue: 0.1228 time to fit residues: 27.9452 Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 9 THR 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 15 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 105 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 0.0000 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 61 ASN c 64 ASN m 105 ASN ** 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 = 0.3506 r_free = 0.3506 target = 0.077141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065747 restraints weight = 50807.290| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.52 r_work: 0.3095 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16313 Z= 0.273 Angle : 1.262 14.576 23969 Z= 0.512 Chirality : 0.110 1.264 3005 Planarity : 0.006 0.066 1570 Dihedral : 18.600 171.762 5831 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 10.92 % Allowed : 22.41 % Favored : 66.67 % 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: -2.21 (0.28), residues: 819 helix: -0.30 (0.30), residues: 302 sheet: -0.59 (0.42), residues: 145 loop : -2.89 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 31 TYR 0.016 0.002 TYR i 72 PHE 0.015 0.002 PHE s 74 TRP 0.015 0.002 TRP c 200 HIS 0.005 0.001 HIS g 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.27 (16309) covalent geometry : angle 1.26000 / 0.51 (23963) hydrogen bonds : bond 0.08002 / 4.08 ( 569) hydrogen bonds : angle 3.66206 / 1.50 ( 1262) metal coordination : bond 0.00747 / 0.37 ( 4) metal coordination : angle 4.20363 / 1.40 ( 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 168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 92 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8371 (OUTLIER) cc_final: 0.7631 (m100) REVERT: c 205 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: g 13 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7976 (tt) REVERT: g 18 TYR cc_start: 0.7124 (m-80) cc_final: 0.6593 (m-80) REVERT: g 79 ARG cc_start: 0.6419 (ptp-170) cc_final: 0.4866 (ptt180) REVERT: i 16 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8972 (t) REVERT: m 66 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5855 (tm-30) REVERT: m 74 ASN cc_start: 0.8935 (m-40) cc_final: 0.8241 (m-40) REVERT: m 100 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: m 105 ASN cc_start: 0.6593 (t0) cc_final: 0.6372 (t0) REVERT: s 6 LYS cc_start: 0.2462 (OUTLIER) cc_final: 0.2024 (pmtt) REVERT: s 7 LYS cc_start: 0.5422 (OUTLIER) cc_final: 0.3660 (pttt) REVERT: s 17 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8281 (mtpm) REVERT: s 27 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5221 (mptt) REVERT: s 37 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7445 (ptp-170) outliers start: 76 outliers final: 48 residues processed: 157 average time/residue: 0.1200 time to fit residues: 28.0820 Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 91 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 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 65 VAL Chi-restraints excluded: chain i residue 83 ILE 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 76 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU 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 7 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 17 LYS Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG 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: 7.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 86 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067257 restraints weight = 50752.772| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.50 r_work: 0.3136 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16313 Z= 0.208 Angle : 1.139 12.447 23969 Z= 0.462 Chirality : 0.098 0.998 3005 Planarity : 0.005 0.059 1570 Dihedral : 18.548 173.596 5827 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 10.63 % Allowed : 22.41 % Favored : 66.95 % 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: -1.94 (0.29), residues: 819 helix: -0.20 (0.30), residues: 317 sheet: -0.25 (0.42), residues: 147 loop : -2.82 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 31 TYR 0.012 0.001 TYR i 72 PHE 0.011 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.005 0.001 HIS g 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (16309) covalent geometry : angle 1.13755 / 0.46 (23963) hydrogen bonds : bond 0.07224 / 3.66 ( 569) hydrogen bonds : angle 3.49400 / 1.43 ( 1262) metal coordination : bond 0.00649 / 0.32 ( 4) metal coordination : angle 3.93148 / 1.31 ( 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 165 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 91 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7605 (m100) REVERT: c 205 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: g 13 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7835 (tt) REVERT: g 18 TYR cc_start: 0.7107 (m-80) cc_final: 0.6590 (m-80) REVERT: g 79 ARG cc_start: 0.6437 (ptp-170) cc_final: 0.4903 (ptt180) REVERT: i 16 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8964 (t) REVERT: i 113 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8536 (ttt180) REVERT: m 66 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5815 (tm-30) REVERT: m 74 ASN cc_start: 0.8967 (m-40) cc_final: 0.8316 (m-40) REVERT: m 100 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: m 109 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7617 (tpt-90) REVERT: n 6 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: s 7 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.3626 (pttt) REVERT: s 17 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8375 (mtpm) REVERT: s 27 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.4898 (mptt) REVERT: s 37 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7340 (ptp-170) outliers start: 74 outliers final: 50 residues processed: 156 average time/residue: 0.1148 time to fit residues: 26.7248 Evaluate side-chains 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 88 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 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 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 75 VAL 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 i residue 16 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 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 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 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 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 36 ARG 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: 1.9990 chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3568 r_free = 0.3568 target = 0.079795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.068651 restraints weight = 50817.143| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.48 r_work: 0.3171 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16313 Z= 0.153 Angle : 1.082 11.691 23969 Z= 0.438 Chirality : 0.093 0.867 3005 Planarity : 0.005 0.068 1570 Dihedral : 18.535 177.135 5821 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 8.76 % Allowed : 24.71 % Favored : 66.52 % 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: -1.65 (0.29), residues: 819 helix: 0.10 (0.31), residues: 310 sheet: -0.01 (0.43), residues: 147 loop : -2.73 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 31 TYR 0.019 0.001 TYR g 154 PHE 0.008 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.011 0.001 HIS g 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (16309) covalent geometry : angle 1.08064 / 0.44 (23963) hydrogen bonds : bond 0.06732 / 3.40 ( 569) hydrogen bonds : angle 3.45109 / 1.41 ( 1262) metal coordination : bond 0.00417 / 0.21 ( 4) metal coordination : angle 3.48253 / 1.16 ( 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 151 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 90 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7578 (m100) REVERT: c 205 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: g 13 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7813 (tt) REVERT: g 18 TYR cc_start: 0.7053 (m-80) cc_final: 0.6554 (m-80) REVERT: g 79 ARG cc_start: 0.6495 (ptp-170) cc_final: 0.4961 (ptt180) REVERT: i 16 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8951 (t) REVERT: j 48 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8799 (tp) REVERT: m 66 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5676 (tm-30) REVERT: m 74 ASN cc_start: 0.8959 (m-40) cc_final: 0.8361 (m-40) REVERT: m 100 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: m 105 ASN cc_start: 0.6452 (t0) cc_final: 0.6119 (t0) REVERT: m 109 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7600 (tpt-90) REVERT: n 6 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7590 (mmp) REVERT: s 7 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.3665 (pttt) REVERT: s 17 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8360 (mtpm) REVERT: s 27 LYS cc_start: 0.5698 (OUTLIER) cc_final: 0.4762 (mptt) outliers start: 61 outliers final: 46 residues processed: 144 average time/residue: 0.1120 time to fit residues: 24.4841 Evaluate side-chains 146 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 88 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 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 16 VAL Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 65 VAL 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 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 61 ASN g 86 GLN ** m 105 ASN ** 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 = 0.3551 r_free = 0.3551 target = 0.079093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067912 restraints weight = 50671.892| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.46 r_work: 0.3152 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16313 Z= 0.188 Angle : 1.100 12.746 23969 Z= 0.446 Chirality : 0.094 0.926 3005 Planarity : 0.005 0.071 1570 Dihedral : 18.481 179.118 5821 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 10.06 % Allowed : 23.56 % Favored : 66.38 % 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: -1.61 (0.29), residues: 819 helix: 0.06 (0.30), residues: 318 sheet: 0.05 (0.43), residues: 147 loop : -2.69 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 31 TYR 0.013 0.001 TYR g 154 PHE 0.011 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.005 0.001 HIS g 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (16309) covalent geometry : angle 1.09900 / 0.45 (23963) hydrogen bonds : bond 0.06981 / 3.53 ( 569) hydrogen bonds : angle 3.39997 / 1.40 ( 1262) metal coordination : bond 0.00570 / 0.29 ( 4) metal coordination : angle 3.70689 / 1.24 ( 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 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 92 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7637 (m100) REVERT: c 205 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: g 13 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7857 (tt) REVERT: g 18 TYR cc_start: 0.7084 (m-80) cc_final: 0.6592 (m-80) REVERT: g 79 ARG cc_start: 0.6403 (ptp-170) cc_final: 0.4862 (ptt180) REVERT: i 16 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8960 (t) REVERT: i 113 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.6967 (ptt90) REVERT: m 66 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: m 74 ASN cc_start: 0.8934 (m-40) cc_final: 0.8304 (m-40) REVERT: m 100 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: n 6 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7948 (mmt) REVERT: s 6 LYS cc_start: 0.2571 (OUTLIER) cc_final: 0.2123 (pmtt) REVERT: s 7 LYS cc_start: 0.5342 (OUTLIER) cc_final: 0.3578 (pttt) REVERT: s 27 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.4852 (mptt) REVERT: s 37 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7327 (ptp-170) outliers start: 70 outliers final: 51 residues processed: 152 average time/residue: 0.1086 time to fit residues: 25.0410 Evaluate side-chains 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 92 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 164 SER 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 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 16 VAL Chi-restraints excluded: chain i residue 29 THR 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 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 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 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 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 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 36 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3512 r_free = 0.3512 target = 0.077439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066197 restraints weight = 51289.186| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.51 r_work: 0.3104 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16313 Z= 0.248 Angle : 1.199 14.572 23969 Z= 0.487 Chirality : 0.103 1.039 3005 Planarity : 0.006 0.072 1570 Dihedral : 18.583 177.638 5817 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 10.34 % Allowed : 23.99 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.81 (0.29), residues: 819 helix: -0.06 (0.30), residues: 313 sheet: -0.02 (0.43), residues: 147 loop : -2.84 (0.29), residues: 359 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 0.014 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/Z covalent geometry : bond 0.00519 / 0.25 (16309) covalent geometry : angle 1.19758 / 0.49 (23963) hydrogen bonds : bond 0.07727 / 3.93 ( 569) hydrogen bonds : angle 3.53368 / 1.45 ( 1262) metal coordination : bond 0.00636 / 0.32 ( 4) metal coordination : angle 3.99791 / 1.33 ( 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 166 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 94 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7625 (m100) REVERT: c 205 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: g 13 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7964 (tt) REVERT: g 18 TYR cc_start: 0.7145 (m-80) cc_final: 0.6628 (m-80) REVERT: g 79 ARG cc_start: 0.6237 (ptp-170) cc_final: 0.4845 (ptt180) REVERT: i 16 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8976 (t) REVERT: i 113 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.6968 (ptt90) REVERT: m 66 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: m 74 ASN cc_start: 0.8975 (m-40) cc_final: 0.8289 (m-40) REVERT: m 100 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: m 105 ASN cc_start: 0.6716 (t0) cc_final: 0.6339 (t0) REVERT: m 109 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7669 (tpt-90) REVERT: n 6 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8288 (mtp) REVERT: n 41 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: s 6 LYS cc_start: 0.2375 (OUTLIER) cc_final: 0.1981 (pmtt) REVERT: s 7 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.3637 (pttt) REVERT: s 27 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.4948 (mptt) REVERT: s 37 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7385 (ptp-170) outliers start: 72 outliers final: 53 residues processed: 155 average time/residue: 0.1193 time to fit residues: 27.2702 Evaluate side-chains 160 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 93 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 103 VAL Chi-restraints excluded: chain c residue 110 LEU 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 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 131 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 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 48 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 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 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 41 ARG 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 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3575 r_free = 0.3575 target = 0.080185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069133 restraints weight = 51077.819| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.47 r_work: 0.3184 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16313 Z= 0.161 Angle : 1.054 11.743 23969 Z= 0.426 Chirality : 0.089 0.740 3005 Planarity : 0.005 0.066 1570 Dihedral : 18.465 178.546 5817 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 8.91 % Allowed : 25.29 % Favored : 65.80 % 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: -1.49 (0.29), residues: 819 helix: 0.06 (0.30), residues: 323 sheet: 0.17 (0.43), residues: 147 loop : -2.58 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 31 TYR 0.013 0.001 TYR g 154 PHE 0.007 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/Z covalent geometry : bond 0.00332 / 0.16 (16309) covalent geometry : angle 1.05203 / 0.43 (23963) hydrogen bonds : bond 0.06710 / 3.39 ( 569) hydrogen bonds : angle 3.33382 / 1.37 ( 1262) metal coordination : bond 0.00555 / 0.28 ( 4) metal coordination : angle 3.69004 / 1.23 ( 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 156 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 94 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7668 (m100) REVERT: c 205 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: g 13 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7786 (tt) REVERT: g 18 TYR cc_start: 0.7057 (m-80) cc_final: 0.6603 (m-80) REVERT: g 70 MET cc_start: 0.7494 (mtp) cc_final: 0.7211 (mtm) REVERT: g 79 ARG cc_start: 0.6223 (ptp-170) cc_final: 0.4842 (ptt180) REVERT: i 16 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8970 (t) REVERT: j 48 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8788 (tp) REVERT: m 66 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5690 (tm-30) REVERT: m 74 ASN cc_start: 0.8838 (m-40) cc_final: 0.8232 (m-40) REVERT: m 100 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: m 105 ASN cc_start: 0.6592 (t0) cc_final: 0.6198 (t0) REVERT: m 109 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7518 (tpt-90) REVERT: n 6 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7887 (mmt) REVERT: n 41 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7431 (ttm170) REVERT: s 7 LYS cc_start: 0.5298 (OUTLIER) cc_final: 0.3573 (pttt) REVERT: s 27 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.4820 (mptt) REVERT: s 37 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7259 (ptp-170) outliers start: 62 outliers final: 45 residues processed: 146 average time/residue: 0.1130 time to fit residues: 24.9155 Evaluate side-chains 150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 164 SER 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 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 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 26 VAL 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 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 VAL 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 41 ARG 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 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3553 r_free = 0.3553 target = 0.079196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068002 restraints weight = 51379.857| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.50 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16313 Z= 0.188 Angle : 1.089 12.465 23969 Z= 0.442 Chirality : 0.092 0.806 3005 Planarity : 0.005 0.073 1570 Dihedral : 18.436 178.111 5816 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 8.91 % Allowed : 25.43 % Favored : 65.66 % 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: -1.48 (0.29), residues: 819 helix: 0.10 (0.30), residues: 321 sheet: 0.16 (0.43), residues: 147 loop : -2.58 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 31 TYR 0.013 0.001 TYR c 192 PHE 0.010 0.001 PHE s 74 TRP 0.014 0.001 TRP c 200 HIS 0.007 0.001 HIS g 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (16309) covalent geometry : angle 1.08718 / 0.44 (23963) hydrogen bonds : bond 0.06929 / 3.51 ( 569) hydrogen bonds : angle 3.39644 / 1.40 ( 1262) metal coordination : bond 0.00582 / 0.29 ( 4) metal coordination : angle 3.66846 / 1.22 ( 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 155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 93 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: c 200 TRP cc_start: 0.8342 (OUTLIER) cc_final: 0.7630 (m100) REVERT: c 205 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: g 13 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (tt) REVERT: g 18 TYR cc_start: 0.7097 (m-80) cc_final: 0.6619 (m-80) REVERT: g 70 MET cc_start: 0.7575 (mtp) cc_final: 0.7315 (mtm) REVERT: g 79 ARG cc_start: 0.6238 (ptp-170) cc_final: 0.4812 (ptt180) REVERT: i 16 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.8980 (t) REVERT: j 101 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7958 (tptp) REVERT: m 66 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6139 (tt0) REVERT: m 74 ASN cc_start: 0.8847 (m-40) cc_final: 0.8179 (m-40) REVERT: m 100 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: m 105 ASN cc_start: 0.6666 (t0) cc_final: 0.6286 (t0) REVERT: m 109 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7555 (tpt-90) REVERT: n 6 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7962 (mmt) REVERT: n 41 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: s 7 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.3481 (pttt) REVERT: s 27 LYS cc_start: 0.5728 (OUTLIER) cc_final: 0.4777 (mptt) REVERT: s 37 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7301 (ptp-170) outliers start: 62 outliers final: 48 residues processed: 146 average time/residue: 0.1086 time to fit residues: 23.8329 Evaluate side-chains 153 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 93 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 84 GLU Chi-restraints excluded: chain c residue 103 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 164 SER 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 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 105 THR Chi-restraints excluded: chain i residue 130 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 26 VAL 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 73 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 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 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 41 ARG 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 26 GLU Chi-restraints excluded: chain s residue 27 LYS Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 36 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3485 r_free = 0.3485 target = 0.076238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065065 restraints weight = 50790.347| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.53 r_work: 0.3073 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16313 Z= 0.306 Angle : 1.293 16.413 23969 Z= 0.526 Chirality : 0.110 1.050 3005 Planarity : 0.006 0.075 1570 Dihedral : 18.649 179.915 5816 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 9.77 % Allowed : 25.00 % Favored : 65.23 % 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: -1.79 (0.29), residues: 819 helix: -0.10 (0.30), residues: 312 sheet: -0.13 (0.43), residues: 149 loop : -2.71 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG j 31 TYR 0.021 0.002 TYR c 192 PHE 0.018 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/Z covalent geometry : bond 0.00644 / 0.31 (16309) covalent geometry : angle 1.29191 / 0.53 (23963) hydrogen bonds : bond 0.08482 / 4.34 ( 569) hydrogen bonds : angle 3.65583 / 1.50 ( 1262) metal coordination : bond 0.00676 / 0.34 ( 4) metal coordination : angle 4.14364 / 1.38 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.66 seconds wall clock time: 62 minutes 47.08 seconds (3767.08 seconds total)