Starting phenix.real_space_refine on Fri Aug 7 03:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967.map" model { file = "/net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9k_51967/08_2026/9h9k_51967_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 478 5.49 5 Mg 30 5.21 5 S 27 5.16 5 C 9970 2.51 5 N 3505 2.21 5 O 4858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18869 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "2" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "3" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1023 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Unusual residues: {' MG': 28} Classifications: {'undetermined': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.26 Number of scatterers: 18869 At special positions: 0 Unit cell: (140.238, 115.752, 168.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 478 15.00 Mg 30 11.99 O 4858 8.00 N 3505 7.00 C 9970 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 559.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 50.2% alpha, 10.4% beta 123 base pairs and 221 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix removed outlier: 3.667A pdb=" N LYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.606A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.468A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 149 removed outlier: 4.068A pdb=" N SER B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 5.841A pdb=" N ASP B 153 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.741A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.223A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 226 Processing helix chain 'C' and resid 6 through 13 removed outlier: 4.349A pdb=" N GLY C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.440A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.633A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 removed outlier: 4.130A pdb=" N GLU C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'C' and resid 157 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 52 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.648A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 4.298A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 4.112A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN I 50 " --> pdb=" O MET I 46 " (cutoff:3.500A) Proline residue: I 51 - end of helix removed outlier: 3.558A pdb=" N VAL I 55 " --> pdb=" O PRO I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.714A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'M' and resid 14 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.611A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 82 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 33 removed outlier: 3.506A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 49 removed outlier: 3.634A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.794A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 71 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.693A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 58 removed outlier: 6.822A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 164 through 170 Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 74 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12 removed outlier: 3.501A pdb=" N ARG I 12 " --> pdb=" O SER I 15 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 15 through 23 current: chain 'I' and resid 33 through 34 Processing sheet with id=AA7, first strand: chain 'J' and resid 5 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 5 through 12 current: chain 'J' and resid 63 through 77 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'N' and resid 73 through 74 Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.071A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 221 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2236 1.32 - 1.44: 7994 1.44 - 1.57: 8948 1.57 - 1.69: 953 1.69 - 1.81: 51 Bond restraints: 20182 Sorted by residual: bond pdb=" N9 A 11163 " pdb=" C4 A 11163 " ideal model delta sigma weight residual 1.374 1.344 0.030 6.00e-03 2.78e+04 2.58e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.469 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N9 G 11104 " pdb=" C4 G 11104 " ideal model delta sigma weight residual 1.375 1.342 0.033 8.00e-03 1.56e+04 1.75e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.465 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" N9 A 11101 " pdb=" C8 A 11101 " ideal model delta sigma weight residual 1.373 1.343 0.030 8.00e-03 1.56e+04 1.41e+01 ... (remaining 20177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28894 2.56 - 5.11: 603 5.11 - 7.67: 48 7.67 - 10.22: 18 10.22 - 12.78: 7 Bond angle restraints: 29570 Sorted by residual: angle pdb=" N6 A 11101 " pdb=" C6 A 11101 " pdb=" N1 A 11101 " ideal model delta sigma weight residual 118.60 111.14 7.46 6.00e-01 2.78e+00 1.54e+02 angle pdb=" N LYS G 114 " pdb=" CA LYS G 114 " pdb=" C LYS G 114 " ideal model delta sigma weight residual 111.07 123.85 -12.78 1.07e+00 8.73e-01 1.43e+02 angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 110.62 121.00 -10.38 1.02e+00 9.61e-01 1.04e+02 angle pdb=" C8 G 11104 " pdb=" N9 G 11104 " pdb=" C4 G 11104 " ideal model delta sigma weight residual 106.40 109.55 -3.15 4.00e-01 6.25e+00 6.18e+01 angle pdb=" N HIS J 56 " pdb=" CA HIS J 56 " pdb=" C HIS J 56 " ideal model delta sigma weight residual 108.00 118.17 -10.17 1.48e+00 4.57e-01 4.72e+01 ... (remaining 29565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 11599 34.93 - 69.86: 1149 69.86 - 104.80: 141 104.80 - 139.73: 7 139.73 - 174.66: 3 Dihedral angle restraints: 12899 sinusoidal: 9780 harmonic: 3119 Sorted by residual: dihedral pdb=" C4' A 11101 " pdb=" C3' A 11101 " pdb=" C2' A 11101 " pdb=" C1' A 11101 " ideal model delta sinusoidal sigma weight residual -35.00 30.03 -65.03 1 8.00e+00 1.56e-02 8.67e+01 dihedral pdb=" C5' A 11101 " pdb=" C4' A 11101 " pdb=" C3' A 11101 " pdb=" O3' A 11101 " ideal model delta sinusoidal sigma weight residual 147.00 83.23 63.77 1 8.00e+00 1.56e-02 8.37e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 46.66 -174.66 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 12896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 3697 0.336 - 0.672: 2 0.672 - 1.009: 0 1.009 - 1.345: 0 1.345 - 1.681: 1 Chirality restraints: 3700 Sorted by residual: chirality pdb=" CG LEU S 15 " pdb=" CB LEU S 15 " pdb=" CD1 LEU S 15 " pdb=" CD2 LEU S 15 " both_signs ideal model delta sigma weight residual False -2.59 -0.91 -1.68 2.00e-01 2.50e+01 7.07e+01 chirality pdb=" P A 2 15 " pdb=" OP1 A 2 15 " pdb=" OP2 A 2 15 " pdb=" O5' A 2 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" P C 1 931 " pdb=" OP1 C 1 931 " pdb=" OP2 C 1 931 " pdb=" O5' C 1 931 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 3697 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.024 2.00e-02 2.50e+03 4.63e-02 6.96e+01 pdb=" N9 2MG 1 966 " -0.004 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.022 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.031 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.009 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.006 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.024 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.022 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.043 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.069 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.041 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.016 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.031 2.00e-02 2.50e+03 4.36e-02 6.17e+01 pdb=" N9 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.019 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.029 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.007 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.005 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.023 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.022 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.040 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.065 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.035 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.013 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 129 " 0.031 2.00e-02 2.50e+03 6.17e-02 3.81e+01 pdb=" C LYS I 129 " -0.107 2.00e-02 2.50e+03 pdb=" O LYS I 129 " 0.040 2.00e-02 2.50e+03 pdb=" N ARG I 130 " 0.036 2.00e-02 2.50e+03 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 255 2.48 - 3.08: 15242 3.08 - 3.69: 36835 3.69 - 4.29: 51201 4.29 - 4.90: 71323 Nonbonded interactions: 174856 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb="ZN ZN B 301 " model vdw 1.872 2.230 nonbonded pdb=" O2' C 11226 " pdb=" O THR M 102 " model vdw 1.885 3.040 nonbonded pdb=" O2' A 11067 " pdb=" O2' A 11093 " model vdw 1.894 3.040 nonbonded pdb=" OD2 ASP B 188 " pdb="ZN ZN B 301 " model vdw 1.908 2.230 nonbonded pdb=" O2' C 11237 " pdb=" O4' U 11335 " model vdw 1.919 3.040 ... (remaining 174851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 20184 Z= 0.559 Angle : 0.971 12.776 29570 Z= 0.802 Chirality : 0.062 1.681 3700 Planarity : 0.007 0.098 1992 Dihedral : 22.145 174.660 10881 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.33 % Allowed : 7.71 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1075 helix: -0.78 (0.22), residues: 475 sheet: -0.55 (0.40), residues: 152 loop : -1.32 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 41 TYR 0.015 0.002 TYR I 38 PHE 0.023 0.002 PHE B 90 TRP 0.013 0.002 TRP C 167 HIS 0.011 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.55 (20182) covalent geometry : angle 0.97123 / 0.80 (29570) hydrogen bonds : bond 0.24963 / 26.61 ( 700) hydrogen bonds : angle 9.12110 / 11.24 ( 1598) metal coordination : bond 0.17457 / 8.73 ( 1) Misc. bond : bond 0.14563 / 7.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 PHE cc_start: 0.6918 (m-80) cc_final: 0.6412 (m-80) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.2178 time to fit residues: 37.0684 Evaluate side-chains 73 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 90 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN B 89 GLN B 103 ASN C 25 ASN G 9 GLN J 58 ASN M 8 ASN M 14 HIS S 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.057424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.050586 restraints weight = 230804.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.051240 restraints weight = 163836.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.051699 restraints weight = 128999.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.052042 restraints weight = 108014.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.052232 restraints weight = 95465.876| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20184 Z= 0.189 Angle : 0.728 11.735 29570 Z= 0.399 Chirality : 0.046 0.345 3700 Planarity : 0.006 0.083 1992 Dihedral : 22.739 175.888 8694 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.32 % Allowed : 11.78 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1075 helix: 0.25 (0.22), residues: 483 sheet: -0.60 (0.36), residues: 175 loop : -0.84 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 49 TYR 0.017 0.003 TYR C 193 PHE 0.020 0.003 PHE S 74 TRP 0.019 0.002 TRP C 167 HIS 0.013 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (20182) covalent geometry : angle 0.72844 / 0.40 (29570) hydrogen bonds : bond 0.10114 / 10.42 ( 700) hydrogen bonds : angle 4.76976 / 5.98 ( 1598) metal coordination : bond 0.01106 / 0.55 ( 1) Misc. bond : bond 0.00550 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8567 (mtp) cc_final: 0.8184 (mpp) REVERT: B 88 ASP cc_start: 0.9139 (t0) cc_final: 0.8816 (m-30) REVERT: B 100 MET cc_start: 0.8844 (mtp) cc_final: 0.8224 (mpp) REVERT: C 29 PHE cc_start: 0.5372 (OUTLIER) cc_final: 0.3680 (t80) REVERT: G 31 MET cc_start: 0.6864 (ttp) cc_final: 0.6341 (mtp) REVERT: M 75 MET cc_start: 0.8728 (mmm) cc_final: 0.8472 (mmm) REVERT: S 81 ARG cc_start: 0.7714 (tmm160) cc_final: 0.7471 (tmm160) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1978 time to fit residues: 26.9502 Evaluate side-chains 78 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 86 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 40.0000 chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 31 optimal weight: 40.0000 chunk 141 optimal weight: 0.0020 chunk 85 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.056855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.050145 restraints weight = 237435.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.050825 restraints weight = 165327.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.051444 restraints weight = 127204.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.051649 restraints weight = 104325.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.051945 restraints weight = 93699.704| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20184 Z= 0.165 Angle : 0.598 9.188 29570 Z= 0.341 Chirality : 0.039 0.465 3700 Planarity : 0.005 0.055 1992 Dihedral : 22.506 176.767 8692 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 13.55 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1075 helix: 0.65 (0.23), residues: 484 sheet: -0.31 (0.38), residues: 158 loop : -0.70 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 5 TYR 0.023 0.002 TYR C 168 PHE 0.017 0.002 PHE S 74 TRP 0.017 0.002 TRP C 167 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (20182) covalent geometry : angle 0.59779 / 0.34 (29570) hydrogen bonds : bond 0.08391 / 8.78 ( 700) hydrogen bonds : angle 4.48428 / 5.59 ( 1598) metal coordination : bond 0.00140 / 0.07 ( 1) Misc. bond : bond 0.00319 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8354 (ptp) REVERT: B 88 ASP cc_start: 0.9150 (t0) cc_final: 0.8883 (m-30) REVERT: B 109 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8922 (mp10) REVERT: C 29 PHE cc_start: 0.5008 (OUTLIER) cc_final: 0.3406 (t80) REVERT: M 75 MET cc_start: 0.8733 (mmm) cc_final: 0.8434 (mmm) REVERT: S 32 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7670 (ttt-90) REVERT: S 44 MET cc_start: 0.8779 (ppp) cc_final: 0.8411 (ppp) outliers start: 22 outliers final: 15 residues processed: 93 average time/residue: 0.1784 time to fit residues: 24.3712 Evaluate side-chains 84 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 18 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 38 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 40.0000 chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN G 9 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.054340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.047707 restraints weight = 240664.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.048438 restraints weight = 166104.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.048825 restraints weight = 127664.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.049058 restraints weight = 108549.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.049355 restraints weight = 98527.157| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20184 Z= 0.238 Angle : 0.705 9.025 29570 Z= 0.391 Chirality : 0.044 0.237 3700 Planarity : 0.006 0.054 1992 Dihedral : 22.680 177.073 8692 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.96 % Allowed : 15.20 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1075 helix: 0.37 (0.23), residues: 482 sheet: -0.56 (0.39), residues: 160 loop : -0.98 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 81 TYR 0.025 0.003 TYR I 38 PHE 0.022 0.003 PHE G 26 TRP 0.017 0.002 TRP B 23 HIS 0.009 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.24 (20182) covalent geometry : angle 0.70453 / 0.39 (29570) hydrogen bonds : bond 0.09298 / 9.86 ( 700) hydrogen bonds : angle 4.62692 / 5.76 ( 1598) metal coordination : bond 0.00269 / 0.13 ( 1) Misc. bond : bond 0.00081 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8830 (mtp) cc_final: 0.8612 (ptp) REVERT: B 109 GLN cc_start: 0.9293 (mm-40) cc_final: 0.8934 (mp10) REVERT: B 161 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 29 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: M 75 MET cc_start: 0.8716 (mmm) cc_final: 0.8381 (mmm) REVERT: N 92 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7800 (tp30) REVERT: S 44 MET cc_start: 0.8595 (ppp) cc_final: 0.8259 (ppp) outliers start: 36 outliers final: 20 residues processed: 103 average time/residue: 0.1695 time to fit residues: 25.4403 Evaluate side-chains 85 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 13 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 9 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.054462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.047603 restraints weight = 235288.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.048254 restraints weight = 167608.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.048686 restraints weight = 132699.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.049012 restraints weight = 112220.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.049147 restraints weight = 98606.187| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20184 Z= 0.183 Angle : 0.620 14.745 29570 Z= 0.350 Chirality : 0.040 0.227 3700 Planarity : 0.005 0.079 1992 Dihedral : 22.685 176.658 8692 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.52 % Allowed : 16.74 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1075 helix: 0.51 (0.23), residues: 483 sheet: -0.38 (0.41), residues: 145 loop : -0.92 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 164 TYR 0.024 0.003 TYR C 168 PHE 0.012 0.002 PHE B 90 TRP 0.053 0.003 TRP B 23 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (20182) covalent geometry : angle 0.62005 / 0.35 (29570) hydrogen bonds : bond 0.08381 / 8.84 ( 700) hydrogen bonds : angle 4.51469 / 5.61 ( 1598) metal coordination : bond 0.00291 / 0.15 ( 1) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8770 (mtp) cc_final: 0.8391 (ptp) REVERT: B 88 ASP cc_start: 0.9146 (t0) cc_final: 0.8840 (m-30) REVERT: B 161 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 29 PHE cc_start: 0.5046 (OUTLIER) cc_final: 0.4433 (m-80) REVERT: M 75 MET cc_start: 0.8717 (mmm) cc_final: 0.8397 (mmm) REVERT: N 89 MET cc_start: 0.8483 (mmm) cc_final: 0.8254 (mmm) REVERT: N 92 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7593 (tp30) REVERT: S 44 MET cc_start: 0.8753 (ppp) cc_final: 0.8500 (ppp) outliers start: 32 outliers final: 22 residues processed: 93 average time/residue: 0.1597 time to fit residues: 22.1303 Evaluate side-chains 86 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 40.0000 chunk 54 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.053122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.046554 restraints weight = 241184.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.047149 restraints weight = 169207.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.047578 restraints weight = 133244.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.047923 restraints weight = 112610.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.048134 restraints weight = 99384.763| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20184 Z= 0.221 Angle : 0.664 9.010 29570 Z= 0.374 Chirality : 0.043 0.258 3700 Planarity : 0.006 0.066 1992 Dihedral : 22.788 176.616 8692 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.30 % Allowed : 18.17 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1075 helix: 0.26 (0.23), residues: 485 sheet: -0.45 (0.41), residues: 146 loop : -1.15 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 7 TYR 0.027 0.003 TYR C 193 PHE 0.016 0.002 PHE C 37 TRP 0.024 0.002 TRP B 23 HIS 0.007 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.22 (20182) covalent geometry : angle 0.66409 / 0.37 (29570) hydrogen bonds : bond 0.08976 / 9.59 ( 700) hydrogen bonds : angle 4.58024 / 5.75 ( 1598) metal coordination : bond 0.00240 / 0.12 ( 1) Misc. bond : bond 0.00109 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8965 (mtp) cc_final: 0.8751 (ptp) REVERT: B 161 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 29 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.4363 (m-80) REVERT: J 88 MET cc_start: 0.7035 (ptp) cc_final: 0.6728 (ptp) REVERT: M 75 MET cc_start: 0.8738 (mmm) cc_final: 0.8415 (mmm) REVERT: N 92 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7609 (tp30) REVERT: S 32 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7574 (ttt-90) REVERT: S 44 MET cc_start: 0.8772 (ppp) cc_final: 0.8502 (ppp) outliers start: 39 outliers final: 26 residues processed: 96 average time/residue: 0.1595 time to fit residues: 22.6931 Evaluate side-chains 87 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 5 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 117 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 9 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.053869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.047425 restraints weight = 244295.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.047993 restraints weight = 169882.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.048460 restraints weight = 132852.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.048841 restraints weight = 109914.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.049034 restraints weight = 95796.925| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20184 Z= 0.153 Angle : 0.583 14.583 29570 Z= 0.331 Chirality : 0.038 0.236 3700 Planarity : 0.005 0.061 1992 Dihedral : 22.737 176.449 8692 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.41 % Allowed : 20.59 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1075 helix: 0.48 (0.23), residues: 487 sheet: -0.31 (0.41), residues: 146 loop : -0.99 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 81 TYR 0.025 0.003 TYR C 42 PHE 0.015 0.002 PHE C 37 TRP 0.026 0.002 TRP B 23 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20182) covalent geometry : angle 0.58326 / 0.33 (29570) hydrogen bonds : bond 0.07799 / 8.25 ( 700) hydrogen bonds : angle 4.43125 / 5.56 ( 1598) metal coordination : bond 0.00203 / 0.10 ( 1) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8926 (mtp) cc_final: 0.8682 (ptp) REVERT: B 100 MET cc_start: 0.8656 (mtp) cc_final: 0.8113 (mpp) REVERT: B 161 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 187 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7600 (t) REVERT: C 29 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4373 (m-80) REVERT: C 164 ARG cc_start: 0.8662 (ppt170) cc_final: 0.8186 (ppt170) REVERT: M 75 MET cc_start: 0.8749 (mmm) cc_final: 0.8426 (mmm) REVERT: N 92 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7213 (tp30) REVERT: S 32 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7659 (ttt-90) REVERT: S 44 MET cc_start: 0.8907 (ppp) cc_final: 0.8665 (ppp) REVERT: S 66 MET cc_start: 0.7861 (mmm) cc_final: 0.7130 (mmm) outliers start: 31 outliers final: 24 residues processed: 88 average time/residue: 0.1759 time to fit residues: 22.3863 Evaluate side-chains 88 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 37 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 135 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 26 optimal weight: 30.0000 chunk 133 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.053232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.046597 restraints weight = 245697.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.047415 restraints weight = 172300.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.047863 restraints weight = 132991.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.048195 restraints weight = 111422.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.048400 restraints weight = 99105.621| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20184 Z= 0.179 Angle : 0.613 14.479 29570 Z= 0.342 Chirality : 0.039 0.232 3700 Planarity : 0.005 0.061 1992 Dihedral : 22.736 176.559 8692 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.41 % Allowed : 21.92 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.25), residues: 1075 helix: 0.44 (0.23), residues: 483 sheet: -0.49 (0.40), residues: 147 loop : -1.04 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 81 TYR 0.020 0.003 TYR I 38 PHE 0.018 0.002 PHE B 90 TRP 0.019 0.002 TRP B 23 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (20182) covalent geometry : angle 0.61288 / 0.34 (29570) hydrogen bonds : bond 0.08180 / 8.71 ( 700) hydrogen bonds : angle 4.49062 / 5.56 ( 1598) metal coordination : bond 0.00207 / 0.10 ( 1) Misc. bond : bond 0.00131 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.9010 (mtp) cc_final: 0.8791 (ptp) REVERT: B 100 MET cc_start: 0.8622 (mtp) cc_final: 0.8126 (mpp) REVERT: B 161 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8228 (tp) REVERT: C 29 PHE cc_start: 0.5195 (OUTLIER) cc_final: 0.4487 (m-80) REVERT: C 164 ARG cc_start: 0.8677 (ppt170) cc_final: 0.8229 (ppt170) REVERT: G 31 MET cc_start: 0.4248 (mtp) cc_final: 0.3425 (ttt) REVERT: M 75 MET cc_start: 0.8762 (mmm) cc_final: 0.8435 (mmm) REVERT: N 92 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7262 (tp30) REVERT: S 32 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7645 (ttt-90) REVERT: S 44 MET cc_start: 0.8865 (ppp) cc_final: 0.8606 (ppp) REVERT: S 66 MET cc_start: 0.7959 (mmm) cc_final: 0.7295 (mmm) outliers start: 31 outliers final: 25 residues processed: 86 average time/residue: 0.1801 time to fit residues: 22.8883 Evaluate side-chains 85 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 37 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 5 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 136 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.051924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.045265 restraints weight = 243716.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.045891 restraints weight = 176923.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.046324 restraints weight = 137756.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.046691 restraints weight = 116130.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.046877 restraints weight = 101984.258| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 20184 Z= 0.226 Angle : 0.687 13.998 29570 Z= 0.382 Chirality : 0.043 0.258 3700 Planarity : 0.006 0.075 1992 Dihedral : 22.932 176.046 8692 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.52 % Allowed : 22.69 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1075 helix: 0.16 (0.23), residues: 483 sheet: -0.61 (0.40), residues: 142 loop : -1.35 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG S 81 TYR 0.022 0.003 TYR I 38 PHE 0.015 0.002 PHE B 90 TRP 0.024 0.002 TRP B 23 HIS 0.006 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (20182) covalent geometry : angle 0.68664 / 0.38 (29570) hydrogen bonds : bond 0.09164 / 9.85 ( 700) hydrogen bonds : angle 4.64686 / 5.78 ( 1598) metal coordination : bond 0.11504 / 5.75 ( 1) Misc. bond : bond 0.00168 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.8994 (mtp) cc_final: 0.8789 (ptp) REVERT: B 161 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8279 (tp) REVERT: C 29 PHE cc_start: 0.5219 (OUTLIER) cc_final: 0.4499 (m-80) REVERT: G 31 MET cc_start: 0.5056 (mtp) cc_final: 0.4458 (ttt) REVERT: I 52 LEU cc_start: 0.9030 (mm) cc_final: 0.8815 (mt) REVERT: M 75 MET cc_start: 0.8798 (mmm) cc_final: 0.8487 (mmm) REVERT: N 92 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7389 (tp30) REVERT: S 32 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7647 (ttt-90) REVERT: S 44 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8649 (ppp) outliers start: 32 outliers final: 26 residues processed: 83 average time/residue: 0.1618 time to fit residues: 19.9772 Evaluate side-chains 85 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain S residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 40.0000 chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 31 optimal weight: 40.0000 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 52 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.053237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.046597 restraints weight = 239924.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047254 restraints weight = 168785.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.047686 restraints weight = 130708.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.047933 restraints weight = 109506.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.048237 restraints weight = 98630.638| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20184 Z= 0.135 Angle : 0.581 15.974 29570 Z= 0.327 Chirality : 0.037 0.237 3700 Planarity : 0.005 0.052 1992 Dihedral : 22.785 176.222 8692 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 23.35 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.25), residues: 1075 helix: 0.43 (0.23), residues: 486 sheet: -0.52 (0.41), residues: 138 loop : -1.05 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 81 TYR 0.020 0.003 TYR C 168 PHE 0.028 0.002 PHE B 90 TRP 0.030 0.002 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (20182) covalent geometry : angle 0.58110 / 0.33 (29570) hydrogen bonds : bond 0.07631 / 8.07 ( 700) hydrogen bonds : angle 4.38732 / 5.43 ( 1598) metal coordination : bond 0.00131 / 0.07 ( 1) Misc. bond : bond 0.00157 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8397 (tp) REVERT: C 29 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4358 (m-80) REVERT: C 164 ARG cc_start: 0.8685 (ppt170) cc_final: 0.8269 (ppt170) REVERT: G 31 MET cc_start: 0.4282 (mtp) cc_final: 0.3385 (ttt) REVERT: J 88 MET cc_start: 0.6775 (ppp) cc_final: 0.6531 (pmm) REVERT: M 75 MET cc_start: 0.8818 (mmm) cc_final: 0.8519 (mmm) REVERT: N 92 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7299 (tp30) REVERT: S 32 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7568 (ttt-90) REVERT: S 44 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8650 (ppp) outliers start: 29 outliers final: 21 residues processed: 81 average time/residue: 0.1794 time to fit residues: 21.1694 Evaluate side-chains 82 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain S residue 44 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 64 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.053512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.046767 restraints weight = 240748.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.047506 restraints weight = 169070.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.047933 restraints weight = 131530.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.048341 restraints weight = 110901.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.048529 restraints weight = 96576.653| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20184 Z= 0.132 Angle : 0.561 10.629 29570 Z= 0.317 Chirality : 0.036 0.242 3700 Planarity : 0.005 0.059 1992 Dihedral : 22.671 176.571 8692 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.64 % Allowed : 24.12 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1075 helix: 0.59 (0.23), residues: 486 sheet: -0.33 (0.41), residues: 144 loop : -0.99 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 81 TYR 0.018 0.002 TYR C 42 PHE 0.020 0.002 PHE S 74 TRP 0.030 0.002 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (20182) covalent geometry : angle 0.56145 / 0.32 (29570) hydrogen bonds : bond 0.07386 / 7.82 ( 700) hydrogen bonds : angle 4.28428 / 5.37 ( 1598) metal coordination : bond 0.00082 / 0.04 ( 1) Misc. bond : bond 0.00169 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.81 seconds wall clock time: 60 minutes 46.93 seconds (3646.93 seconds total)