Starting phenix.real_space_refine on Sat Oct 31 14:05:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pna_71748/10_2026/9pna_71748.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 13608 2.51 5 N 3780 2.21 5 O 4131 1.98 5 H 21501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43092 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 843 Classifications: {'peptide': 57} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Restraints were copied for chains: B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R Time building chain proxies: 5.32, per 1000 atoms: 0.12 Number of scatterers: 43092 At special positions: 0 Unit cell: (133.44, 133.44, 124.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 4131 8.00 N 3780 7.00 C 13608 6.00 H 21501 1.00 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: 3.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 1 sheets defined 41.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 41 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 41 Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 18 through 41 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 18 through 41 Processing helix chain 'D' and resid 43 through 57 Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 18 through 41 Processing helix chain 'E' and resid 43 through 57 Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 41 Processing helix chain 'F' and resid 43 through 57 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 18 through 41 Processing helix chain 'G' and resid 43 through 57 Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 18 through 41 Processing helix chain 'H' and resid 43 through 57 Processing helix chain 'I' and resid 9 through 13 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 18 through 41 Processing helix chain 'I' and resid 43 through 57 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 63 through 75 Processing helix chain 'J' and resid 85 through 103 Processing helix chain 'J' and resid 211 through 234 Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG J 245 " --> pdb=" O LYS J 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN J 246 " --> pdb=" O ALA J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 Processing helix chain 'K' and resid 18 through 26 Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 85 through 103 Processing helix chain 'K' and resid 211 through 234 Processing helix chain 'K' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG K 245 " --> pdb=" O LYS K 242 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN K 246 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 256 Processing helix chain 'L' and resid 18 through 26 Processing helix chain 'L' and resid 63 through 75 Processing helix chain 'L' and resid 85 through 103 Processing helix chain 'L' and resid 211 through 234 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.577A pdb=" N ARG L 245 " --> pdb=" O LYS L 242 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 85 through 103 Processing helix chain 'M' and resid 211 through 234 Processing helix chain 'M' and resid 241 through 246 removed outlier: 3.577A pdb=" N ARG M 245 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN M 246 " --> pdb=" O ALA M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 256 Processing helix chain 'N' and resid 18 through 26 Processing helix chain 'N' and resid 63 through 75 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 211 through 234 Processing helix chain 'N' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG N 245 " --> pdb=" O LYS N 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN N 246 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 256 Processing helix chain 'O' and resid 18 through 26 Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 103 Processing helix chain 'O' and resid 211 through 234 Processing helix chain 'O' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG O 245 " --> pdb=" O LYS O 242 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN O 246 " --> pdb=" O ALA O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 256 Processing helix chain 'P' and resid 18 through 26 Processing helix chain 'P' and resid 63 through 75 Processing helix chain 'P' and resid 85 through 103 Processing helix chain 'P' and resid 211 through 234 Processing helix chain 'P' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG P 245 " --> pdb=" O LYS P 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN P 246 " --> pdb=" O ALA P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 256 Processing helix chain 'Q' and resid 18 through 26 Processing helix chain 'Q' and resid 63 through 75 Processing helix chain 'Q' and resid 85 through 103 Processing helix chain 'Q' and resid 211 through 234 Processing helix chain 'Q' and resid 241 through 246 removed outlier: 3.577A pdb=" N ARG Q 245 " --> pdb=" O LYS Q 242 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN Q 246 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 256 Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 63 through 75 Processing helix chain 'R' and resid 85 through 103 Processing helix chain 'R' and resid 211 through 234 Processing helix chain 'R' and resid 241 through 246 removed outlier: 3.576A pdb=" N ARG R 245 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN R 246 " --> pdb=" O ALA R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 14 current: chain 'J' and resid 146 through 165 removed outlier: 3.708A pdb=" N SER J 173 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN J 165 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE J 171 " --> pdb=" O ASN J 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 198 through 209 current: chain 'K' and resid 146 through 165 removed outlier: 3.707A pdb=" N SER K 173 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN K 165 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE K 171 " --> pdb=" O ASN K 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 198 through 209 current: chain 'L' and resid 146 through 165 removed outlier: 3.708A pdb=" N SER L 173 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN L 165 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE L 171 " --> pdb=" O ASN L 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 198 through 209 current: chain 'M' and resid 146 through 165 removed outlier: 3.708A pdb=" N SER M 173 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN M 165 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE M 171 " --> pdb=" O ASN M 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 198 through 209 current: chain 'N' and resid 146 through 165 removed outlier: 3.707A pdb=" N SER N 173 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN N 165 " --> pdb=" O ILE N 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE N 171 " --> pdb=" O ASN N 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 198 through 209 current: chain 'O' and resid 146 through 165 removed outlier: 3.707A pdb=" N SER O 173 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN O 165 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE O 171 " --> pdb=" O ASN O 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 198 through 209 current: chain 'P' and resid 146 through 165 removed outlier: 3.707A pdb=" N SER P 173 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN P 165 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE P 171 " --> pdb=" O ASN P 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 198 through 209 current: chain 'Q' and resid 146 through 165 removed outlier: 3.708A pdb=" N SER Q 173 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN Q 165 " --> pdb=" O ILE Q 171 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE Q 171 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 198 through 209 current: chain 'R' and resid 146 through 165 removed outlier: 3.707A pdb=" N SER R 173 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN R 165 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE R 171 " --> pdb=" O ASN R 165 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.99 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21492 1.03 - 1.23: 22 1.23 - 1.42: 9158 1.42 - 1.62: 12672 1.62 - 1.81: 135 Bond restraints: 43479 Sorted by residual: bond pdb=" N ALA M 10 " pdb=" CA ALA M 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N ALA K 10 " pdb=" CA ALA K 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ALA P 10 " pdb=" CA ALA P 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ALA L 10 " pdb=" CA ALA L 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ALA O 10 " pdb=" CA ALA O 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 43474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 74814 1.19 - 2.38: 3320 2.38 - 3.57: 256 3.57 - 4.76: 27 4.76 - 5.95: 9 Bond angle restraints: 78426 Sorted by residual: angle pdb=" CA ASP E 45 " pdb=" CB ASP E 45 " pdb=" HB3 ASP E 45 " ideal model delta sigma weight residual 109.00 114.95 -5.95 3.00e+00 1.11e-01 3.94e+00 angle pdb=" CA ASP F 45 " pdb=" CB ASP F 45 " pdb=" HB3 ASP F 45 " ideal model delta sigma weight residual 109.00 114.95 -5.95 3.00e+00 1.11e-01 3.94e+00 angle pdb=" CA ASP B 45 " pdb=" CB ASP B 45 " pdb=" HB3 ASP B 45 " ideal model delta sigma weight residual 109.00 114.93 -5.93 3.00e+00 1.11e-01 3.91e+00 angle pdb=" CA ASP H 45 " pdb=" CB ASP H 45 " pdb=" HB3 ASP H 45 " ideal model delta sigma weight residual 109.00 114.89 -5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" CA ASP A 45 " pdb=" CB ASP A 45 " pdb=" HB3 ASP A 45 " ideal model delta sigma weight residual 109.00 114.88 -5.88 3.00e+00 1.11e-01 3.85e+00 ... (remaining 78421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 18318 17.88 - 35.77: 1540 35.77 - 53.65: 446 53.65 - 71.54: 126 71.54 - 89.42: 72 Dihedral angle restraints: 20502 sinusoidal: 11331 harmonic: 9171 Sorted by residual: dihedral pdb=" CB GLU K 82 " pdb=" CG GLU K 82 " pdb=" CD GLU K 82 " pdb=" OE1 GLU K 82 " ideal model delta sinusoidal sigma weight residual 0.00 -88.65 88.65 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU M 82 " pdb=" CG GLU M 82 " pdb=" CD GLU M 82 " pdb=" OE1 GLU M 82 " ideal model delta sinusoidal sigma weight residual 0.00 -88.63 88.63 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU N 82 " pdb=" CG GLU N 82 " pdb=" CD GLU N 82 " pdb=" OE1 GLU N 82 " ideal model delta sinusoidal sigma weight residual 0.00 -88.62 88.62 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 20499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2133 0.028 - 0.056: 792 0.056 - 0.083: 198 0.083 - 0.111: 165 0.111 - 0.139: 96 Chirality restraints: 3384 Sorted by residual: chirality pdb=" CA ILE N 79 " pdb=" N ILE N 79 " pdb=" C ILE N 79 " pdb=" CB ILE N 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE R 79 " pdb=" N ILE R 79 " pdb=" C ILE R 79 " pdb=" CB ILE R 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE Q 79 " pdb=" N ILE Q 79 " pdb=" C ILE Q 79 " pdb=" CB ILE Q 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 3381 not shown) Planarity restraints: 6597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 43 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" CG ASP A 43 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 43 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 43 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 31 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ALA C 31 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA C 31 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY C 32 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 43 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" CG ASP I 43 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP I 43 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP I 43 " -0.013 2.00e-02 2.50e+03 ... (remaining 6594 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.46: 25883 2.46 - 2.99: 97026 2.99 - 3.53: 114322 3.53 - 4.06: 153325 4.06 - 4.60: 228623 Nonbonded interactions: 619179 Sorted by model distance: nonbonded pdb=" HD2 ARG J 110 " pdb="HH11 ARG J 110 " model vdw 1.920 2.270 nonbonded pdb=" HD2 ARG L 110 " pdb="HH11 ARG L 110 " model vdw 1.920 2.270 nonbonded pdb=" HD2 ARG Q 110 " pdb="HH11 ARG Q 110 " model vdw 1.920 2.270 nonbonded pdb=" HD2 ARG O 110 " pdb="HH11 ARG O 110 " model vdw 1.921 2.270 nonbonded pdb=" HD2 ARG R 110 " pdb="HH11 ARG R 110 " model vdw 1.921 2.270 ... (remaining 619174 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.760 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21978 Z= 0.120 Angle : 0.501 3.650 29853 Z= 0.282 Chirality : 0.041 0.139 3384 Planarity : 0.004 0.053 3951 Dihedral : 15.676 89.421 8082 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.43 % Allowed : 11.54 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.14 (0.16), residues: 2754 helix: 2.65 (0.16), residues: 1008 sheet: 0.90 (0.19), residues: 684 loop : 0.67 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.010 0.001 TYR N 152 PHE 0.014 0.001 PHE F 51 TRP 0.007 0.001 TRP F 39 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (21978) covalent geometry : angle 0.50051 / 0.28 (29853) hydrogen bonds : bond 0.18187 / 12.12 ( 1062) hydrogen bonds : angle 5.62214 / 4.00 ( 3078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 480 time to evaluate : 1.237 Fit side-chains REVERT: A 6 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6101 (mm-40) REVERT: A 44 TYR cc_start: 0.7767 (m-80) cc_final: 0.7423 (m-80) REVERT: B 6 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.5988 (tp-100) REVERT: C 6 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.5937 (tp40) REVERT: C 11 ASN cc_start: 0.6417 (p0) cc_final: 0.6194 (p0) REVERT: D 6 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.5889 (mm-40) REVERT: D 41 ASN cc_start: 0.7687 (m-40) cc_final: 0.7453 (t0) REVERT: E 6 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.5827 (tp-100) REVERT: E 11 ASN cc_start: 0.6583 (p0) cc_final: 0.6067 (p0) REVERT: F 6 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6146 (tp40) REVERT: F 41 ASN cc_start: 0.7924 (m-40) cc_final: 0.7717 (t0) REVERT: G 6 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.5927 (tp40) REVERT: H 6 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.5972 (mm-40) REVERT: H 9 ASN cc_start: 0.7248 (t0) cc_final: 0.6948 (t0) REVERT: I 6 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6108 (mm-40) REVERT: I 11 ASN cc_start: 0.6370 (p0) cc_final: 0.6155 (p0) REVERT: J 11 ARG cc_start: 0.5976 (pmm150) cc_final: 0.4667 (mmp-170) REVERT: J 22 LYS cc_start: 0.6864 (mtpp) cc_final: 0.5654 (mmtt) REVERT: J 42 GLN cc_start: 0.7244 (mt0) cc_final: 0.6051 (tp-100) REVERT: J 56 GLN cc_start: 0.7583 (mt0) cc_final: 0.7286 (mt0) REVERT: J 185 GLU cc_start: 0.7920 (tt0) cc_final: 0.7557 (tt0) REVERT: J 203 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8086 (mt-10) REVERT: J 245 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6506 (mtp-110) REVERT: K 11 ARG cc_start: 0.6045 (pmm150) cc_final: 0.4761 (mmp-170) REVERT: K 22 LYS cc_start: 0.6952 (mtpp) cc_final: 0.5946 (mttt) REVERT: K 56 GLN cc_start: 0.7620 (mt0) cc_final: 0.7230 (mt0) REVERT: K 170 GLU cc_start: 0.7674 (tt0) cc_final: 0.7018 (mt-10) REVERT: K 185 GLU cc_start: 0.7987 (tt0) cc_final: 0.7722 (tt0) REVERT: K 203 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7958 (mt-10) REVERT: K 245 ARG cc_start: 0.6873 (mtp-110) cc_final: 0.6308 (ttt-90) REVERT: L 11 ARG cc_start: 0.5982 (pmm150) cc_final: 0.4953 (mmp-170) REVERT: L 22 LYS cc_start: 0.6792 (mtpp) cc_final: 0.5860 (mttt) REVERT: L 42 GLN cc_start: 0.7195 (mt0) cc_final: 0.6026 (tp-100) REVERT: L 56 GLN cc_start: 0.7585 (mt0) cc_final: 0.7201 (mt0) REVERT: L 170 GLU cc_start: 0.7665 (tt0) cc_final: 0.6918 (mt-10) REVERT: L 185 GLU cc_start: 0.7999 (tt0) cc_final: 0.7716 (tt0) REVERT: L 203 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8060 (mt-10) REVERT: L 245 ARG cc_start: 0.6766 (mtp-110) cc_final: 0.6417 (ttt-90) REVERT: M 11 ARG cc_start: 0.6006 (pmm150) cc_final: 0.4734 (mmp-170) REVERT: M 22 LYS cc_start: 0.6791 (mtpp) cc_final: 0.5884 (mttt) REVERT: M 56 GLN cc_start: 0.7661 (mt0) cc_final: 0.7459 (mt0) REVERT: M 150 THR cc_start: 0.8092 (p) cc_final: 0.7836 (m) REVERT: M 185 GLU cc_start: 0.8012 (tt0) cc_final: 0.7575 (tt0) REVERT: M 203 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8063 (mt-10) REVERT: M 245 ARG cc_start: 0.6816 (mtp-110) cc_final: 0.6258 (mtp-110) REVERT: N 11 ARG cc_start: 0.5938 (pmm150) cc_final: 0.4806 (mmp-170) REVERT: N 22 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6009 (mttt) REVERT: N 170 GLU cc_start: 0.7805 (tt0) cc_final: 0.7058 (mt-10) REVERT: N 203 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8336 (mt-10) REVERT: N 245 ARG cc_start: 0.6917 (mtp-110) cc_final: 0.6359 (mtp-110) REVERT: O 11 ARG cc_start: 0.6124 (pmm150) cc_final: 0.4766 (mmp-170) REVERT: O 22 LYS cc_start: 0.6804 (mtpp) cc_final: 0.5566 (mmtt) REVERT: O 42 GLN cc_start: 0.7264 (mt0) cc_final: 0.6085 (tp-100) REVERT: O 56 GLN cc_start: 0.7652 (mt0) cc_final: 0.7427 (mt0) REVERT: O 170 GLU cc_start: 0.7702 (tt0) cc_final: 0.6951 (mt-10) REVERT: O 185 GLU cc_start: 0.8035 (tt0) cc_final: 0.7703 (tt0) REVERT: O 203 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7861 (mt-10) REVERT: O 240 GLN cc_start: 0.6998 (tp40) cc_final: 0.6734 (tt0) REVERT: O 245 ARG cc_start: 0.6956 (mtp-110) cc_final: 0.6319 (mtp-110) REVERT: P 11 ARG cc_start: 0.6073 (pmm150) cc_final: 0.4968 (mmp-170) REVERT: P 22 LYS cc_start: 0.6872 (mtpp) cc_final: 0.5868 (mttt) REVERT: P 42 GLN cc_start: 0.7412 (mt0) cc_final: 0.6088 (tp-100) REVERT: P 150 THR cc_start: 0.8184 (p) cc_final: 0.7865 (m) REVERT: P 170 GLU cc_start: 0.7569 (tt0) cc_final: 0.6805 (mt-10) REVERT: P 185 GLU cc_start: 0.7828 (tt0) cc_final: 0.7400 (tt0) REVERT: P 203 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8257 (mt-10) REVERT: P 240 GLN cc_start: 0.6951 (tp40) cc_final: 0.6747 (tt0) REVERT: P 245 ARG cc_start: 0.6946 (mtp-110) cc_final: 0.6418 (mtp-110) REVERT: P 256 MET cc_start: 0.5497 (mtp) cc_final: 0.5295 (mtp) REVERT: Q 11 ARG cc_start: 0.6202 (pmm150) cc_final: 0.4828 (mmp-170) REVERT: Q 22 LYS cc_start: 0.6928 (mtpp) cc_final: 0.5942 (mttt) REVERT: Q 42 GLN cc_start: 0.7307 (mt0) cc_final: 0.5974 (tp-100) REVERT: Q 170 GLU cc_start: 0.7694 (tt0) cc_final: 0.6966 (mt-10) REVERT: Q 185 GLU cc_start: 0.7896 (tt0) cc_final: 0.7536 (tt0) REVERT: Q 203 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8089 (mt-10) REVERT: Q 245 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6549 (mtp-110) REVERT: R 11 ARG cc_start: 0.6110 (pmm150) cc_final: 0.4677 (mmp-170) REVERT: R 22 LYS cc_start: 0.6940 (mtpp) cc_final: 0.5781 (mmtt) REVERT: R 42 GLN cc_start: 0.7149 (mt0) cc_final: 0.5995 (tp-100) REVERT: R 84 GLN cc_start: 0.7383 (tt0) cc_final: 0.7182 (tt0) REVERT: R 150 THR cc_start: 0.8174 (p) cc_final: 0.7930 (m) REVERT: R 170 GLU cc_start: 0.7817 (tt0) cc_final: 0.7048 (mt-10) REVERT: R 185 GLU cc_start: 0.7974 (tt0) cc_final: 0.7544 (tt0) REVERT: R 240 GLN cc_start: 0.7103 (tp40) cc_final: 0.6892 (tt0) REVERT: R 245 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.6478 (mtp-110) outliers start: 10 outliers final: 0 residues processed: 480 average time/residue: 1.1923 time to fit residues: 664.5886 Evaluate side-chains 360 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 351 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain I residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN B 40 ASN C 30 ASN F 30 ASN H 18 ASN H 56 GLN K 42 GLN M 165 ASN N 241 ASN O 114 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100282 restraints weight = 63725.036| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 0.97 r_work: 0.2903 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21978 Z= 0.243 Angle : 0.628 6.409 29853 Z= 0.343 Chirality : 0.047 0.162 3384 Planarity : 0.006 0.066 3951 Dihedral : 6.010 44.475 3051 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.54 % Allowed : 12.31 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2754 helix: 2.40 (0.15), residues: 1053 sheet: 1.22 (0.20), residues: 585 loop : 0.39 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 162 TYR 0.013 0.002 TYR J 51 PHE 0.013 0.002 PHE F 5 TRP 0.006 0.002 TRP P 77 HIS 0.007 0.003 HIS J 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (21978) covalent geometry : angle 0.62780 / 0.34 (29853) hydrogen bonds : bond 0.06354 / 4.22 ( 1062) hydrogen bonds : angle 4.31317 / 3.06 ( 3078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.903 Fit side-chains REVERT: A 6 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7643 (mm-40) REVERT: A 11 ASN cc_start: 0.8179 (p0) cc_final: 0.7775 (m-40) REVERT: B 6 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7748 (tp-100) REVERT: C 6 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7753 (mm-40) REVERT: D 6 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7851 (mm-40) REVERT: G 6 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: H 6 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7753 (mm-40) REVERT: I 6 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: J 11 ARG cc_start: 0.7623 (pmm150) cc_final: 0.6962 (mmp-170) REVERT: J 22 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7555 (mptt) REVERT: J 25 THR cc_start: 0.8909 (m) cc_final: 0.8682 (p) REVERT: J 170 GLU cc_start: 0.8329 (tt0) cc_final: 0.8063 (mt-10) REVERT: J 240 GLN cc_start: 0.8243 (tp40) cc_final: 0.7883 (tt0) REVERT: J 245 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7546 (ttt-90) REVERT: K 11 ARG cc_start: 0.7686 (pmm150) cc_final: 0.7029 (mmp-170) REVERT: K 22 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7554 (mttt) REVERT: K 25 THR cc_start: 0.8824 (m) cc_final: 0.8610 (p) REVERT: K 170 GLU cc_start: 0.8352 (tt0) cc_final: 0.8094 (mt-10) REVERT: K 203 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8330 (mt-10) REVERT: K 240 GLN cc_start: 0.8158 (tp40) cc_final: 0.7886 (tt0) REVERT: K 245 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7430 (mtp-110) REVERT: L 11 ARG cc_start: 0.7642 (pmm150) cc_final: 0.7053 (mmp-170) REVERT: L 22 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7399 (mttt) REVERT: L 25 THR cc_start: 0.8908 (m) cc_final: 0.8656 (p) REVERT: L 42 GLN cc_start: 0.8500 (mt0) cc_final: 0.8114 (tp-100) REVERT: L 245 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7459 (ttt-90) REVERT: M 11 ARG cc_start: 0.7703 (pmm150) cc_final: 0.7014 (mmp-170) REVERT: M 22 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7527 (mttp) REVERT: M 240 GLN cc_start: 0.8111 (tp40) cc_final: 0.7890 (tt0) REVERT: M 245 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7387 (mtp-110) REVERT: N 11 ARG cc_start: 0.7511 (pmm150) cc_final: 0.6877 (mmp-170) REVERT: N 22 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7573 (mptt) REVERT: N 170 GLU cc_start: 0.8472 (tt0) cc_final: 0.8195 (mt-10) REVERT: N 245 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.7476 (mtp-110) REVERT: O 11 ARG cc_start: 0.7686 (pmm150) cc_final: 0.6985 (mmp-170) REVERT: O 22 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7265 (mmtt) REVERT: O 170 GLU cc_start: 0.8303 (tt0) cc_final: 0.8085 (mt-10) REVERT: O 245 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7299 (mtp-110) REVERT: P 11 ARG cc_start: 0.7603 (pmm150) cc_final: 0.6972 (mmp-170) REVERT: P 22 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7647 (mtmt) REVERT: P 25 THR cc_start: 0.8859 (m) cc_final: 0.8641 (p) REVERT: P 170 GLU cc_start: 0.8374 (tt0) cc_final: 0.8099 (mt-10) REVERT: P 203 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8482 (mt-10) REVERT: P 245 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7379 (ttt-90) REVERT: Q 11 ARG cc_start: 0.7728 (pmm150) cc_final: 0.7011 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7472 (mptt) REVERT: Q 25 THR cc_start: 0.8839 (m) cc_final: 0.8573 (p) REVERT: Q 170 GLU cc_start: 0.8308 (tt0) cc_final: 0.8057 (mt-10) REVERT: Q 240 GLN cc_start: 0.8171 (tp40) cc_final: 0.7863 (tt0) REVERT: Q 245 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7485 (mtp-110) REVERT: R 11 ARG cc_start: 0.7600 (pmm150) cc_final: 0.6960 (mmp-170) REVERT: R 22 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7505 (mttt) REVERT: R 25 THR cc_start: 0.8860 (m) cc_final: 0.8634 (p) REVERT: R 42 GLN cc_start: 0.8428 (mt0) cc_final: 0.8069 (tp-100) REVERT: R 245 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7473 (mtp-110) outliers start: 36 outliers final: 13 residues processed: 302 average time/residue: 1.2294 time to fit residues: 431.1156 Evaluate side-chains 295 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [263, 172, 114, 31, 96, 176, 69, 228, 183, 92, 78] chunk 263 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 42 GLN K 114 GLN M 42 GLN N 42 GLN N 241 ASN O 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.098831 restraints weight = 64409.478| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.09 r_work: 0.2899 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21978 Z= 0.155 Angle : 0.516 4.328 29853 Z= 0.279 Chirality : 0.043 0.148 3384 Planarity : 0.005 0.048 3951 Dihedral : 5.483 45.505 3045 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.89 % Allowed : 12.87 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.24 (0.16), residues: 2754 helix: 2.61 (0.15), residues: 1053 sheet: 1.54 (0.20), residues: 585 loop : 0.41 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 162 TYR 0.007 0.001 TYR Q 253 PHE 0.008 0.002 PHE M 35 TRP 0.003 0.001 TRP M 237 HIS 0.004 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21978) covalent geometry : angle 0.51574 / 0.28 (29853) hydrogen bonds : bond 0.05232 / 3.48 ( 1062) hydrogen bonds : angle 4.11963 / 2.92 ( 3078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 1.207 Fit side-chains REVERT: A 6 GLN cc_start: 0.8438 (mt0) cc_final: 0.7683 (mm-40) REVERT: A 11 ASN cc_start: 0.8226 (p0) cc_final: 0.7830 (m110) REVERT: B 11 ASN cc_start: 0.8152 (p0) cc_final: 0.7820 (m-40) REVERT: C 6 GLN cc_start: 0.8455 (mt0) cc_final: 0.7751 (mm-40) REVERT: D 6 GLN cc_start: 0.8478 (mt0) cc_final: 0.7869 (mm-40) REVERT: E 6 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: F 6 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7670 (mm-40) REVERT: H 6 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: H 11 ASN cc_start: 0.8239 (p0) cc_final: 0.7932 (m-40) REVERT: I 6 GLN cc_start: 0.8470 (mt0) cc_final: 0.7832 (mm-40) REVERT: I 11 ASN cc_start: 0.8316 (p0) cc_final: 0.7905 (m-40) REVERT: J 11 ARG cc_start: 0.7690 (pmm150) cc_final: 0.6955 (mmp-170) REVERT: J 22 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7387 (mptt) REVERT: J 25 THR cc_start: 0.8864 (m) cc_final: 0.8575 (p) REVERT: J 170 GLU cc_start: 0.8362 (tt0) cc_final: 0.8075 (mt-10) REVERT: J 240 GLN cc_start: 0.8167 (tp40) cc_final: 0.7836 (tt0) REVERT: J 245 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7539 (mtp-110) REVERT: K 11 ARG cc_start: 0.7615 (pmm150) cc_final: 0.6967 (mmp-170) REVERT: K 22 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7393 (mttt) REVERT: K 25 THR cc_start: 0.8831 (m) cc_final: 0.8578 (p) REVERT: K 42 GLN cc_start: 0.8439 (mt0) cc_final: 0.8097 (tp40) REVERT: K 170 GLU cc_start: 0.8371 (tt0) cc_final: 0.8086 (mt-10) REVERT: K 240 GLN cc_start: 0.8109 (tp40) cc_final: 0.7884 (tt0) REVERT: K 245 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7384 (mtp-110) REVERT: L 11 ARG cc_start: 0.7638 (pmm150) cc_final: 0.7069 (mmp-170) REVERT: L 22 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7271 (mttt) REVERT: L 25 THR cc_start: 0.8851 (m) cc_final: 0.8557 (p) REVERT: L 42 GLN cc_start: 0.8534 (mt0) cc_final: 0.8059 (tp-100) REVERT: L 245 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7378 (mtp-110) REVERT: M 11 ARG cc_start: 0.7737 (pmm150) cc_final: 0.7024 (mmp-170) REVERT: M 22 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7346 (mttp) REVERT: M 240 GLN cc_start: 0.8143 (tp40) cc_final: 0.7880 (tt0) REVERT: M 245 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7351 (mtp-110) REVERT: N 11 ARG cc_start: 0.7548 (pmm150) cc_final: 0.6869 (mmp-170) REVERT: N 22 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7237 (mptt) REVERT: N 25 THR cc_start: 0.8842 (m) cc_final: 0.8583 (p) REVERT: N 170 GLU cc_start: 0.8441 (tt0) cc_final: 0.8164 (mt-10) REVERT: N 240 GLN cc_start: 0.8103 (tp40) cc_final: 0.7870 (tt0) REVERT: N 245 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7441 (mtp-110) REVERT: O 11 ARG cc_start: 0.7714 (pmm150) cc_final: 0.7002 (mmp-170) REVERT: O 22 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7154 (mmtt) REVERT: O 170 GLU cc_start: 0.8316 (tt0) cc_final: 0.8056 (mt-10) REVERT: O 245 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7240 (mtp-110) REVERT: P 11 ARG cc_start: 0.7639 (pmm150) cc_final: 0.6960 (mmp-170) REVERT: P 22 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7445 (mttp) REVERT: P 25 THR cc_start: 0.8847 (m) cc_final: 0.8580 (p) REVERT: P 170 GLU cc_start: 0.8357 (tt0) cc_final: 0.8087 (mt-10) REVERT: P 245 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7321 (ttt-90) REVERT: Q 11 ARG cc_start: 0.7739 (pmm150) cc_final: 0.6910 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7351 (mptt) REVERT: Q 25 THR cc_start: 0.8781 (m) cc_final: 0.8497 (p) REVERT: Q 170 GLU cc_start: 0.8324 (tt0) cc_final: 0.8071 (mt-10) REVERT: Q 203 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8449 (mt-10) REVERT: Q 240 GLN cc_start: 0.8176 (tp40) cc_final: 0.7843 (tt0) REVERT: Q 245 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7408 (mtp-110) REVERT: R 11 ARG cc_start: 0.7609 (pmm150) cc_final: 0.6987 (mmp-170) REVERT: R 22 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7145 (mmtt) REVERT: R 25 THR cc_start: 0.8811 (m) cc_final: 0.8525 (p) REVERT: R 42 GLN cc_start: 0.8513 (mt0) cc_final: 0.8070 (tp-100) REVERT: R 170 GLU cc_start: 0.8505 (tt0) cc_final: 0.8191 (mt-10) REVERT: R 245 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7413 (mtp-110) outliers start: 44 outliers final: 19 residues processed: 308 average time/residue: 1.2601 time to fit residues: 448.9686 Evaluate side-chains 300 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [187, 231, 123, 248, 125, 74, 151, 189, 236, 164, 139] chunk 187 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 42 GLN N 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097882 restraints weight = 64342.442| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.09 r_work: 0.2880 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21978 Z= 0.155 Angle : 0.523 5.414 29853 Z= 0.281 Chirality : 0.043 0.144 3384 Planarity : 0.005 0.055 3951 Dihedral : 4.719 45.357 3027 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.72 % Allowed : 13.30 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.24 (0.16), residues: 2754 helix: 2.62 (0.15), residues: 1053 sheet: 1.54 (0.20), residues: 585 loop : 0.40 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 162 TYR 0.009 0.001 TYR O 253 PHE 0.008 0.002 PHE H 7 TRP 0.003 0.001 TRP M 237 HIS 0.003 0.001 HIS M 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21978) covalent geometry : angle 0.52326 / 0.28 (29853) hydrogen bonds : bond 0.04926 / 3.27 ( 1062) hydrogen bonds : angle 4.03845 / 2.86 ( 3078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 1.178 Fit side-chains REVERT: A 6 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: A 11 ASN cc_start: 0.8211 (p0) cc_final: 0.7888 (m110) REVERT: B 6 GLN cc_start: 0.8475 (mt0) cc_final: 0.7926 (mm-40) REVERT: B 11 ASN cc_start: 0.8153 (p0) cc_final: 0.7919 (m-40) REVERT: C 6 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: D 6 GLN cc_start: 0.8460 (mt0) cc_final: 0.7868 (mm-40) REVERT: E 6 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: F 6 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7695 (mm-40) REVERT: G 6 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7713 (mm-40) REVERT: H 6 GLN cc_start: 0.8442 (mt0) cc_final: 0.7764 (mm-40) REVERT: H 11 ASN cc_start: 0.8139 (p0) cc_final: 0.7926 (m110) REVERT: I 6 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7823 (mm-40) REVERT: I 11 ASN cc_start: 0.8285 (p0) cc_final: 0.7951 (m-40) REVERT: J 11 ARG cc_start: 0.7684 (pmm150) cc_final: 0.6967 (mmp-170) REVERT: J 22 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7371 (mptt) REVERT: J 25 THR cc_start: 0.8870 (m) cc_final: 0.8621 (p) REVERT: J 170 GLU cc_start: 0.8340 (tt0) cc_final: 0.8059 (mt-10) REVERT: J 240 GLN cc_start: 0.8161 (tp40) cc_final: 0.7807 (tt0) REVERT: J 245 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7524 (mtp-110) REVERT: K 11 ARG cc_start: 0.7641 (pmm150) cc_final: 0.6934 (mmp-170) REVERT: K 22 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7278 (mttt) REVERT: K 25 THR cc_start: 0.8863 (m) cc_final: 0.8629 (p) REVERT: K 245 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7355 (mtp-110) REVERT: L 11 ARG cc_start: 0.7606 (pmm150) cc_final: 0.7052 (mmm160) REVERT: L 22 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7265 (mttt) REVERT: L 25 THR cc_start: 0.8865 (m) cc_final: 0.8598 (p) REVERT: L 42 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8132 (tp-100) REVERT: L 245 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7369 (mtp-110) REVERT: M 11 ARG cc_start: 0.7671 (pmm150) cc_final: 0.7003 (mmp-170) REVERT: M 22 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7301 (mttp) REVERT: M 240 GLN cc_start: 0.8112 (tp40) cc_final: 0.7821 (tt0) REVERT: M 245 ARG cc_start: 0.7656 (mtp-110) cc_final: 0.7308 (mtp-110) REVERT: N 11 ARG cc_start: 0.7555 (pmm150) cc_final: 0.6883 (mmp-170) REVERT: N 22 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7184 (mptt) REVERT: N 170 GLU cc_start: 0.8454 (tt0) cc_final: 0.8171 (mt-10) REVERT: N 240 GLN cc_start: 0.8081 (tp40) cc_final: 0.7848 (tt0) REVERT: N 245 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7402 (mtp-110) REVERT: O 11 ARG cc_start: 0.7683 (pmm150) cc_final: 0.7001 (mmp-170) REVERT: O 22 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7122 (mmtt) REVERT: O 170 GLU cc_start: 0.8370 (tt0) cc_final: 0.8114 (mt-10) REVERT: O 245 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7405 (mtp-110) REVERT: P 11 ARG cc_start: 0.7658 (pmm150) cc_final: 0.7040 (mmp-170) REVERT: P 22 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7488 (mtmt) REVERT: P 25 THR cc_start: 0.8816 (m) cc_final: 0.8593 (p) REVERT: P 170 GLU cc_start: 0.8362 (tt0) cc_final: 0.8081 (mt-10) REVERT: P 245 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7332 (ttt-90) REVERT: Q 11 ARG cc_start: 0.7747 (pmm150) cc_final: 0.6920 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7332 (mptt) REVERT: Q 25 THR cc_start: 0.8803 (m) cc_final: 0.8547 (p) REVERT: Q 170 GLU cc_start: 0.8308 (tt0) cc_final: 0.8074 (mt-10) REVERT: Q 240 GLN cc_start: 0.8189 (tp40) cc_final: 0.7835 (tt0) REVERT: Q 245 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7384 (mtp-110) REVERT: R 11 ARG cc_start: 0.7612 (pmm150) cc_final: 0.6999 (mmp-170) REVERT: R 22 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7240 (mttt) REVERT: R 25 THR cc_start: 0.8851 (m) cc_final: 0.8593 (p) REVERT: R 42 GLN cc_start: 0.8533 (mt0) cc_final: 0.8111 (tp-100) REVERT: R 170 GLU cc_start: 0.8501 (tt0) cc_final: 0.8180 (mt-10) REVERT: R 245 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7379 (mtp-110) REVERT: R 254 ARG cc_start: 0.8309 (ttp-170) cc_final: 0.8084 (mtp180) outliers start: 40 outliers final: 19 residues processed: 288 average time/residue: 1.3435 time to fit residues: 443.6360 Evaluate side-chains 301 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [254, 191, 4, 192, 32, 253, 166, 61, 86, 215, 67] chunk 254 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 42 GLN M 42 GLN N 42 GLN N 241 ASN O 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.095067 restraints weight = 64479.934| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.10 r_work: 0.2833 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21978 Z= 0.236 Angle : 0.610 6.422 29853 Z= 0.329 Chirality : 0.046 0.148 3384 Planarity : 0.006 0.083 3951 Dihedral : 4.951 20.186 3024 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.36 % Allowed : 12.40 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.15), residues: 2754 helix: 2.24 (0.15), residues: 1053 sheet: 1.36 (0.20), residues: 594 loop : 0.30 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 76 TYR 0.012 0.002 TYR J 51 PHE 0.010 0.002 PHE D 5 TRP 0.005 0.002 TRP R 237 HIS 0.004 0.001 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (21978) covalent geometry : angle 0.60964 / 0.33 (29853) hydrogen bonds : bond 0.06015 / 3.99 ( 1062) hydrogen bonds : angle 4.22144 / 3.00 ( 3078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: A 11 ASN cc_start: 0.8278 (p0) cc_final: 0.7961 (m110) REVERT: B 6 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7869 (mm-40) REVERT: C 6 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: D 6 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7792 (mm-40) REVERT: E 6 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: G 6 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: H 6 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: H 41 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8177 (m110) REVERT: I 6 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7824 (mm-40) REVERT: I 11 ASN cc_start: 0.8334 (p0) cc_final: 0.8045 (m-40) REVERT: J 11 ARG cc_start: 0.7697 (pmm150) cc_final: 0.7000 (mmp-170) REVERT: J 22 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7427 (mptt) REVERT: J 42 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8017 (tp40) REVERT: J 170 GLU cc_start: 0.8385 (tt0) cc_final: 0.8119 (mt-10) REVERT: J 240 GLN cc_start: 0.8215 (tp40) cc_final: 0.7856 (tt0) REVERT: J 245 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7390 (mtp-110) REVERT: K 11 ARG cc_start: 0.7734 (pmm150) cc_final: 0.6994 (mmp-170) REVERT: K 22 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7434 (mttt) REVERT: K 245 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7339 (mtp-110) REVERT: L 11 ARG cc_start: 0.7653 (pmm150) cc_final: 0.7097 (mmp-170) REVERT: L 22 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7309 (mttt) REVERT: L 25 THR cc_start: 0.8925 (m) cc_final: 0.8723 (p) REVERT: L 42 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8108 (tp-100) REVERT: L 217 MET cc_start: 0.9114 (tpp) cc_final: 0.8861 (tpt) REVERT: L 245 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7330 (mtp-110) REVERT: M 11 ARG cc_start: 0.7664 (pmm150) cc_final: 0.7046 (mmp-170) REVERT: M 22 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7449 (mttp) REVERT: M 245 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7339 (mtp-110) REVERT: N 11 ARG cc_start: 0.7587 (pmm150) cc_final: 0.6914 (mmp-170) REVERT: N 22 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7350 (mptt) REVERT: N 170 GLU cc_start: 0.8454 (tt0) cc_final: 0.8168 (mt-10) REVERT: N 240 GLN cc_start: 0.8138 (tp40) cc_final: 0.7900 (tt0) REVERT: N 245 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7330 (mtp-110) REVERT: O 11 ARG cc_start: 0.7682 (pmm150) cc_final: 0.7009 (mmp-170) REVERT: O 22 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7207 (mmtt) REVERT: O 170 GLU cc_start: 0.8386 (tt0) cc_final: 0.8159 (mt-10) REVERT: O 245 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.7397 (mtp-110) REVERT: P 11 ARG cc_start: 0.7668 (pmm150) cc_final: 0.7054 (mmp-170) REVERT: P 170 GLU cc_start: 0.8338 (tt0) cc_final: 0.8103 (mt-10) REVERT: P 245 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7423 (mtp-110) REVERT: Q 11 ARG cc_start: 0.7831 (pmm150) cc_final: 0.6990 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7439 (mptt) REVERT: Q 170 GLU cc_start: 0.8328 (tt0) cc_final: 0.8098 (mt-10) REVERT: Q 240 GLN cc_start: 0.8215 (tp40) cc_final: 0.7849 (tt0) REVERT: Q 245 ARG cc_start: 0.7670 (mtp-110) cc_final: 0.7320 (mtp-110) REVERT: R 11 ARG cc_start: 0.7600 (pmm150) cc_final: 0.6952 (mmp-170) REVERT: R 22 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7090 (mmtt) REVERT: R 42 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8066 (tp-100) REVERT: R 245 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7393 (mtp-110) outliers start: 55 outliers final: 28 residues processed: 275 average time/residue: 1.3884 time to fit residues: 435.2277 Evaluate side-chains 302 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain F residue 3 MET Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [267, 186, 165, 201, 156, 123, 78, 89, 131, 82, 33] chunk 267 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 GLN K 42 GLN O 42 GLN Q 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.096354 restraints weight = 64633.735| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.10 r_work: 0.2851 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21978 Z= 0.164 Angle : 0.536 5.426 29853 Z= 0.288 Chirality : 0.043 0.146 3384 Planarity : 0.005 0.050 3951 Dihedral : 4.749 18.617 3024 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.97 % Allowed : 13.17 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.01 (0.16), residues: 2754 helix: 2.38 (0.15), residues: 1053 sheet: 1.53 (0.20), residues: 585 loop : 0.26 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 76 TYR 0.008 0.001 TYR N 51 PHE 0.008 0.002 PHE P 191 TRP 0.003 0.001 TRP Q 237 HIS 0.004 0.001 HIS J 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (21978) covalent geometry : angle 0.53642 / 0.29 (29853) hydrogen bonds : bond 0.05147 / 3.42 ( 1062) hydrogen bonds : angle 4.12231 / 2.93 ( 3078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: A 11 ASN cc_start: 0.8230 (p0) cc_final: 0.7953 (m110) REVERT: B 6 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: C 6 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: D 6 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7782 (mm-40) REVERT: E 6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: F 6 GLN cc_start: 0.8405 (mt0) cc_final: 0.7996 (mp10) REVERT: G 6 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7709 (mm-40) REVERT: H 6 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: H 41 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8151 (m110) REVERT: I 6 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7804 (mm-40) REVERT: I 11 ASN cc_start: 0.8282 (p0) cc_final: 0.8039 (m-40) REVERT: J 11 ARG cc_start: 0.7675 (pmm150) cc_final: 0.6960 (mmp-170) REVERT: J 22 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7376 (mptt) REVERT: J 42 GLN cc_start: 0.8542 (mt0) cc_final: 0.8020 (tp40) REVERT: J 170 GLU cc_start: 0.8383 (tt0) cc_final: 0.8123 (mt-10) REVERT: J 240 GLN cc_start: 0.8202 (tp40) cc_final: 0.7867 (tt0) REVERT: J 245 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7392 (mtp-110) REVERT: K 11 ARG cc_start: 0.7696 (pmm150) cc_final: 0.6964 (mmp-170) REVERT: K 22 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7378 (mttt) REVERT: K 245 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.7364 (mtp-110) REVERT: L 11 ARG cc_start: 0.7684 (pmm150) cc_final: 0.7102 (mmp-170) REVERT: L 25 THR cc_start: 0.8892 (m) cc_final: 0.8638 (p) REVERT: L 42 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8109 (tp-100) REVERT: L 76 ARG cc_start: 0.8065 (mpp80) cc_final: 0.7828 (mpp-170) REVERT: L 217 MET cc_start: 0.9099 (tpp) cc_final: 0.8846 (tpt) REVERT: L 245 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7331 (mtp-110) REVERT: M 11 ARG cc_start: 0.7635 (pmm150) cc_final: 0.7009 (mmp-170) REVERT: M 22 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7363 (mttp) REVERT: M 245 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7313 (mtp-110) REVERT: N 11 ARG cc_start: 0.7564 (pmm150) cc_final: 0.6895 (mmp-170) REVERT: N 22 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7249 (mptt) REVERT: N 170 GLU cc_start: 0.8459 (tt0) cc_final: 0.8179 (mt-10) REVERT: N 240 GLN cc_start: 0.8121 (tp40) cc_final: 0.7878 (tt0) REVERT: N 245 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7332 (mtp-110) REVERT: O 11 ARG cc_start: 0.7693 (pmm150) cc_final: 0.7017 (mmp-170) REVERT: O 22 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7159 (mmtt) REVERT: O 170 GLU cc_start: 0.8366 (tt0) cc_final: 0.8146 (mt-10) REVERT: O 245 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7406 (mtp-110) REVERT: P 11 ARG cc_start: 0.7624 (pmm150) cc_final: 0.7032 (mmp-170) REVERT: P 22 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7544 (mttp) REVERT: P 170 GLU cc_start: 0.8347 (tt0) cc_final: 0.8108 (mt-10) REVERT: P 245 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7422 (mtp-110) REVERT: Q 11 ARG cc_start: 0.7781 (pmm150) cc_final: 0.7005 (mmp-170) REVERT: Q 170 GLU cc_start: 0.8320 (tt0) cc_final: 0.8097 (mt-10) REVERT: Q 240 GLN cc_start: 0.8181 (tp40) cc_final: 0.7785 (tt0) REVERT: Q 245 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7329 (mtp-110) REVERT: R 11 ARG cc_start: 0.7591 (pmm150) cc_final: 0.6941 (mmp-170) REVERT: R 22 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7122 (mmtt) REVERT: R 42 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8045 (tp-100) REVERT: R 245 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7355 (mtp-110) REVERT: R 254 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.8095 (mtp180) outliers start: 46 outliers final: 23 residues processed: 272 average time/residue: 1.4257 time to fit residues: 440.2474 Evaluate side-chains 291 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [262, 21, 35, 17, 137, 22, 87, 199, 222, 119, 69] chunk 262 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 222 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 GLN K 42 GLN N 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096126 restraints weight = 64271.238| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.10 r_work: 0.2849 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21978 Z= 0.178 Angle : 0.546 5.636 29853 Z= 0.293 Chirality : 0.044 0.143 3384 Planarity : 0.005 0.055 3951 Dihedral : 4.733 19.049 3024 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.10 % Allowed : 13.17 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2754 helix: 2.36 (0.15), residues: 1053 sheet: 1.52 (0.20), residues: 585 loop : 0.22 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 76 TYR 0.009 0.002 TYR N 51 PHE 0.008 0.002 PHE P 191 TRP 0.004 0.001 TRP R 237 HIS 0.003 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (21978) covalent geometry : angle 0.54579 / 0.29 (29853) hydrogen bonds : bond 0.05236 / 3.48 ( 1062) hydrogen bonds : angle 4.12229 / 2.93 ( 3078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7657 (mm-40) REVERT: A 11 ASN cc_start: 0.8222 (p0) cc_final: 0.7997 (m110) REVERT: B 6 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7925 (mm-40) REVERT: C 6 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7755 (mm-40) REVERT: D 6 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7775 (mm-40) REVERT: E 6 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: F 6 GLN cc_start: 0.8429 (mt0) cc_final: 0.8052 (mp10) REVERT: G 6 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7718 (mm-40) REVERT: H 6 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7813 (mm-40) REVERT: I 6 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7832 (mm-40) REVERT: I 11 ASN cc_start: 0.8326 (p0) cc_final: 0.8094 (m-40) REVERT: J 11 ARG cc_start: 0.7688 (pmm150) cc_final: 0.6980 (mmp-170) REVERT: J 22 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7386 (mptt) REVERT: J 42 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8032 (tp40) REVERT: J 170 GLU cc_start: 0.8370 (tt0) cc_final: 0.8117 (mt-10) REVERT: J 240 GLN cc_start: 0.8206 (tp40) cc_final: 0.7869 (tt0) REVERT: J 245 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7380 (mtp-110) REVERT: K 11 ARG cc_start: 0.7695 (pmm150) cc_final: 0.6973 (mmp-170) REVERT: K 22 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7405 (mttt) REVERT: K 245 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7359 (mtp-110) REVERT: L 11 ARG cc_start: 0.7695 (pmm150) cc_final: 0.7111 (mmp-170) REVERT: L 22 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7137 (mmtt) REVERT: L 25 THR cc_start: 0.8917 (m) cc_final: 0.8681 (p) REVERT: L 42 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8112 (tp-100) REVERT: L 76 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7787 (mpp-170) REVERT: L 217 MET cc_start: 0.9101 (tpp) cc_final: 0.8860 (tpt) REVERT: L 245 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7322 (mtp-110) REVERT: M 11 ARG cc_start: 0.7595 (pmm150) cc_final: 0.7031 (mmp-170) REVERT: M 22 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7377 (mttp) REVERT: M 245 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7308 (mtp-110) REVERT: N 11 ARG cc_start: 0.7563 (pmm150) cc_final: 0.6896 (mmp-170) REVERT: N 22 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7323 (mptt) REVERT: N 170 GLU cc_start: 0.8457 (tt0) cc_final: 0.8182 (mt-10) REVERT: N 240 GLN cc_start: 0.8099 (tp40) cc_final: 0.7871 (tt0) REVERT: N 245 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7344 (mtp-110) REVERT: O 11 ARG cc_start: 0.7690 (pmm150) cc_final: 0.7033 (mmp-170) REVERT: O 22 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7169 (mmtt) REVERT: O 170 GLU cc_start: 0.8379 (tt0) cc_final: 0.8155 (mt-10) REVERT: O 245 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7398 (mtp-110) REVERT: P 11 ARG cc_start: 0.7607 (pmm150) cc_final: 0.7038 (mmp-170) REVERT: P 22 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7517 (mttp) REVERT: P 170 GLU cc_start: 0.8349 (tt0) cc_final: 0.8109 (mt-10) REVERT: P 245 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7422 (mtp-110) REVERT: Q 11 ARG cc_start: 0.7768 (pmm150) cc_final: 0.7008 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7449 (mptt) REVERT: Q 170 GLU cc_start: 0.8339 (tt0) cc_final: 0.8116 (mt-10) REVERT: Q 240 GLN cc_start: 0.8178 (tp40) cc_final: 0.7794 (tt0) REVERT: Q 245 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7425 (mtp-110) REVERT: R 11 ARG cc_start: 0.7572 (pmm150) cc_final: 0.6939 (mmp-170) REVERT: R 42 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8078 (tp-100) REVERT: R 245 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7357 (mtp-110) REVERT: R 254 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.8108 (mtp180) outliers start: 49 outliers final: 27 residues processed: 269 average time/residue: 1.4253 time to fit residues: 437.5527 Evaluate side-chains 295 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain N residue 194 ILE Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [37, 14, 263, 16, 246, 184, 239, 117, 91, 126, 218] chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 246 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 GLN M 42 GLN N 42 GLN O 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.116532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.097292 restraints weight = 64680.716| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.10 r_work: 0.2865 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21978 Z= 0.137 Angle : 0.507 5.130 29853 Z= 0.270 Chirality : 0.042 0.142 3384 Planarity : 0.005 0.051 3951 Dihedral : 4.571 18.548 3024 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.54 % Allowed : 14.16 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.13 (0.16), residues: 2754 helix: 2.55 (0.15), residues: 1053 sheet: 1.59 (0.20), residues: 585 loop : 0.26 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 76 TYR 0.007 0.001 TYR Q 253 PHE 0.007 0.001 PHE K 191 TRP 0.003 0.001 TRP N 77 HIS 0.003 0.001 HIS Q 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21978) covalent geometry : angle 0.50676 / 0.27 (29853) hydrogen bonds : bond 0.04677 / 3.11 ( 1062) hydrogen bonds : angle 4.03575 / 2.86 ( 3078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.928 Fit side-chains REVERT: A 6 GLN cc_start: 0.8432 (mt0) cc_final: 0.7660 (mm-40) REVERT: B 6 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7910 (mm-40) REVERT: C 6 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7743 (mm-40) REVERT: D 6 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7806 (mm-40) REVERT: F 6 GLN cc_start: 0.8403 (mt0) cc_final: 0.7696 (mm-40) REVERT: H 6 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7781 (mm-40) REVERT: I 6 GLN cc_start: 0.8503 (mt0) cc_final: 0.7829 (mm-40) REVERT: J 11 ARG cc_start: 0.7647 (pmm150) cc_final: 0.6963 (mmp-170) REVERT: J 22 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7377 (mptt) REVERT: J 42 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8024 (tp40) REVERT: J 170 GLU cc_start: 0.8378 (tt0) cc_final: 0.8127 (mt-10) REVERT: J 240 GLN cc_start: 0.8175 (tp40) cc_final: 0.7839 (tt0) REVERT: J 245 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7372 (mtp-110) REVERT: K 11 ARG cc_start: 0.7633 (pmm150) cc_final: 0.6946 (mmp-170) REVERT: K 22 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7377 (mttt) REVERT: K 245 ARG cc_start: 0.7724 (mtp-110) cc_final: 0.7353 (mtp-110) REVERT: L 11 ARG cc_start: 0.7652 (pmm150) cc_final: 0.7103 (mmp-170) REVERT: L 22 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7019 (mmtt) REVERT: L 25 THR cc_start: 0.8899 (m) cc_final: 0.8633 (p) REVERT: L 42 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8121 (tp-100) REVERT: L 76 ARG cc_start: 0.8024 (mpp80) cc_final: 0.7781 (mpp-170) REVERT: L 217 MET cc_start: 0.9092 (tpp) cc_final: 0.8852 (tpt) REVERT: L 245 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7324 (mtp-110) REVERT: M 11 ARG cc_start: 0.7569 (pmm150) cc_final: 0.6971 (mmp-170) REVERT: M 22 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7333 (mttp) REVERT: M 245 ARG cc_start: 0.7670 (mtp-110) cc_final: 0.7307 (mtp-110) REVERT: N 11 ARG cc_start: 0.7528 (pmm150) cc_final: 0.6881 (mmp-170) REVERT: N 22 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7291 (mptt) REVERT: N 170 GLU cc_start: 0.8454 (tt0) cc_final: 0.8193 (mt-10) REVERT: N 240 GLN cc_start: 0.8081 (tp40) cc_final: 0.7856 (tt0) REVERT: N 245 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7346 (mtp-110) REVERT: O 11 ARG cc_start: 0.7665 (pmm150) cc_final: 0.7036 (mmp-170) REVERT: O 170 GLU cc_start: 0.8400 (tt0) cc_final: 0.8182 (mt-10) REVERT: O 245 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7399 (mtp-110) REVERT: P 11 ARG cc_start: 0.7590 (pmm150) cc_final: 0.7030 (mmp-170) REVERT: P 22 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7479 (mttp) REVERT: P 170 GLU cc_start: 0.8354 (tt0) cc_final: 0.8114 (mt-10) REVERT: P 245 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7411 (mtp-110) REVERT: Q 11 ARG cc_start: 0.7733 (pmm150) cc_final: 0.6985 (mmp-170) REVERT: Q 22 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7363 (mptt) REVERT: Q 170 GLU cc_start: 0.8336 (tt0) cc_final: 0.8116 (mt-10) REVERT: Q 240 GLN cc_start: 0.8161 (tp40) cc_final: 0.7780 (tt0) REVERT: Q 245 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7404 (mtp-110) REVERT: R 11 ARG cc_start: 0.7548 (pmm150) cc_final: 0.6924 (mmp-170) REVERT: R 22 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7081 (mmtt) REVERT: R 42 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8047 (tp-100) REVERT: R 170 GLU cc_start: 0.8496 (tt0) cc_final: 0.8171 (mt-10) REVERT: R 245 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7339 (mtp-110) REVERT: R 254 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.8093 (mtp180) outliers start: 36 outliers final: 25 residues processed: 274 average time/residue: 1.4118 time to fit residues: 441.9882 Evaluate side-chains 294 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [92, 37, 25, 64, 256, 123, 104, 264, 11, 75, 63] chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 264 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 37 GLN K 42 GLN N 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098378 restraints weight = 64129.033| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.09 r_work: 0.2887 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21978 Z= 0.120 Angle : 0.488 5.894 29853 Z= 0.259 Chirality : 0.042 0.141 3384 Planarity : 0.004 0.058 3951 Dihedral : 4.414 18.081 3024 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.37 % Allowed : 14.59 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.28 (0.16), residues: 2754 helix: 2.71 (0.15), residues: 1053 sheet: 1.64 (0.20), residues: 585 loop : 0.32 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 76 TYR 0.007 0.001 TYR Q 253 PHE 0.007 0.001 PHE K 191 TRP 0.003 0.001 TRP N 77 HIS 0.002 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21978) covalent geometry : angle 0.48847 / 0.26 (29853) hydrogen bonds : bond 0.04353 / 2.89 ( 1062) hydrogen bonds : angle 3.95344 / 2.81 ( 3078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.956 Fit side-chains REVERT: A 6 GLN cc_start: 0.8406 (mt0) cc_final: 0.7662 (mm-40) REVERT: B 6 GLN cc_start: 0.8441 (mt0) cc_final: 0.7936 (mm-40) REVERT: C 6 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: D 6 GLN cc_start: 0.8425 (mt0) cc_final: 0.7804 (mm-40) REVERT: F 6 GLN cc_start: 0.8403 (mt0) cc_final: 0.7719 (mm-40) REVERT: H 6 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: I 6 GLN cc_start: 0.8488 (mt0) cc_final: 0.7835 (mm-40) REVERT: J 11 ARG cc_start: 0.7618 (pmm150) cc_final: 0.6959 (mmp-170) REVERT: J 22 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7365 (mptt) REVERT: J 42 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8015 (tp40) REVERT: J 76 ARG cc_start: 0.8003 (mpp80) cc_final: 0.7762 (mpp-170) REVERT: J 170 GLU cc_start: 0.8373 (tt0) cc_final: 0.8124 (mt-10) REVERT: J 240 GLN cc_start: 0.8149 (tp40) cc_final: 0.7834 (tt0) REVERT: K 11 ARG cc_start: 0.7635 (pmm150) cc_final: 0.6946 (mmp-170) REVERT: K 22 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7356 (mttt) REVERT: K 245 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: L 11 ARG cc_start: 0.7653 (pmm150) cc_final: 0.7115 (mmp-170) REVERT: L 22 LYS cc_start: 0.7913 (mtpp) cc_final: 0.6948 (mmtt) REVERT: L 25 THR cc_start: 0.8898 (m) cc_final: 0.8628 (p) REVERT: L 42 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8079 (tp-100) REVERT: L 76 ARG cc_start: 0.7996 (mpp80) cc_final: 0.7745 (mpp-170) REVERT: L 217 MET cc_start: 0.9077 (tpp) cc_final: 0.8841 (tpt) REVERT: L 245 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7354 (mtp-110) REVERT: M 11 ARG cc_start: 0.7569 (pmm150) cc_final: 0.7000 (mmm160) REVERT: M 22 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7313 (mttp) REVERT: M 170 GLU cc_start: 0.8356 (tt0) cc_final: 0.8131 (mt-10) REVERT: M 245 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7290 (mtp-110) REVERT: N 11 ARG cc_start: 0.7525 (pmm150) cc_final: 0.6898 (mmp-170) REVERT: N 22 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7305 (mptt) REVERT: N 170 GLU cc_start: 0.8449 (tt0) cc_final: 0.8224 (mt-10) REVERT: N 240 GLN cc_start: 0.8085 (tp40) cc_final: 0.7876 (tt0) REVERT: N 245 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: O 11 ARG cc_start: 0.7643 (pmm150) cc_final: 0.7042 (mmp-170) REVERT: O 22 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7090 (mmtt) REVERT: O 170 GLU cc_start: 0.8402 (tt0) cc_final: 0.8188 (mt-10) REVERT: O 245 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7398 (mtp-110) REVERT: P 11 ARG cc_start: 0.7576 (pmm150) cc_final: 0.7087 (mmm160) REVERT: P 22 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7455 (mttp) REVERT: P 170 GLU cc_start: 0.8344 (tt0) cc_final: 0.8097 (mt-10) REVERT: Q 11 ARG cc_start: 0.7705 (pmm150) cc_final: 0.6988 (mmp-170) REVERT: Q 22 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7315 (mptt) REVERT: Q 170 GLU cc_start: 0.8305 (tt0) cc_final: 0.8095 (mt-10) REVERT: Q 240 GLN cc_start: 0.8147 (tp40) cc_final: 0.7772 (tt0) REVERT: Q 245 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.7418 (mtp-110) REVERT: R 11 ARG cc_start: 0.7570 (pmm150) cc_final: 0.6945 (mmp-170) REVERT: R 22 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7052 (mmtt) REVERT: R 42 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8049 (tp-100) REVERT: R 170 GLU cc_start: 0.8481 (tt0) cc_final: 0.8172 (mt-10) REVERT: R 245 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7337 (mtp-110) REVERT: R 254 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8096 (mtp180) outliers start: 32 outliers final: 23 residues processed: 287 average time/residue: 1.3765 time to fit residues: 451.7947 Evaluate side-chains 298 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [216, 193, 6, 268, 96, 226, 131, 233, 17, 200, 171] chunk 216 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN H 37 GLN K 42 GLN N 42 GLN N 241 ASN Q 108 ASN Q 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096137 restraints weight = 64678.844| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.10 r_work: 0.2852 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21978 Z= 0.183 Angle : 0.546 5.705 29853 Z= 0.292 Chirality : 0.044 0.141 3384 Planarity : 0.005 0.054 3951 Dihedral : 4.601 19.623 3024 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.54 % Allowed : 14.50 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: 2.08 (0.16), residues: 2754 helix: 2.47 (0.15), residues: 1053 sheet: 1.49 (0.20), residues: 594 loop : 0.31 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 76 TYR 0.011 0.002 TYR O 51 PHE 0.008 0.002 PHE P 191 TRP 0.004 0.001 TRP R 237 HIS 0.003 0.001 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (21978) covalent geometry : angle 0.54579 / 0.29 (29853) hydrogen bonds : bond 0.05146 / 3.42 ( 1062) hydrogen bonds : angle 4.06012 / 2.88 ( 3078) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.235 Fit side-chains REVERT: B 6 GLN cc_start: 0.8498 (mt0) cc_final: 0.7929 (mm-40) REVERT: C 6 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7743 (mm-40) REVERT: D 6 GLN cc_start: 0.8460 (mt0) cc_final: 0.7823 (mm-40) REVERT: F 6 GLN cc_start: 0.8452 (mt0) cc_final: 0.8077 (mp10) REVERT: G 6 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7712 (mm-40) REVERT: H 6 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: I 6 GLN cc_start: 0.8514 (mt0) cc_final: 0.7838 (mm-40) REVERT: J 11 ARG cc_start: 0.7674 (pmm150) cc_final: 0.6984 (mmp-170) REVERT: J 22 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7398 (mptt) REVERT: J 42 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8038 (tp40) REVERT: J 170 GLU cc_start: 0.8364 (tt0) cc_final: 0.8114 (mt-10) REVERT: J 240 GLN cc_start: 0.8163 (tp40) cc_final: 0.7852 (tt0) REVERT: K 11 ARG cc_start: 0.7672 (pmm150) cc_final: 0.6969 (mmp-170) REVERT: K 22 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7428 (mttt) REVERT: K 245 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7341 (mtp-110) REVERT: L 11 ARG cc_start: 0.7691 (pmm150) cc_final: 0.7107 (mmp-170) REVERT: L 22 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7084 (mmtt) REVERT: L 25 THR cc_start: 0.8918 (m) cc_final: 0.8705 (p) REVERT: L 42 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8148 (tp-100) REVERT: L 76 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7778 (mpp-170) REVERT: L 217 MET cc_start: 0.9100 (tpp) cc_final: 0.8871 (tpt) REVERT: L 245 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7344 (mtp-110) REVERT: M 11 ARG cc_start: 0.7547 (pmm150) cc_final: 0.6977 (mmp-170) REVERT: M 22 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7340 (mttp) REVERT: M 245 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7289 (mtp-110) REVERT: N 11 ARG cc_start: 0.7517 (pmm150) cc_final: 0.6882 (mmp-170) REVERT: N 22 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7328 (mptt) REVERT: N 170 GLU cc_start: 0.8469 (tt0) cc_final: 0.8228 (mt-10) REVERT: N 245 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.7386 (mtp-110) REVERT: O 11 ARG cc_start: 0.7666 (pmm150) cc_final: 0.7035 (mmp-170) REVERT: O 170 GLU cc_start: 0.8396 (tt0) cc_final: 0.8184 (mt-10) REVERT: O 245 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7335 (mtp-110) REVERT: P 11 ARG cc_start: 0.7582 (pmm150) cc_final: 0.7036 (mmp-170) REVERT: P 22 LYS cc_start: 0.8095 (mtpp) cc_final: 0.7486 (mttp) REVERT: P 170 GLU cc_start: 0.8356 (tt0) cc_final: 0.8116 (mt-10) REVERT: Q 11 ARG cc_start: 0.7745 (pmm150) cc_final: 0.7001 (mmp-170) REVERT: Q 22 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7409 (mptt) REVERT: Q 170 GLU cc_start: 0.8340 (tt0) cc_final: 0.8105 (mt-10) REVERT: Q 240 GLN cc_start: 0.8163 (tp40) cc_final: 0.7788 (tt0) REVERT: Q 245 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7465 (mtp-110) REVERT: R 11 ARG cc_start: 0.7580 (pmm150) cc_final: 0.6943 (mmp-170) REVERT: R 22 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7123 (mmtt) REVERT: R 42 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8057 (tp-100) REVERT: R 245 ARG cc_start: 0.7698 (mtp-110) cc_final: 0.7335 (mtp-110) REVERT: R 254 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8090 (mtp180) outliers start: 36 outliers final: 26 residues processed: 272 average time/residue: 1.4198 time to fit residues: 440.2620 Evaluate side-chains 290 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 43 ASP Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 20 SER Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 GLN Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [11, 72, 163, 74, 114, 26, 160, 246, 226, 58, 242] chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 11 ASN H 37 GLN K 42 GLN M 42 GLN N 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.097664 restraints weight = 64720.873| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.10 r_work: 0.2874 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21978 Z= 0.132 Angle : 0.502 5.187 29853 Z= 0.267 Chirality : 0.042 0.142 3384 Planarity : 0.005 0.055 3951 Dihedral : 4.471 18.741 3024 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 14.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.16), residues: 2754 helix: 2.63 (0.15), residues: 1053 sheet: 1.63 (0.20), residues: 585 loop : 0.30 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 76 TYR 0.008 0.001 TYR O 51 PHE 0.007 0.001 PHE R 191 TRP 0.003 0.001 TRP N 77 HIS 0.002 0.001 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21978) covalent geometry : angle 0.50162 / 0.27 (29853) hydrogen bonds : bond 0.04548 / 3.02 ( 1062) hydrogen bonds : angle 3.98644 / 2.83 ( 3078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13320.73 seconds wall clock time: 225 minutes 30.37 seconds (13530.37 seconds total)