Starting phenix.real_space_refine on Sat Aug 23 11:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9m_34573/08_2025/8h9m_34573.cif" } resolution = 3.0 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7930 2.51 5 N 1932 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12083 Number of models: 1 Model: "" Number of chains: 19 Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.66, per 1000 atoms: 0.22 Number of scatterers: 12083 At special positions: 0 Unit cell: (111.69, 103.66, 139.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2158 8.00 N 1932 7.00 C 7930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 548.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 5 sheets defined 76.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain '3' and resid 1 through 17 removed outlier: 3.970A pdb=" N LYS 3 7 " --> pdb=" O ASP 3 3 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE 3 8 " --> pdb=" O THR 3 4 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 3.911A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain '6' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 49 removed outlier: 4.230A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.682A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.675A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.529A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.713A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.250A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.660A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.777A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.730A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 4.010A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 138 Processing helix chain 'N' and resid 139 through 181 removed outlier: 4.184A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.794A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 13 through 19 removed outlier: 3.722A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 removed outlier: 3.666A pdb=" N ALA P 41 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 8 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 29 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.777A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 85 removed outlier: 4.261A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.300A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.996A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.250A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.225A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.267A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'N' and resid 13 through 14 957 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3714 1.34 - 1.46: 2248 1.46 - 1.57: 6247 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12324 Sorted by residual: bond pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 1.333 1.249 0.083 1.37e-02 5.33e+03 3.67e+01 bond pdb=" C ARG 7 38 " pdb=" N ASN 7 39 " ideal model delta sigma weight residual 1.332 1.413 -0.081 1.48e-02 4.57e+03 3.01e+01 bond pdb=" N ARG 1 38 " pdb=" CA ARG 1 38 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 7.32e+00 bond pdb=" N ARG 4 38 " pdb=" CA ARG 4 38 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.24e-02 6.50e+03 6.67e+00 bond pdb=" N ARG 7 38 " pdb=" CA ARG 7 38 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.27e-02 6.20e+03 6.61e+00 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 15961 1.29 - 2.57: 600 2.57 - 3.86: 92 3.86 - 5.14: 26 5.14 - 6.43: 10 Bond angle restraints: 16689 Sorted by residual: angle pdb=" O ALA 7 37 " pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 122.39 115.96 6.43 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C ARG 7 38 " pdb=" N ASN 7 39 " pdb=" CA ASN 7 39 " ideal model delta sigma weight residual 123.16 117.57 5.59 1.23e+00 6.61e-01 2.07e+01 angle pdb=" CA ALA 7 37 " pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 118.08 123.68 -5.60 1.30e+00 5.92e-01 1.86e+01 angle pdb=" N ALA 3 5 " pdb=" CA ALA 3 5 " pdb=" C ALA 3 5 " ideal model delta sigma weight residual 112.68 108.62 4.06 1.33e+00 5.65e-01 9.30e+00 angle pdb=" N THR 3 4 " pdb=" CA THR 3 4 " pdb=" C THR 3 4 " ideal model delta sigma weight residual 113.38 109.91 3.47 1.23e+00 6.61e-01 7.94e+00 ... (remaining 16684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6536 17.76 - 35.52: 609 35.52 - 53.28: 76 53.28 - 71.04: 15 71.04 - 88.80: 13 Dihedral angle restraints: 7249 sinusoidal: 2711 harmonic: 4538 Sorted by residual: dihedral pdb=" CA TYR G 193 " pdb=" C TYR G 193 " pdb=" N ASP G 194 " pdb=" CA ASP G 194 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CG ARG R 45 " pdb=" CD ARG R 45 " pdb=" NE ARG R 45 " pdb=" CZ ARG R 45 " ideal model delta sinusoidal sigma weight residual 180.00 135.12 44.88 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1294 0.034 - 0.069: 495 0.069 - 0.103: 122 0.103 - 0.137: 57 0.137 - 0.172: 3 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA ILE 3 2 " pdb=" N ILE 3 2 " pdb=" C ILE 3 2 " pdb=" CB ILE 3 2 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE G 178 " pdb=" N ILE G 178 " pdb=" C ILE G 178 " pdb=" CB ILE G 178 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CB ILE N 144 " pdb=" CA ILE N 144 " pdb=" CG1 ILE N 144 " pdb=" CG2 ILE N 144 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1968 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 38 " 0.281 9.50e-02 1.11e+02 1.26e-01 9.78e+00 pdb=" NE ARG 6 38 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG 6 38 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 38 " -0.254 9.50e-02 1.11e+02 1.14e-01 7.92e+00 pdb=" NE ARG 4 38 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG 4 38 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 38 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 38 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 38 " 0.178 9.50e-02 1.11e+02 7.96e-02 3.89e+00 pdb=" NE ARG 5 38 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 38 " 0.006 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1886 2.75 - 3.29: 12877 3.29 - 3.83: 20518 3.83 - 4.36: 24258 4.36 - 4.90: 41412 Nonbonded interactions: 100951 Sorted by model distance: nonbonded pdb=" O ILE K 50 " pdb=" OH TYR R 77 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR G 52 " pdb=" OE1 GLN G 205 " model vdw 2.220 3.040 nonbonded pdb=" O LYS N 55 " pdb=" OG1 THR N 59 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR G 214 " pdb=" O PRO H 23 " model vdw 2.250 3.040 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.251 3.120 ... (remaining 100946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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: 12.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:10.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 12324 Z= 0.226 Angle : 0.599 6.430 16689 Z= 0.365 Chirality : 0.041 0.172 1971 Planarity : 0.007 0.126 2066 Dihedral : 13.764 88.796 4353 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: -2.47 (0.19), residues: 1558 helix: -1.23 (0.14), residues: 1107 sheet: -1.80 (0.50), residues: 85 loop : -2.28 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 38 TYR 0.018 0.001 TYR G 193 PHE 0.021 0.001 PHE H 45 TRP 0.008 0.001 TRP R 28 HIS 0.003 0.001 HIS G 120 Details of bonding type rmsd covalent geometry : bond 0.00409 (12324) covalent geometry : angle 0.59899 (16689) hydrogen bonds : bond 0.12343 ( 951) hydrogen bonds : angle 6.69048 ( 2805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 75 ARG cc_start: 0.7454 (mtp85) cc_final: 0.6562 (tmt170) REVERT: H 118 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6675 (mm-30) REVERT: K 14 TYR cc_start: 0.8452 (m-80) cc_final: 0.8179 (m-80) REVERT: N 140 MET cc_start: 0.5061 (tpt) cc_final: 0.4811 (ptm) REVERT: N 181 MET cc_start: 0.7860 (tpp) cc_final: 0.7575 (tpt) REVERT: P 5 ILE cc_start: 0.7536 (mp) cc_final: 0.7031 (mp) REVERT: P 31 MET cc_start: 0.8101 (tmm) cc_final: 0.7846 (tmm) REVERT: R 85 LYS cc_start: 0.8817 (ptmt) cc_final: 0.8485 (ptmm) REVERT: R 91 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7661 (tptt) REVERT: T 36 ARG cc_start: 0.7203 (mpt-90) cc_final: 0.6393 (mpt90) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5941 time to fit residues: 168.5114 Evaluate side-chains 208 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 39 ASN 8 39 ASN G 120 HIS G 150 ASN G 163 ASN G 182 ASN H 85 ASN H 111 ASN M 159 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 90 HIS N 172 HIS R 83 HIS S 75 ASN T 6 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119486 restraints weight = 15918.238| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.18 r_work: 0.3443 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12324 Z= 0.174 Angle : 0.590 9.795 16689 Z= 0.309 Chirality : 0.042 0.175 1971 Planarity : 0.004 0.036 2066 Dihedral : 4.254 19.906 1686 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 12.13 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: -0.08 (0.21), residues: 1558 helix: 0.72 (0.15), residues: 1093 sheet: -1.42 (0.52), residues: 85 loop : -1.81 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 113 TYR 0.015 0.001 TYR G 44 PHE 0.023 0.001 PHE 3 54 TRP 0.013 0.001 TRP P 10 HIS 0.003 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00379 (12324) covalent geometry : angle 0.59007 (16689) hydrogen bonds : bond 0.05946 ( 951) hydrogen bonds : angle 4.53860 ( 2805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: 3 1 ASP cc_start: 0.6330 (t0) cc_final: 0.6105 (p0) REVERT: 5 75 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5380 (mtt) REVERT: 7 69 PHE cc_start: 0.7578 (m-80) cc_final: 0.7307 (t80) REVERT: 1 75 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5586 (mtm) REVERT: G 75 ARG cc_start: 0.7753 (mtp85) cc_final: 0.6248 (ppt170) REVERT: G 113 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7863 (ttp80) REVERT: H 132 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7491 (tm-30) REVERT: H 136 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7260 (mt-10) REVERT: I 30 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: K 13 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7276 (ttm170) REVERT: K 14 TYR cc_start: 0.8838 (m-80) cc_final: 0.8433 (m-80) REVERT: K 23 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7264 (mm110) REVERT: N 181 MET cc_start: 0.7759 (tpp) cc_final: 0.7246 (tpt) REVERT: N 203 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8628 (mm-30) REVERT: P 5 ILE cc_start: 0.7224 (mp) cc_final: 0.6979 (tp) REVERT: P 31 MET cc_start: 0.8395 (tmm) cc_final: 0.8074 (tmm) REVERT: R 85 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8125 (ptmm) REVERT: R 91 LYS cc_start: 0.7946 (tmmt) cc_final: 0.7630 (tptt) outliers start: 38 outliers final: 7 residues processed: 240 average time/residue: 0.5039 time to fit residues: 131.6878 Evaluate side-chains 220 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 3 residue 66 MET Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain Q residue 28 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 74 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN G 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120271 restraints weight = 16273.870| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.21 r_work: 0.3480 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12324 Z= 0.152 Angle : 0.537 7.620 16689 Z= 0.281 Chirality : 0.041 0.192 1971 Planarity : 0.004 0.037 2066 Dihedral : 4.095 18.146 1686 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.75 % Allowed : 15.08 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 0.84 (0.21), residues: 1558 helix: 1.27 (0.15), residues: 1119 sheet: -1.29 (0.53), residues: 86 loop : -1.15 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 134 TYR 0.015 0.001 TYR R 77 PHE 0.020 0.001 PHE 3 69 TRP 0.011 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00318 (12324) covalent geometry : angle 0.53665 (16689) hydrogen bonds : bond 0.05407 ( 951) hydrogen bonds : angle 4.30098 ( 2805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: 4 66 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7126 (mtt) REVERT: 6 75 MET cc_start: 0.8100 (mpp) cc_final: 0.7898 (mpt) REVERT: 7 69 PHE cc_start: 0.7673 (m-80) cc_final: 0.7349 (t80) REVERT: 1 75 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6071 (mpp) REVERT: G 75 ARG cc_start: 0.7795 (mtp85) cc_final: 0.6326 (ppt170) REVERT: G 110 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7588 (t0) REVERT: H 132 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7399 (tm-30) REVERT: H 136 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7372 (mt-10) REVERT: I 30 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: K 14 TYR cc_start: 0.8837 (m-80) cc_final: 0.8559 (m-80) REVERT: K 23 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7302 (mm110) REVERT: N 140 MET cc_start: 0.6769 (ptm) cc_final: 0.5620 (mmp) REVERT: N 181 MET cc_start: 0.7841 (tpp) cc_final: 0.7352 (tpt) REVERT: P 31 MET cc_start: 0.8419 (tmm) cc_final: 0.8122 (tmm) REVERT: R 19 GLU cc_start: 0.2945 (OUTLIER) cc_final: 0.2482 (tm-30) REVERT: R 53 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.5677 (tttt) REVERT: R 85 LYS cc_start: 0.8528 (ptmt) cc_final: 0.7959 (ptmm) REVERT: R 91 LYS cc_start: 0.7965 (tmmt) cc_final: 0.7633 (tptt) REVERT: T 34 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8124 (mmmm) outliers start: 47 outliers final: 14 residues processed: 246 average time/residue: 0.4773 time to fit residues: 128.5690 Evaluate side-chains 226 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 53 LYS Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 147 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119547 restraints weight = 16157.658| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.19 r_work: 0.3475 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12324 Z= 0.156 Angle : 0.534 7.486 16689 Z= 0.280 Chirality : 0.040 0.189 1971 Planarity : 0.004 0.036 2066 Dihedral : 4.044 17.139 1686 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.07 % Allowed : 17.40 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.32 (0.21), residues: 1558 helix: 1.60 (0.15), residues: 1123 sheet: -1.16 (0.55), residues: 86 loop : -0.88 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 113 TYR 0.014 0.001 TYR G 44 PHE 0.023 0.001 PHE 3 69 TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00331 (12324) covalent geometry : angle 0.53387 (16689) hydrogen bonds : bond 0.05271 ( 951) hydrogen bonds : angle 4.20768 ( 2805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: 3 4 THR cc_start: 0.8459 (p) cc_final: 0.8258 (p) REVERT: 3 39 ASN cc_start: 0.8462 (t0) cc_final: 0.8245 (t0) REVERT: 4 66 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7351 (mtp) REVERT: 5 75 MET cc_start: 0.6746 (mpp) cc_final: 0.6321 (mpt) REVERT: 6 70 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7785 (mp) REVERT: 6 75 MET cc_start: 0.8144 (mpp) cc_final: 0.7904 (mpt) REVERT: 7 66 MET cc_start: 0.8134 (mtm) cc_final: 0.7691 (mtp) REVERT: 7 69 PHE cc_start: 0.7724 (m-80) cc_final: 0.7364 (t80) REVERT: 8 7 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7368 (mtmp) REVERT: 1 75 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6439 (mtm) REVERT: G 75 ARG cc_start: 0.7813 (mtp85) cc_final: 0.6320 (ppt170) REVERT: H 132 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7389 (tm-30) REVERT: H 136 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7366 (mt-10) REVERT: K 13 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6909 (ttp-170) REVERT: K 14 TYR cc_start: 0.8844 (m-80) cc_final: 0.8155 (m-80) REVERT: K 23 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7416 (mm110) REVERT: N 140 MET cc_start: 0.6816 (ptm) cc_final: 0.5600 (mmp) REVERT: N 181 MET cc_start: 0.7757 (tpp) cc_final: 0.7285 (tpt) REVERT: P 5 ILE cc_start: 0.7206 (mp) cc_final: 0.6870 (tt) REVERT: P 31 MET cc_start: 0.8402 (tmm) cc_final: 0.8135 (tmm) REVERT: R 19 GLU cc_start: 0.2867 (OUTLIER) cc_final: 0.2326 (tm-30) REVERT: R 85 LYS cc_start: 0.8511 (ptmt) cc_final: 0.7974 (ptmm) REVERT: R 91 LYS cc_start: 0.8037 (tmmt) cc_final: 0.7684 (tptt) REVERT: T 34 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8245 (mmmm) outliers start: 51 outliers final: 16 residues processed: 240 average time/residue: 0.4951 time to fit residues: 129.9493 Evaluate side-chains 227 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 7 LYS Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.162128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122075 restraints weight = 16046.165| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.18 r_work: 0.3485 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12324 Z= 0.129 Angle : 0.511 7.408 16689 Z= 0.268 Chirality : 0.040 0.209 1971 Planarity : 0.004 0.038 2066 Dihedral : 3.960 16.830 1686 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.59 % Allowed : 18.91 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.74 (0.22), residues: 1558 helix: 1.90 (0.15), residues: 1121 sheet: -1.03 (0.56), residues: 84 loop : -0.66 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 134 TYR 0.012 0.001 TYR G 44 PHE 0.025 0.001 PHE 3 69 TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00257 (12324) covalent geometry : angle 0.51142 (16689) hydrogen bonds : bond 0.04837 ( 951) hydrogen bonds : angle 4.05829 ( 2805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: 3 39 ASN cc_start: 0.8447 (t0) cc_final: 0.8176 (t0) REVERT: 6 70 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7809 (mp) REVERT: 6 75 MET cc_start: 0.8164 (mpp) cc_final: 0.7913 (mpt) REVERT: 7 66 MET cc_start: 0.8092 (mtm) cc_final: 0.7294 (mmp) REVERT: 7 69 PHE cc_start: 0.7737 (m-80) cc_final: 0.7372 (t80) REVERT: 1 75 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6306 (mpp) REVERT: G 75 ARG cc_start: 0.7848 (mtp85) cc_final: 0.6363 (ppt170) REVERT: H 34 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: H 132 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7395 (tm-30) REVERT: H 136 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7356 (mt-10) REVERT: K 13 ARG cc_start: 0.7222 (ttm170) cc_final: 0.6895 (ttp-110) REVERT: K 14 TYR cc_start: 0.8833 (m-80) cc_final: 0.7985 (m-80) REVERT: K 23 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7404 (mm110) REVERT: N 140 MET cc_start: 0.6860 (ptm) cc_final: 0.5691 (mmp) REVERT: N 181 MET cc_start: 0.7707 (tpp) cc_final: 0.7248 (tpt) REVERT: P 5 ILE cc_start: 0.7172 (mp) cc_final: 0.6841 (tt) REVERT: P 31 MET cc_start: 0.8431 (tmm) cc_final: 0.8211 (tmm) REVERT: R 19 GLU cc_start: 0.2825 (OUTLIER) cc_final: 0.2303 (tm-30) REVERT: R 91 LYS cc_start: 0.8042 (tmmt) cc_final: 0.7662 (tptt) REVERT: T 34 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8323 (mmmm) outliers start: 45 outliers final: 15 residues processed: 241 average time/residue: 0.4844 time to fit residues: 128.0061 Evaluate side-chains 230 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 66 MET Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121439 restraints weight = 16128.881| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.22 r_work: 0.3472 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12324 Z= 0.141 Angle : 0.531 10.857 16689 Z= 0.274 Chirality : 0.040 0.194 1971 Planarity : 0.004 0.037 2066 Dihedral : 3.919 15.446 1686 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.11 % Allowed : 20.91 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 1.93 (0.22), residues: 1558 helix: 2.05 (0.15), residues: 1117 sheet: -1.03 (0.56), residues: 86 loop : -0.55 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 113 TYR 0.014 0.001 TYR R 77 PHE 0.024 0.001 PHE 3 69 TRP 0.010 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00294 (12324) covalent geometry : angle 0.53146 (16689) hydrogen bonds : bond 0.04923 ( 951) hydrogen bonds : angle 4.03382 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: 3 39 ASN cc_start: 0.8501 (t0) cc_final: 0.8149 (t0) REVERT: 6 75 MET cc_start: 0.8251 (mpp) cc_final: 0.7995 (mpt) REVERT: 7 66 MET cc_start: 0.8070 (mtm) cc_final: 0.7291 (mmp) REVERT: 7 69 PHE cc_start: 0.7747 (m-80) cc_final: 0.7383 (t80) REVERT: 1 75 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6319 (mpp) REVERT: G 36 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7891 (ptt-90) REVERT: G 75 ARG cc_start: 0.7845 (mtp85) cc_final: 0.6302 (ppt170) REVERT: H 34 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: H 132 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7284 (tm-30) REVERT: H 136 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7275 (mt-10) REVERT: K 13 ARG cc_start: 0.7183 (ttm170) cc_final: 0.6895 (ttp-110) REVERT: K 14 TYR cc_start: 0.8835 (m-80) cc_final: 0.7902 (m-10) REVERT: K 23 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7419 (mm110) REVERT: N 140 MET cc_start: 0.6808 (ptm) cc_final: 0.5686 (mmp) REVERT: N 181 MET cc_start: 0.7745 (tpp) cc_final: 0.7230 (tpp) REVERT: P 5 ILE cc_start: 0.7236 (mp) cc_final: 0.6919 (tt) REVERT: R 19 GLU cc_start: 0.2674 (OUTLIER) cc_final: 0.2116 (tm-30) REVERT: R 91 LYS cc_start: 0.8041 (tmmt) cc_final: 0.7662 (tptt) outliers start: 39 outliers final: 21 residues processed: 227 average time/residue: 0.4802 time to fit residues: 119.5432 Evaluate side-chains 228 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 112 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN G 182 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122318 restraints weight = 16031.435| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.20 r_work: 0.3479 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12324 Z= 0.138 Angle : 0.530 9.460 16689 Z= 0.274 Chirality : 0.040 0.191 1971 Planarity : 0.004 0.037 2066 Dihedral : 3.919 16.013 1686 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 21.79 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 2.01 (0.22), residues: 1558 helix: 2.07 (0.15), residues: 1130 sheet: -1.06 (0.55), residues: 89 loop : -0.44 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 113 TYR 0.013 0.001 TYR R 77 PHE 0.026 0.001 PHE 6 69 TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00287 (12324) covalent geometry : angle 0.52966 (16689) hydrogen bonds : bond 0.04866 ( 951) hydrogen bonds : angle 3.99648 ( 2805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: 3 39 ASN cc_start: 0.8517 (t0) cc_final: 0.8149 (t0) REVERT: 6 70 LEU cc_start: 0.8323 (mt) cc_final: 0.8029 (mp) REVERT: 6 75 MET cc_start: 0.8225 (mpp) cc_final: 0.7965 (mpt) REVERT: 7 66 MET cc_start: 0.8098 (mtm) cc_final: 0.7322 (mmp) REVERT: 7 69 PHE cc_start: 0.7784 (m-80) cc_final: 0.7386 (t80) REVERT: G 36 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7902 (ptt-90) REVERT: G 75 ARG cc_start: 0.7859 (mtp85) cc_final: 0.6306 (ppt170) REVERT: H 34 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: H 132 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7285 (tm-30) REVERT: H 136 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7291 (mt-10) REVERT: K 14 TYR cc_start: 0.8844 (m-80) cc_final: 0.7951 (m-10) REVERT: K 23 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7374 (mm110) REVERT: N 140 MET cc_start: 0.6892 (ptm) cc_final: 0.5780 (mmp) REVERT: N 181 MET cc_start: 0.7722 (tpp) cc_final: 0.7282 (tpp) REVERT: P 5 ILE cc_start: 0.7216 (mp) cc_final: 0.6899 (tt) REVERT: P 13 MET cc_start: 0.8787 (mmm) cc_final: 0.8565 (mmm) REVERT: R 19 GLU cc_start: 0.2473 (OUTLIER) cc_final: 0.1950 (tm-30) REVERT: R 91 LYS cc_start: 0.8054 (tmmt) cc_final: 0.7672 (tptt) outliers start: 38 outliers final: 17 residues processed: 228 average time/residue: 0.4560 time to fit residues: 114.0605 Evaluate side-chains 224 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 4 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122550 restraints weight = 15959.458| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.20 r_work: 0.3502 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12324 Z= 0.135 Angle : 0.540 13.293 16689 Z= 0.276 Chirality : 0.040 0.184 1971 Planarity : 0.004 0.037 2066 Dihedral : 3.898 16.175 1686 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.63 % Allowed : 22.51 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 2.08 (0.22), residues: 1558 helix: 2.09 (0.15), residues: 1133 sheet: -0.97 (0.55), residues: 89 loop : -0.37 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 134 TYR 0.017 0.001 TYR K 14 PHE 0.026 0.001 PHE 3 69 TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00281 (12324) covalent geometry : angle 0.53963 (16689) hydrogen bonds : bond 0.04819 ( 951) hydrogen bonds : angle 3.97818 ( 2805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: 3 39 ASN cc_start: 0.8490 (t0) cc_final: 0.8121 (t0) REVERT: 6 70 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8038 (mp) REVERT: 6 75 MET cc_start: 0.8235 (mpp) cc_final: 0.7991 (mpt) REVERT: 7 66 MET cc_start: 0.8081 (mtm) cc_final: 0.7335 (mmp) REVERT: 7 69 PHE cc_start: 0.7759 (m-80) cc_final: 0.7338 (t80) REVERT: 1 75 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6113 (mtt) REVERT: G 36 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7920 (ptt-90) REVERT: G 75 ARG cc_start: 0.7860 (mtp85) cc_final: 0.6305 (ppt170) REVERT: H 34 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: H 132 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7247 (tm-30) REVERT: H 136 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7220 (mt-10) REVERT: I 44 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7644 (mttp) REVERT: K 14 TYR cc_start: 0.8842 (m-80) cc_final: 0.8269 (m-10) REVERT: K 49 GLU cc_start: 0.8075 (tp30) cc_final: 0.7786 (tp30) REVERT: K 77 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) REVERT: N 140 MET cc_start: 0.6935 (ptm) cc_final: 0.5796 (mmp) REVERT: N 181 MET cc_start: 0.7861 (tpp) cc_final: 0.7376 (tpp) REVERT: P 5 ILE cc_start: 0.7190 (mp) cc_final: 0.6894 (tt) REVERT: R 19 GLU cc_start: 0.2688 (OUTLIER) cc_final: 0.2092 (tm-30) REVERT: R 91 LYS cc_start: 0.8088 (tmmt) cc_final: 0.7695 (tptt) REVERT: S 94 LYS cc_start: 0.7901 (ptmm) cc_final: 0.7688 (ptmm) outliers start: 33 outliers final: 18 residues processed: 227 average time/residue: 0.4277 time to fit residues: 106.0730 Evaluate side-chains 228 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122554 restraints weight = 16090.828| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.20 r_work: 0.3487 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12324 Z= 0.140 Angle : 0.553 11.735 16689 Z= 0.281 Chirality : 0.040 0.185 1971 Planarity : 0.003 0.036 2066 Dihedral : 3.902 17.577 1686 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.23 % Allowed : 23.30 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 2.07 (0.22), residues: 1558 helix: 2.04 (0.15), residues: 1142 sheet: -0.91 (0.55), residues: 89 loop : -0.30 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 134 TYR 0.015 0.001 TYR K 14 PHE 0.027 0.001 PHE 3 69 TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00295 (12324) covalent geometry : angle 0.55278 (16689) hydrogen bonds : bond 0.04860 ( 951) hydrogen bonds : angle 3.98120 ( 2805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: 3 39 ASN cc_start: 0.8545 (t0) cc_final: 0.8178 (t0) REVERT: 6 70 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (mp) REVERT: 6 75 MET cc_start: 0.8262 (mpp) cc_final: 0.8034 (mpt) REVERT: 7 66 MET cc_start: 0.8115 (mtm) cc_final: 0.7395 (mmp) REVERT: 7 69 PHE cc_start: 0.7778 (m-80) cc_final: 0.7349 (t80) REVERT: 1 75 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6273 (mtt) REVERT: G 36 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7935 (ptt-90) REVERT: G 75 ARG cc_start: 0.7871 (mtp85) cc_final: 0.6325 (ppt170) REVERT: H 34 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (ttp80) REVERT: H 132 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7252 (tm-30) REVERT: H 136 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7222 (mt-10) REVERT: I 44 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7625 (mttp) REVERT: K 13 ARG cc_start: 0.7361 (ttp-110) cc_final: 0.6948 (ttp-170) REVERT: K 14 TYR cc_start: 0.8848 (m-80) cc_final: 0.8187 (m-10) REVERT: K 23 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7271 (mm110) REVERT: K 77 PHE cc_start: 0.7926 (t80) cc_final: 0.7547 (t80) REVERT: N 140 MET cc_start: 0.6892 (ptm) cc_final: 0.5776 (mmp) REVERT: N 181 MET cc_start: 0.7866 (tpp) cc_final: 0.7372 (tpp) REVERT: N 225 ASN cc_start: 0.8745 (m-40) cc_final: 0.8520 (m-40) REVERT: P 5 ILE cc_start: 0.7191 (mp) cc_final: 0.6887 (tt) REVERT: R 19 GLU cc_start: 0.2620 (OUTLIER) cc_final: 0.2065 (tm-30) REVERT: R 91 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7714 (tptt) outliers start: 28 outliers final: 18 residues processed: 226 average time/residue: 0.4573 time to fit residues: 112.9428 Evaluate side-chains 234 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.163307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123141 restraints weight = 15940.615| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.19 r_work: 0.3500 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12324 Z= 0.135 Angle : 0.570 13.330 16689 Z= 0.286 Chirality : 0.040 0.180 1971 Planarity : 0.004 0.037 2066 Dihedral : 3.884 18.395 1686 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.15 % Allowed : 24.34 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 2.12 (0.22), residues: 1558 helix: 2.06 (0.15), residues: 1137 sheet: -0.73 (0.54), residues: 89 loop : -0.23 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 134 TYR 0.017 0.001 TYR T 32 PHE 0.028 0.001 PHE 3 69 TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00281 (12324) covalent geometry : angle 0.57044 (16689) hydrogen bonds : bond 0.04741 ( 951) hydrogen bonds : angle 3.96301 ( 2805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (mp) REVERT: 6 75 MET cc_start: 0.8227 (mpp) cc_final: 0.7958 (mpt) REVERT: 7 66 MET cc_start: 0.8060 (mtm) cc_final: 0.7378 (mmp) REVERT: 7 69 PHE cc_start: 0.7780 (m-80) cc_final: 0.7359 (t80) REVERT: 1 75 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6224 (mtt) REVERT: 2 38 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (tpp80) REVERT: G 36 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7930 (ptt-90) REVERT: G 75 ARG cc_start: 0.7837 (mtp85) cc_final: 0.6334 (ppt170) REVERT: H 34 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7739 (ttp80) REVERT: H 132 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7206 (tm-30) REVERT: H 136 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7119 (mt-10) REVERT: I 44 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7558 (mttp) REVERT: K 13 ARG cc_start: 0.7355 (ttp-110) cc_final: 0.6983 (ttp-170) REVERT: K 14 TYR cc_start: 0.8873 (m-80) cc_final: 0.8264 (m-10) REVERT: K 77 PHE cc_start: 0.7902 (t80) cc_final: 0.7479 (t80) REVERT: N 140 MET cc_start: 0.6888 (ptm) cc_final: 0.5748 (mmp) REVERT: N 181 MET cc_start: 0.7863 (tpp) cc_final: 0.7375 (tpp) REVERT: N 225 ASN cc_start: 0.8744 (m-40) cc_final: 0.8525 (m-40) REVERT: P 5 ILE cc_start: 0.7174 (mp) cc_final: 0.6880 (tt) REVERT: R 19 GLU cc_start: 0.2629 (OUTLIER) cc_final: 0.2072 (tm-30) REVERT: R 91 LYS cc_start: 0.8100 (tmmt) cc_final: 0.7740 (tptt) outliers start: 27 outliers final: 16 residues processed: 222 average time/residue: 0.4503 time to fit residues: 109.3522 Evaluate side-chains 230 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 133 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 146 optimal weight: 0.0670 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123635 restraints weight = 15898.032| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.20 r_work: 0.3503 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12324 Z= 0.134 Angle : 0.576 13.533 16689 Z= 0.289 Chirality : 0.040 0.202 1971 Planarity : 0.003 0.037 2066 Dihedral : 3.900 18.888 1686 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.92 % Allowed : 24.50 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 aren not related in a simple way. whole: 2.13 (0.22), residues: 1558 helix: 2.08 (0.15), residues: 1140 sheet: -0.73 (0.54), residues: 89 loop : -0.27 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 134 TYR 0.015 0.001 TYR R 77 PHE 0.027 0.001 PHE 3 69 TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00279 (12324) covalent geometry : angle 0.57648 (16689) hydrogen bonds : bond 0.04677 ( 951) hydrogen bonds : angle 3.93609 ( 2805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4650.83 seconds wall clock time: 79 minutes 57.26 seconds (4797.26 seconds total)