Starting phenix.real_space_refine on Wed May 14 14:03:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9m_34573/05_2025/8h9m_34573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9m_34573/05_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_34573/05_2025/8h9m_34573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9m_34573/05_2025/8h9m_34573.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9m_34573/05_2025/8h9m_34573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9m_34573/05_2025/8h9m_34573.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.28, per 1000 atoms: 0.77 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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.21 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: 3.68 Time building geometry restraints manager: 3.46 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: 11.560 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (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 TRP 0.008 0.001 TRP R 28 HIS 0.003 0.001 HIS G 120 PHE 0.021 0.001 PHE H 45 TYR 0.018 0.001 TYR G 193 ARG 0.006 0.000 ARG 3 38 Details of bonding type rmsd hydrogen bonds : bond 0.12343 ( 951) hydrogen bonds : angle 6.69048 ( 2805) covalent geometry : bond 0.00409 (12324) covalent geometry : angle 0.59899 (16689) *********************** 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 : 1.234 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: 0.6692 (mm-30) REVERT: K 14 TYR cc_start: 0.8452 (m-80) cc_final: 0.8180 (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: 0.7573 (tpt) REVERT: P 5 ILE cc_start: 0.7536 (mp) cc_final: 0.7033 (mp) REVERT: P 31 MET cc_start: 0.8101 (tmm) cc_final: 0.7847 (tmm) REVERT: R 85 LYS cc_start: 0.8817 (ptmt) cc_final: 0.8486 (ptmm) REVERT: R 91 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7662 (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: 1.2543 time to fit residues: 356.9993 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 : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.157000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120173 restraints weight = 15740.791| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.01 r_work: 0.3458 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12324 Z= 0.172 Angle : 0.588 9.868 16689 Z= 0.308 Chirality : 0.042 0.176 1971 Planarity : 0.004 0.037 2066 Dihedral : 4.260 20.136 1686 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 12.37 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1558 helix: 0.74 (0.15), residues: 1098 sheet: -1.41 (0.52), residues: 85 loop : -1.82 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.003 0.001 HIS H 66 PHE 0.024 0.001 PHE 3 54 TYR 0.016 0.001 TYR G 44 ARG 0.006 0.001 ARG G 113 Details of bonding type rmsd hydrogen bonds : bond 0.05928 ( 951) hydrogen bonds : angle 4.53171 ( 2805) covalent geometry : bond 0.00371 (12324) covalent geometry : angle 0.58763 (16689) *********************** 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 : 1.280 Fit side-chains revert: symmetry clash REVERT: 3 1 ASP cc_start: 0.6343 (t0) cc_final: 0.6122 (p0) REVERT: 5 75 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5364 (mtt) REVERT: 7 69 PHE cc_start: 0.7589 (m-80) cc_final: 0.7344 (t80) REVERT: 1 75 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.5579 (mtm) REVERT: G 75 ARG cc_start: 0.7741 (mtp85) cc_final: 0.6271 (ppt170) REVERT: G 113 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7851 (ttp80) REVERT: H 132 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7517 (tm-30) REVERT: H 136 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7230 (mt-10) REVERT: I 30 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: K 13 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7391 (ttm170) REVERT: K 14 TYR cc_start: 0.8823 (m-80) cc_final: 0.8463 (m-80) REVERT: K 23 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7289 (mm110) REVERT: N 181 MET cc_start: 0.7752 (tpp) cc_final: 0.7249 (tpt) REVERT: P 5 ILE cc_start: 0.7262 (mp) cc_final: 0.7014 (tp) REVERT: P 31 MET cc_start: 0.8400 (tmm) cc_final: 0.8074 (tmm) REVERT: Q 6 THR cc_start: 0.8979 (p) cc_final: 0.8572 (m) REVERT: R 85 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8160 (ptmm) REVERT: R 91 LYS cc_start: 0.7948 (tmmt) cc_final: 0.7639 (tptt) outliers start: 38 outliers final: 6 residues processed: 239 average time/residue: 1.1076 time to fit residues: 288.8949 Evaluate side-chains 220 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.161528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121409 restraints weight = 16184.809| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.20 r_work: 0.3483 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2109 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= 0.142 Angle : 0.529 7.716 16689 Z= 0.277 Chirality : 0.040 0.193 1971 Planarity : 0.004 0.038 2066 Dihedral : 4.075 18.110 1686 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.99 % Allowed : 14.45 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1558 helix: 1.36 (0.16), residues: 1118 sheet: -1.24 (0.53), residues: 86 loop : -1.08 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.019 0.001 PHE 3 69 TYR 0.013 0.001 TYR G 44 ARG 0.006 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 951) hydrogen bonds : angle 4.24496 ( 2805) covalent geometry : bond 0.00287 (12324) covalent geometry : angle 0.52950 (16689) *********************** 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 272 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: 4 66 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7121 (mtt) REVERT: 6 75 MET cc_start: 0.8075 (mpp) cc_final: 0.7847 (mpt) REVERT: 7 69 PHE cc_start: 0.7637 (m-80) cc_final: 0.7349 (t80) REVERT: 1 75 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6165 (mpp) REVERT: G 75 ARG cc_start: 0.7777 (mtp85) cc_final: 0.6356 (ppt170) REVERT: G 110 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7601 (t0) REVERT: H 118 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6531 (mm-30) REVERT: I 30 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: K 14 TYR cc_start: 0.8839 (m-80) cc_final: 0.8533 (m-80) REVERT: K 23 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7300 (mm110) REVERT: N 140 MET cc_start: 0.6716 (ptm) cc_final: 0.5566 (mmp) REVERT: N 181 MET cc_start: 0.7755 (tpp) cc_final: 0.7250 (tpt) REVERT: P 31 MET cc_start: 0.8409 (tmm) cc_final: 0.8106 (tmm) REVERT: R 19 GLU cc_start: 0.2915 (OUTLIER) cc_final: 0.2462 (tm-30) REVERT: R 53 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.5596 (tttt) REVERT: R 85 LYS cc_start: 0.8494 (ptmt) cc_final: 0.8014 (ptmm) REVERT: R 91 LYS cc_start: 0.7982 (tmmt) cc_final: 0.7634 (tptt) REVERT: T 34 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8180 (mmmm) outliers start: 50 outliers final: 14 residues processed: 245 average time/residue: 1.0495 time to fit residues: 281.8247 Evaluate side-chains 223 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 2 residue 42 LEU 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 I residue 30 GLU 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 Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 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 = 0.4032 r_free = 0.4032 target = 0.159984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119764 restraints weight = 16022.644| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.18 r_work: 0.3456 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12324 Z= 0.154 Angle : 0.531 7.125 16689 Z= 0.279 Chirality : 0.041 0.189 1971 Planarity : 0.004 0.037 2066 Dihedral : 4.010 16.955 1686 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.99 % Allowed : 17.64 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1558 helix: 1.68 (0.15), residues: 1116 sheet: -1.11 (0.55), residues: 86 loop : -0.87 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.024 0.001 PHE 3 69 TYR 0.013 0.001 TYR G 44 ARG 0.010 0.001 ARG G 113 Details of bonding type rmsd hydrogen bonds : bond 0.05236 ( 951) hydrogen bonds : angle 4.16461 ( 2805) covalent geometry : bond 0.00330 (12324) covalent geometry : angle 0.53120 (16689) *********************** 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 264 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: 5 75 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6301 (mpt) REVERT: 6 70 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7759 (mp) REVERT: 6 75 MET cc_start: 0.8144 (mpp) cc_final: 0.7905 (mpt) REVERT: 7 66 MET cc_start: 0.8167 (mtm) cc_final: 0.7721 (mtp) REVERT: 7 69 PHE cc_start: 0.7713 (m-80) cc_final: 0.7338 (t80) REVERT: 7 70 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7786 (mp) REVERT: 1 75 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6449 (mpp) REVERT: G 75 ARG cc_start: 0.7781 (mtp85) cc_final: 0.6276 (ppt170) REVERT: H 132 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7793 (mm-40) REVERT: K 13 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7133 (ttp-110) REVERT: K 14 TYR cc_start: 0.8840 (m-80) cc_final: 0.8146 (m-10) REVERT: K 23 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7338 (mm110) REVERT: N 140 MET cc_start: 0.6772 (ptm) cc_final: 0.5615 (mmp) REVERT: N 181 MET cc_start: 0.7760 (tpp) cc_final: 0.7305 (tpt) REVERT: P 5 ILE cc_start: 0.7258 (mp) cc_final: 0.6919 (tt) REVERT: P 31 MET cc_start: 0.8415 (tmm) cc_final: 0.8162 (tmm) REVERT: R 19 GLU cc_start: 0.2904 (OUTLIER) cc_final: 0.2341 (tm-30) REVERT: R 91 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7676 (tptt) REVERT: T 34 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8294 (mmmm) outliers start: 50 outliers final: 17 residues processed: 238 average time/residue: 1.1020 time to fit residues: 287.4966 Evaluate side-chains 223 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 71 ILE 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 87 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 15 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4044 r_free = 0.4044 target = 0.161261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121075 restraints weight = 15995.203| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.18 r_work: 0.3464 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2537 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= 0.142 Angle : 0.520 7.361 16689 Z= 0.271 Chirality : 0.040 0.207 1971 Planarity : 0.004 0.038 2066 Dihedral : 3.982 16.129 1686 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.15 % Allowed : 18.28 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1558 helix: 1.86 (0.15), residues: 1121 sheet: -0.93 (0.56), residues: 84 loop : -0.72 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.025 0.001 PHE 3 69 TYR 0.013 0.001 TYR G 44 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05019 ( 951) hydrogen bonds : angle 4.09267 ( 2805) covalent geometry : bond 0.00298 (12324) covalent geometry : angle 0.52024 (16689) *********************** 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: 52 poor density : 216 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (mp) REVERT: 6 75 MET cc_start: 0.8203 (mpp) cc_final: 0.7882 (mpt) REVERT: 7 66 MET cc_start: 0.8168 (mtm) cc_final: 0.7285 (mmp) REVERT: 7 69 PHE cc_start: 0.7691 (m-80) cc_final: 0.7345 (t80) REVERT: 1 75 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6387 (mpp) REVERT: G 75 ARG cc_start: 0.7829 (mtp85) cc_final: 0.6301 (ppt170) REVERT: H 34 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7800 (ttp80) REVERT: H 132 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7655 (mm-40) REVERT: H 136 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7260 (mt-10) REVERT: K 13 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7211 (ttp-110) REVERT: K 14 TYR cc_start: 0.8826 (m-80) cc_final: 0.8041 (m-10) REVERT: K 23 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7440 (mm110) REVERT: N 140 MET cc_start: 0.6781 (ptm) cc_final: 0.5621 (mmp) REVERT: N 181 MET cc_start: 0.7719 (tpp) cc_final: 0.7249 (tpt) REVERT: P 5 ILE cc_start: 0.7152 (mp) cc_final: 0.6832 (tt) REVERT: P 31 MET cc_start: 0.8389 (tmm) cc_final: 0.8185 (tmm) REVERT: R 19 GLU cc_start: 0.2802 (OUTLIER) cc_final: 0.2237 (tm-30) REVERT: R 53 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5753 (tttt) REVERT: R 91 LYS cc_start: 0.8056 (tmmt) cc_final: 0.7679 (tptt) REVERT: T 34 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8300 (mmmm) outliers start: 52 outliers final: 22 residues processed: 239 average time/residue: 1.0885 time to fit residues: 285.5704 Evaluate side-chains 233 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 72 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 I residue 46 VAL 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 R residue 19 GLU Chi-restraints excluded: chain R residue 53 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 6 optimal weight: 0.7980 chunk 141 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4057 r_free = 0.4057 target = 0.162676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122571 restraints weight = 16244.287| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.22 r_work: 0.3485 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12324 Z= 0.128 Angle : 0.515 10.326 16689 Z= 0.267 Chirality : 0.040 0.196 1971 Planarity : 0.004 0.038 2066 Dihedral : 3.924 15.935 1686 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.03 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1558 helix: 2.10 (0.15), residues: 1115 sheet: -0.96 (0.56), residues: 86 loop : -0.54 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.025 0.001 PHE 3 69 TYR 0.013 0.001 TYR R 77 ARG 0.005 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 951) hydrogen bonds : angle 3.99999 ( 2805) covalent geometry : bond 0.00254 (12324) covalent geometry : angle 0.51487 (16689) *********************** 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 250 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: 6 75 MET cc_start: 0.8239 (mpp) cc_final: 0.7932 (mpt) REVERT: 7 66 MET cc_start: 0.8051 (mtm) cc_final: 0.7272 (mmp) REVERT: 7 69 PHE cc_start: 0.7745 (m-80) cc_final: 0.7371 (t80) REVERT: 1 75 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6329 (mpp) REVERT: G 36 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7926 (ptt-90) REVERT: G 75 ARG cc_start: 0.7831 (mtp85) cc_final: 0.6317 (ppt170) REVERT: H 34 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7800 (ttp80) REVERT: H 132 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7433 (tm-30) REVERT: H 136 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7309 (mt-10) REVERT: K 13 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7172 (ttp-110) REVERT: K 14 TYR cc_start: 0.8836 (m-80) cc_final: 0.8011 (m-10) REVERT: K 23 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7339 (mm110) REVERT: N 140 MET cc_start: 0.6815 (ptm) cc_final: 0.5718 (mmp) REVERT: N 159 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8482 (ttm170) REVERT: N 181 MET cc_start: 0.7708 (tpp) cc_final: 0.7095 (tpp) REVERT: P 5 ILE cc_start: 0.7162 (mp) cc_final: 0.6833 (tt) REVERT: R 19 GLU cc_start: 0.2622 (OUTLIER) cc_final: 0.2097 (tm-30) REVERT: R 91 LYS cc_start: 0.8041 (tmmt) cc_final: 0.7659 (tptt) REVERT: T 34 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8347 (mmmm) outliers start: 38 outliers final: 19 residues processed: 227 average time/residue: 1.0446 time to fit residues: 260.6533 Evaluate side-chains 231 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 42 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain 2 residue 42 LEU 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 159 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 116 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 105 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.162806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122793 restraints weight = 16013.578| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.20 r_work: 0.3491 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2830 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= 0.133 Angle : 0.532 12.571 16689 Z= 0.271 Chirality : 0.040 0.190 1971 Planarity : 0.004 0.037 2066 Dihedral : 3.909 15.750 1686 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.11 % Allowed : 21.39 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1558 helix: 2.13 (0.15), residues: 1119 sheet: -0.90 (0.55), residues: 89 loop : -0.46 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.026 0.001 PHE 6 69 TYR 0.013 0.001 TYR R 77 ARG 0.004 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 951) hydrogen bonds : angle 3.97535 ( 2805) covalent geometry : bond 0.00273 (12324) covalent geometry : angle 0.53189 (16689) *********************** 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: 39 poor density : 208 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8004 (mp) REVERT: 6 75 MET cc_start: 0.8224 (mpp) cc_final: 0.7965 (mpt) REVERT: 7 66 MET cc_start: 0.8055 (mtm) cc_final: 0.7290 (mmp) REVERT: 7 69 PHE cc_start: 0.7742 (m-80) cc_final: 0.7352 (t80) REVERT: 1 75 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6277 (mpp) REVERT: G 36 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7909 (ptt-90) REVERT: G 75 ARG cc_start: 0.7841 (mtp85) cc_final: 0.6329 (ppt170) REVERT: H 34 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: H 132 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7421 (tm-30) REVERT: H 136 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7230 (mt-10) REVERT: K 13 ARG cc_start: 0.7386 (ttp-170) cc_final: 0.7088 (ttp-110) REVERT: K 14 TYR cc_start: 0.8833 (m-80) cc_final: 0.7996 (m-10) REVERT: K 23 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7368 (mm110) REVERT: K 49 GLU cc_start: 0.8104 (tp30) cc_final: 0.7785 (tp30) REVERT: N 140 MET cc_start: 0.6831 (ptm) cc_final: 0.5718 (mmp) REVERT: N 159 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8538 (ttm170) REVERT: N 181 MET cc_start: 0.7684 (tpp) cc_final: 0.7234 (tpp) REVERT: P 5 ILE cc_start: 0.7241 (mp) cc_final: 0.6915 (tt) REVERT: P 9 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8381 (pt) REVERT: R 19 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.2056 (tm-30) REVERT: R 91 LYS cc_start: 0.8057 (tmmt) cc_final: 0.7681 (tptt) outliers start: 39 outliers final: 18 residues processed: 224 average time/residue: 1.0558 time to fit residues: 259.4106 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 : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 72 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 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 N residue 159 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 91 optimal weight: 0.0270 chunk 130 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.163206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122837 restraints weight = 16181.987| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.22 r_work: 0.3495 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12324 Z= 0.130 Angle : 0.527 11.366 16689 Z= 0.270 Chirality : 0.040 0.189 1971 Planarity : 0.003 0.037 2066 Dihedral : 3.872 16.436 1686 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.47 % Allowed : 22.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.22), residues: 1558 helix: 2.15 (0.15), residues: 1130 sheet: -0.52 (0.58), residues: 84 loop : -0.46 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.027 0.001 PHE 3 69 TYR 0.013 0.001 TYR T 32 ARG 0.003 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 951) hydrogen bonds : angle 3.93330 ( 2805) covalent geometry : bond 0.00266 (12324) covalent geometry : angle 0.52694 (16689) *********************** 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 245 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8037 (mp) REVERT: 6 75 MET cc_start: 0.8231 (mpp) cc_final: 0.7975 (mpt) REVERT: 7 66 MET cc_start: 0.8065 (mtm) cc_final: 0.7325 (mmp) REVERT: 7 69 PHE cc_start: 0.7759 (m-80) cc_final: 0.7332 (t80) REVERT: G 36 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7911 (ptt-90) REVERT: G 75 ARG cc_start: 0.7873 (mtp85) cc_final: 0.6315 (ppt170) REVERT: H 34 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: H 132 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7410 (tm-30) REVERT: H 136 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7314 (mt-10) REVERT: I 44 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7632 (mttp) REVERT: K 13 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.7127 (ttp-110) REVERT: K 14 TYR cc_start: 0.8855 (m-80) cc_final: 0.8036 (m-10) REVERT: K 23 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7382 (mm110) REVERT: K 77 PHE cc_start: 0.7927 (t80) cc_final: 0.7558 (t80) REVERT: N 140 MET cc_start: 0.6924 (ptm) cc_final: 0.5777 (mmp) REVERT: N 181 MET cc_start: 0.7857 (tpp) cc_final: 0.7365 (tpp) REVERT: N 225 ASN cc_start: 0.8753 (m-40) cc_final: 0.8519 (m-40) REVERT: P 5 ILE cc_start: 0.7217 (mp) cc_final: 0.6900 (tt) REVERT: R 19 GLU cc_start: 0.2617 (OUTLIER) cc_final: 0.2030 (tm-30) REVERT: R 91 LYS cc_start: 0.8063 (tmmt) cc_final: 0.7686 (tptt) outliers start: 31 outliers final: 18 residues processed: 224 average time/residue: 1.0820 time to fit residues: 265.3197 Evaluate side-chains 226 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 72 LEU 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 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 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 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.161756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121628 restraints weight = 16044.641| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.20 r_work: 0.3473 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12324 Z= 0.152 Angle : 0.555 13.022 16689 Z= 0.283 Chirality : 0.041 0.186 1971 Planarity : 0.004 0.035 2066 Dihedral : 3.898 17.240 1686 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.71 % Allowed : 22.75 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1558 helix: 2.07 (0.15), residues: 1136 sheet: -0.67 (0.56), residues: 87 loop : -0.37 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.027 0.001 PHE 3 69 TYR 0.016 0.001 TYR R 77 ARG 0.005 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 951) hydrogen bonds : angle 3.99135 ( 2805) covalent geometry : bond 0.00332 (12324) covalent geometry : angle 0.55505 (16689) *********************** 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 249 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.5923 (mpm) REVERT: 6 70 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8088 (mp) REVERT: 6 75 MET cc_start: 0.8261 (mpp) cc_final: 0.8018 (mpt) REVERT: 7 66 MET cc_start: 0.8112 (mtm) cc_final: 0.7376 (mmp) REVERT: 7 69 PHE cc_start: 0.7754 (m-80) cc_final: 0.7333 (t80) REVERT: 1 73 PHE cc_start: 0.7456 (m-80) cc_final: 0.7238 (m-80) REVERT: 1 75 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6170 (mtt) REVERT: G 36 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7895 (ptt-90) REVERT: G 75 ARG cc_start: 0.7900 (mtp85) cc_final: 0.6346 (ppt170) REVERT: G 110 ASP cc_start: 0.7696 (t0) cc_final: 0.7458 (t0) REVERT: H 132 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7434 (tm-30) REVERT: H 136 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7413 (mt-10) REVERT: K 13 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7159 (ttp-110) REVERT: K 14 TYR cc_start: 0.8837 (m-80) cc_final: 0.8034 (m-10) REVERT: K 49 GLU cc_start: 0.8062 (tp30) cc_final: 0.7837 (tp30) REVERT: K 77 PHE cc_start: 0.7892 (t80) cc_final: 0.7499 (t80) REVERT: N 140 MET cc_start: 0.6906 (ptm) cc_final: 0.5773 (mmp) REVERT: N 181 MET cc_start: 0.7880 (tpp) cc_final: 0.7372 (tpp) REVERT: N 225 ASN cc_start: 0.8752 (m-40) cc_final: 0.8525 (m-40) REVERT: P 5 ILE cc_start: 0.7208 (mp) cc_final: 0.6904 (tt) REVERT: R 19 GLU cc_start: 0.2661 (OUTLIER) cc_final: 0.2129 (tm-30) REVERT: R 91 LYS cc_start: 0.8096 (tmmt) cc_final: 0.7722 (tptt) outliers start: 34 outliers final: 19 residues processed: 227 average time/residue: 1.0828 time to fit residues: 269.1440 Evaluate side-chains 232 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 75 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.163031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122938 restraints weight = 15919.996| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.19 r_work: 0.3490 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3087 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= 0.136 Angle : 0.551 13.166 16689 Z= 0.280 Chirality : 0.040 0.202 1971 Planarity : 0.004 0.036 2066 Dihedral : 3.890 18.922 1686 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 23.94 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.22), residues: 1558 helix: 2.12 (0.15), residues: 1136 sheet: -0.76 (0.55), residues: 89 loop : -0.31 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.027 0.001 PHE 3 69 TYR 0.015 0.001 TYR T 32 ARG 0.007 0.000 ARG G 113 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 951) hydrogen bonds : angle 3.96210 ( 2805) covalent geometry : bond 0.00287 (12324) covalent geometry : angle 0.55063 (16689) ********************** 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 242 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8024 (mp) REVERT: 6 75 MET cc_start: 0.8254 (mpp) cc_final: 0.7968 (mpt) REVERT: 7 66 MET cc_start: 0.8082 (mtm) cc_final: 0.7366 (mmp) REVERT: 7 69 PHE cc_start: 0.7751 (m-80) cc_final: 0.7330 (t80) REVERT: 1 75 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6129 (mtt) REVERT: G 36 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7919 (ptt-90) REVERT: G 75 ARG cc_start: 0.7839 (mtp85) cc_final: 0.6265 (ppt170) REVERT: G 110 ASP cc_start: 0.7699 (t0) cc_final: 0.7486 (t0) REVERT: H 34 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: H 132 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7643 (mm-40) REVERT: K 13 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.7153 (ttp-110) REVERT: K 14 TYR cc_start: 0.8843 (m-80) cc_final: 0.7989 (m-10) REVERT: K 23 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7283 (mm110) REVERT: K 49 GLU cc_start: 0.8110 (tp30) cc_final: 0.7860 (tp30) REVERT: K 77 PHE cc_start: 0.7881 (t80) cc_final: 0.7481 (t80) REVERT: N 140 MET cc_start: 0.6877 (ptm) cc_final: 0.5734 (mmp) REVERT: N 181 MET cc_start: 0.7839 (tpp) cc_final: 0.7331 (tpp) REVERT: N 225 ASN cc_start: 0.8759 (m-40) cc_final: 0.8547 (m-40) REVERT: P 5 ILE cc_start: 0.7147 (mp) cc_final: 0.6862 (tt) REVERT: R 19 GLU cc_start: 0.2734 (OUTLIER) cc_final: 0.2142 (tm-30) REVERT: R 91 LYS cc_start: 0.8114 (tmmt) cc_final: 0.7753 (tptt) outliers start: 28 outliers final: 19 residues processed: 223 average time/residue: 1.0853 time to fit residues: 265.3094 Evaluate side-chains 232 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 75 MET 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 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 Q residue 22 LEU 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 39 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.162504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122205 restraints weight = 15995.319| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.21 r_work: 0.3483 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12324 Z= 0.147 Angle : 0.577 13.985 16689 Z= 0.291 Chirality : 0.041 0.249 1971 Planarity : 0.004 0.035 2066 Dihedral : 3.920 19.669 1686 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.47 % Allowed : 23.62 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1558 helix: 2.05 (0.15), residues: 1140 sheet: -0.77 (0.55), residues: 89 loop : -0.35 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.027 0.001 PHE 3 69 TYR 0.015 0.001 TYR R 77 ARG 0.004 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 951) hydrogen bonds : angle 3.98947 ( 2805) covalent geometry : bond 0.00319 (12324) covalent geometry : angle 0.57666 (16689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10316.72 seconds wall clock time: 178 minutes 26.63 seconds (10706.63 seconds total)