Starting phenix.real_space_refine on Sat Jul 4 06:47:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9k_51967/07_2026/9h9k_51967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9k_51967/07_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_51967/07_2026/9h9k_51967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9k_51967/07_2026/9h9k_51967.map" model { file = "/net/cci-nas-00/data/ceres_data/9h9k_51967/07_2026/9h9k_51967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9k_51967/07_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-dev-6108/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: 4.65, per 1000 atoms: 0.25 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: 1.87 Conformation dependent library (CDL) restraints added in 479.5 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: 2.86 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: 4.57 Time building geometry restraints manager: 2.41 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: 28978 2.56 - 5.11: 520 5.11 - 7.67: 47 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=" P A 11101 " pdb=" O5' A 11101 " pdb=" C5' A 11101 " ideal model delta sigma weight residual 120.90 131.60 -10.70 1.50e+00 4.44e-01 5.09e+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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- 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= 0.527 Angle : 0.894 12.776 29570 Z= 0.717 Chirality : 0.056 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 0.00635 / 0.52 (20182) covalent geometry : angle 0.89435 / 0.72 (29570) hydrogen bonds : bond 0.24963 / 24.26 ( 700) hydrogen bonds : angle 9.12110 / 10.75 ( 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 : 0.482 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: B 69 PHE cc_start: 0.6918 (m-80) cc_final: 0.6412 (m-80) REVERT: C 195 VAL cc_start: 0.5393 (t) cc_final: 0.5157 (t) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 0.2272 time to fit residues: 38.3607 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 : 0.470 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.9386 ------------------------------------------------------------------------------- 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 ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.057156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.050362 restraints weight = 231869.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.050998 restraints weight = 162722.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.051439 restraints weight = 129515.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.051755 restraints weight = 108724.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.051936 restraints weight = 95635.316| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 20184 Z= 0.200 Angle : 0.640 8.058 29570 Z= 0.375 Chirality : 0.041 0.317 3700 Planarity : 0.005 0.055 1992 Dihedral : 22.955 175.543 8694 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 12.00 % 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: -0.66 (0.24), residues: 1075 helix: 0.16 (0.22), residues: 483 sheet: -0.65 (0.36), residues: 175 loop : -0.90 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 81 TYR 0.016 0.002 TYR I 38 PHE 0.017 0.003 PHE S 74 TRP 0.017 0.002 TRP C 167 HIS 0.014 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.20 (20182) covalent geometry : angle 0.64050 / 0.37 (29570) hydrogen bonds : bond 0.10981 / 10.37 ( 700) hydrogen bonds : angle 4.95239 / 5.98 ( 1598) metal coordination : bond 0.00228 / 0.11 ( 1) Misc. bond : bond 0.00033 / 0.02 ( 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 94 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.408 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 88 ASP cc_start: 0.9131 (t0) cc_final: 0.8757 (m-30) REVERT: B 109 GLN cc_start: 0.8973 (mp10) cc_final: 0.8735 (mp10) REVERT: C 29 PHE cc_start: 0.5140 (OUTLIER) cc_final: 0.4719 (m-80) REVERT: M 75 MET cc_start: 0.8637 (mmm) cc_final: 0.8388 (mmm) REVERT: S 81 ARG cc_start: 0.7631 (tmm160) cc_final: 0.7429 (tmm160) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.1993 time to fit residues: 25.0554 Evaluate side-chains 73 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 62 PHE 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: 30.0000 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 141 optimal weight: 0.0370 chunk 85 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN B 109 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3820 r_free = 0.3820 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.049004 restraints weight = 234792.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.049692 restraints weight = 165857.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.050282 restraints weight = 130670.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.050501 restraints weight = 108396.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.050643 restraints weight = 96420.003| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20184 Z= 0.203 Angle : 0.634 9.664 29570 Z= 0.367 Chirality : 0.041 0.271 3700 Planarity : 0.006 0.054 1992 Dihedral : 22.768 176.682 8692 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.75 % Allowed : 12.89 % Favored : 84.36 % 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: 0.54 (0.23), residues: 482 sheet: -0.57 (0.38), residues: 156 loop : -0.81 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 164 TYR 0.022 0.003 TYR C 168 PHE 0.031 0.003 PHE S 74 TRP 0.022 0.002 TRP C 167 HIS 0.014 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (20182) covalent geometry : angle 0.63374 / 0.37 (29570) hydrogen bonds : bond 0.08613 / 8.13 ( 700) hydrogen bonds : angle 4.53495 / 5.46 ( 1598) metal coordination : bond 0.00036 / 0.02 ( 1) Misc. bond : bond 0.00228 / 0.11 ( 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 102 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.509 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 88 ASP cc_start: 0.9182 (t0) cc_final: 0.8903 (m-30) REVERT: B 109 GLN cc_start: 0.9049 (mp-120) cc_final: 0.8787 (mp10) REVERT: C 29 PHE cc_start: 0.5072 (OUTLIER) cc_final: 0.4755 (m-80) REVERT: M 75 MET cc_start: 0.8733 (mmm) cc_final: 0.8430 (mmm) REVERT: S 32 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7678 (ptt-90) outliers start: 25 outliers final: 16 residues processed: 97 average time/residue: 0.1584 time to fit residues: 22.7323 Evaluate side-chains 83 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 THR 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 C residue 201 TRP 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 J residue 57 VAL 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 38 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 38 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN G 9 GLN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.053329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.046533 restraints weight = 239508.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.047139 restraints weight = 169322.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.047565 restraints weight = 132731.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.047874 restraints weight = 112642.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.048264 restraints weight = 99666.068| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20184 Z= 0.277 Angle : 0.732 10.678 29570 Z= 0.419 Chirality : 0.044 0.261 3700 Planarity : 0.007 0.091 1992 Dihedral : 22.988 176.661 8692 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.30 % Allowed : 14.65 % Favored : 81.06 % 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: -0.97 (0.24), residues: 1075 helix: 0.08 (0.22), residues: 484 sheet: -0.61 (0.38), residues: 156 loop : -1.39 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 41 TYR 0.028 0.003 TYR C 42 PHE 0.023 0.003 PHE G 26 TRP 0.023 0.003 TRP C 167 HIS 0.011 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.28 (20182) covalent geometry : angle 0.73225 / 0.42 (29570) hydrogen bonds : bond 0.10230 / 9.81 ( 700) hydrogen bonds : angle 4.78254 / 5.73 ( 1598) metal coordination : bond 0.00319 / 0.16 ( 1) Misc. bond : bond 0.00107 / 0.05 ( 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: 39 poor density : 69 time to evaluate : 0.363 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: 0.9015 (OUTLIER) cc_final: 0.8767 (ptp) REVERT: B 109 GLN cc_start: 0.9168 (mp-120) cc_final: 0.8877 (mp10) REVERT: B 161 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8148 (tp) REVERT: C 29 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4481 (m-80) REVERT: M 75 MET cc_start: 0.8755 (mmm) cc_final: 0.8438 (mmm) REVERT: N 92 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7748 (tp30) outliers start: 39 outliers final: 22 residues processed: 100 average time/residue: 0.1590 time to fit residues: 23.5751 Evaluate side-chains 89 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 161 LEU 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 41 GLN 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 I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 94 LEU 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 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: 7.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.054851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.048136 restraints weight = 237785.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.048807 restraints weight = 166301.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.049279 restraints weight = 129718.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.049696 restraints weight = 108999.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.049883 restraints weight = 95195.598| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20184 Z= 0.141 Angle : 0.565 9.339 29570 Z= 0.329 Chirality : 0.038 0.249 3700 Planarity : 0.005 0.066 1992 Dihedral : 22.831 176.725 8692 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.75 % Allowed : 16.96 % Favored : 80.29 % 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: -0.30 (0.25), residues: 1075 helix: 0.64 (0.23), residues: 481 sheet: -0.54 (0.38), residues: 157 loop : -0.93 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 81 TYR 0.022 0.003 TYR C 193 PHE 0.039 0.002 PHE S 74 TRP 0.053 0.003 TRP B 23 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (20182) covalent geometry : angle 0.56529 / 0.33 (29570) hydrogen bonds : bond 0.07538 / 7.13 ( 700) hydrogen bonds : angle 4.36726 / 5.24 ( 1598) metal coordination : bond 0.00166 / 0.08 ( 1) Misc. bond : bond 0.00209 / 0.10 ( 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 100 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.556 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 100 MET cc_start: 0.8731 (mtp) cc_final: 0.8181 (mpp) REVERT: B 109 GLN cc_start: 0.9176 (mp-120) cc_final: 0.8870 (mp10) REVERT: B 161 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 29 PHE cc_start: 0.5013 (OUTLIER) cc_final: 0.4240 (m-80) REVERT: G 31 MET cc_start: 0.5530 (mmm) cc_final: 0.5118 (mtp) REVERT: M 75 MET cc_start: 0.8827 (mmm) cc_final: 0.8572 (mmm) REVERT: N 92 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7182 (tp30) REVERT: S 32 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7762 (ptt-90) outliers start: 25 outliers final: 18 residues processed: 93 average time/residue: 0.1800 time to fit residues: 24.3086 Evaluate side-chains 84 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS 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 18 TRP 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 90 TYR Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 54 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.054609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.047911 restraints weight = 238966.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.048617 restraints weight = 166734.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.049027 restraints weight = 128092.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.049292 restraints weight = 107597.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.049659 restraints weight = 97065.334| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20184 Z= 0.145 Angle : 0.558 16.278 29570 Z= 0.320 Chirality : 0.037 0.250 3700 Planarity : 0.005 0.056 1992 Dihedral : 22.725 176.772 8692 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.19 % Allowed : 18.06 % Favored : 78.74 % 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: -0.23 (0.25), residues: 1075 helix: 0.69 (0.23), residues: 485 sheet: -0.31 (0.41), residues: 147 loop : -0.97 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 71 TYR 0.025 0.003 TYR C 193 PHE 0.021 0.002 PHE S 74 TRP 0.021 0.002 TRP B 23 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (20182) covalent geometry : angle 0.55776 / 0.32 (29570) hydrogen bonds : bond 0.07451 / 7.09 ( 700) hydrogen bonds : angle 4.34632 / 5.20 ( 1598) metal coordination : bond 0.00192 / 0.10 ( 1) Misc. bond : bond 0.00107 / 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 97 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.584 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: B 88 ASP cc_start: 0.9237 (t0) cc_final: 0.8975 (m-30) REVERT: B 100 MET cc_start: 0.8725 (mtp) cc_final: 0.8211 (mpp) REVERT: B 109 GLN cc_start: 0.9207 (mp-120) cc_final: 0.8887 (mp10) REVERT: B 154 MET cc_start: 0.5844 (ttp) cc_final: 0.5511 (ttp) REVERT: B 161 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8280 (tp) REVERT: C 29 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4344 (m-80) REVERT: G 31 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5492 (ttt) REVERT: M 75 MET cc_start: 0.8923 (mmm) cc_final: 0.8711 (mmm) REVERT: N 92 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7215 (tp30) REVERT: S 32 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7791 (ptt-90) outliers start: 29 outliers final: 19 residues processed: 90 average time/residue: 0.1698 time to fit residues: 22.2228 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS 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 56 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 31 MET 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 126 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain M residue 7 ILE 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: 20.0000 chunk 4 optimal weight: 30.0000 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 43 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.052690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.046004 restraints weight = 244957.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.046633 restraints weight = 173384.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.047086 restraints weight = 136016.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.047497 restraints weight = 113500.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.047654 restraints weight = 98142.194| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20184 Z= 0.231 Angle : 0.665 12.952 29570 Z= 0.381 Chirality : 0.042 0.251 3700 Planarity : 0.006 0.057 1992 Dihedral : 22.910 176.411 8692 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.86 % Allowed : 20.26 % Favored : 76.87 % 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: -0.75 (0.24), residues: 1075 helix: 0.29 (0.23), residues: 484 sheet: -0.41 (0.41), residues: 139 loop : -1.33 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 81 TYR 0.024 0.003 TYR C 42 PHE 0.018 0.002 PHE S 74 TRP 0.023 0.002 TRP B 23 HIS 0.007 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 (20182) covalent geometry : angle 0.66531 / 0.38 (29570) hydrogen bonds : bond 0.09204 / 8.89 ( 700) hydrogen bonds : angle 4.49491 / 5.36 ( 1598) metal coordination : bond 0.00240 / 0.12 ( 1) Misc. bond : bond 0.00138 / 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 86 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.466 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 88 ASP cc_start: 0.9399 (t0) cc_final: 0.9173 (m-30) REVERT: B 161 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8491 (tp) REVERT: C 29 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.4556 (m-80) REVERT: G 31 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5705 (ttt) REVERT: N 92 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7566 (tp30) outliers start: 26 outliers final: 15 residues processed: 81 average time/residue: 0.1771 time to fit residues: 20.9630 Evaluate side-chains 74 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 161 LEU 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 76 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 135 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.052872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.046251 restraints weight = 244780.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.047020 restraints weight = 171253.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.047454 restraints weight = 133954.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.047857 restraints weight = 112618.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.048046 restraints weight = 98992.670| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20184 Z= 0.186 Angle : 0.600 8.629 29570 Z= 0.346 Chirality : 0.039 0.240 3700 Planarity : 0.005 0.052 1992 Dihedral : 22.908 176.172 8692 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.97 % Allowed : 21.59 % Favored : 75.44 % 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: -0.70 (0.25), residues: 1075 helix: 0.32 (0.23), residues: 486 sheet: -0.40 (0.41), residues: 146 loop : -1.30 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 81 TYR 0.026 0.003 TYR C 42 PHE 0.023 0.002 PHE S 74 TRP 0.018 0.002 TRP C 201 HIS 0.005 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 (20182) covalent geometry : angle 0.59994 / 0.35 (29570) hydrogen bonds : bond 0.08074 / 7.71 ( 700) hydrogen bonds : angle 4.47728 / 5.32 ( 1598) metal coordination : bond 0.00209 / 0.10 ( 1) Misc. bond : bond 0.00182 / 0.09 ( 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 89 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.585 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: 0.8767 (ptp) cc_final: 0.8466 (pmm) REVERT: B 88 ASP cc_start: 0.9411 (t0) cc_final: 0.9192 (m-30) REVERT: B 100 MET cc_start: 0.8666 (mtp) cc_final: 0.8131 (mpp) REVERT: B 161 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 29 PHE cc_start: 0.5150 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: M 75 MET cc_start: 0.8596 (mmm) cc_final: 0.8393 (mmm) REVERT: N 92 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7244 (tp30) outliers start: 27 outliers final: 20 residues processed: 80 average time/residue: 0.1745 time to fit residues: 20.3802 Evaluate side-chains 80 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 94 HIS 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 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 31 MET Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 126 GLN Chi-restraints excluded: chain J residue 17 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 5 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN 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 = 0.054026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.047273 restraints weight = 240364.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.048146 restraints weight = 166707.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.048591 restraints weight = 126759.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.049049 restraints weight = 105867.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.049219 restraints weight = 91628.280| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20184 Z= 0.125 Angle : 0.547 9.134 29570 Z= 0.311 Chirality : 0.036 0.246 3700 Planarity : 0.004 0.048 1992 Dihedral : 22.741 176.457 8692 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 22.25 % Favored : 75.44 % 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: -0.38 (0.25), residues: 1075 helix: 0.59 (0.23), residues: 488 sheet: -0.40 (0.40), residues: 158 loop : -1.08 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 81 TYR 0.015 0.002 TYR I 7 PHE 0.028 0.002 PHE B 90 TRP 0.029 0.002 TRP C 201 HIS 0.002 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (20182) covalent geometry : angle 0.54657 / 0.31 (29570) hydrogen bonds : bond 0.07013 / 6.75 ( 700) hydrogen bonds : angle 4.24890 / 5.10 ( 1598) metal coordination : bond 0.00013 / 0.01 ( 1) Misc. bond : bond 0.00148 / 0.07 ( 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 80 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.449 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: B 100 MET cc_start: 0.8775 (mtp) cc_final: 0.8177 (mpp) REVERT: B 161 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8389 (tp) REVERT: C 29 PHE cc_start: 0.5065 (OUTLIER) cc_final: 0.4305 (m-80) REVERT: G 31 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5405 (mtp) REVERT: I 126 GLN cc_start: 0.4826 (OUTLIER) cc_final: 0.4127 (mt0) REVERT: M 75 MET cc_start: 0.8832 (mmm) cc_final: 0.8619 (mmm) REVERT: N 92 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7191 (tp30) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.1648 time to fit residues: 18.2250 Evaluate side-chains 77 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU 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 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 C residue 211 MET Chi-restraints excluded: chain G residue 31 MET Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL 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 77 VAL Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 2 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3776 r_free = 0.3776 target = 0.053503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.046846 restraints weight = 238023.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.047464 restraints weight = 168143.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.047892 restraints weight = 130877.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.048346 restraints weight = 109484.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.048502 restraints weight = 93064.662| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20184 Z= 0.154 Angle : 0.566 10.554 29570 Z= 0.322 Chirality : 0.037 0.242 3700 Planarity : 0.005 0.047 1992 Dihedral : 22.722 176.480 8692 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.42 % Allowed : 22.14 % Favored : 75.44 % 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: -0.37 (0.25), residues: 1075 helix: 0.62 (0.23), residues: 490 sheet: -0.39 (0.40), residues: 160 loop : -1.12 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 81 TYR 0.031 0.002 TYR C 42 PHE 0.022 0.002 PHE S 74 TRP 0.019 0.002 TRP C 201 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (20182) covalent geometry : angle 0.56576 / 0.32 (29570) hydrogen bonds : bond 0.07361 / 7.10 ( 700) hydrogen bonds : angle 4.31665 / 5.16 ( 1598) metal coordination : bond 0.00127 / 0.06 ( 1) Misc. bond : bond 0.00122 / 0.06 ( 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 81 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.473 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: 0.8640 (ptp) cc_final: 0.8210 (pmm) REVERT: B 100 MET cc_start: 0.8771 (mtp) cc_final: 0.8155 (mpp) REVERT: B 109 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8930 (mp10) REVERT: B 161 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8434 (tp) REVERT: C 29 PHE cc_start: 0.5148 (OUTLIER) cc_final: 0.4396 (m-80) REVERT: G 31 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5643 (mtp) REVERT: N 92 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7271 (tp30) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.1657 time to fit residues: 18.7307 Evaluate side-chains 78 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 MET Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 62 PHE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 58 VAL 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 77 VAL Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 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 = 0.3790 r_free = 0.3790 target = 0.053939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.047242 restraints weight = 242342.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.048069 restraints weight = 167923.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.048502 restraints weight = 127271.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.048935 restraints weight = 106710.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.049126 restraints weight = 93265.093| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20184 Z= 0.127 Angle : 0.542 10.325 29570 Z= 0.308 Chirality : 0.036 0.237 3700 Planarity : 0.005 0.061 1992 Dihedral : 22.662 176.476 8692 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.42 % Allowed : 22.80 % Favored : 74.78 % 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: -0.23 (0.25), residues: 1075 helix: 0.76 (0.23), residues: 488 sheet: -0.43 (0.39), residues: 160 loop : -1.03 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 81 TYR 0.016 0.002 TYR C 193 PHE 0.021 0.002 PHE S 74 TRP 0.029 0.002 TRP C 201 HIS 0.004 0.001 HIS S 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (20182) covalent geometry : angle 0.54160 / 0.31 (29570) hydrogen bonds : bond 0.06946 / 6.70 ( 700) hydrogen bonds : angle 4.25611 / 5.08 ( 1598) metal coordination : bond 0.00066 / 0.03 ( 1) Misc. bond : bond 0.00138 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.82 seconds wall clock time: 62 minutes 39.83 seconds (3759.83 seconds total)