Starting phenix.real_space_refine on Fri Aug 7 03:38:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965.map" model { file = "/net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9i_51965/08_2026/9h9i_51965_neut.cif" } resolution = 3.2 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 477 5.49 5 Mg 49 5.21 5 S 27 5.16 5 C 10016 2.51 5 N 3521 2.21 5 O 4868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18959 Number of models: 1 Model: "" Number of chains: 13 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: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} 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: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1116 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Unusual residues: {' MG': 49} Classifications: {'undetermined': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.18 Number of scatterers: 18959 At special positions: 0 Unit cell: (140.238, 117.978, 166.95, 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 477 15.00 Mg 49 11.99 O 4868 8.00 N 3521 7.00 C 10016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 453.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 52.3% alpha, 15.2% beta 136 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.595A pdb=" N MET B 27 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix 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 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.515A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.973A 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 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.860A 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 12 removed outlier: 3.629A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 4.250A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 59 through 63 removed outlier: 4.452A pdb=" N LYS C 62 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 82 Processing helix chain 'C' and resid 83 through 96 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 68 Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.921A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.667A pdb=" N MET I 46 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Proline residue: I 51 - end of helix 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 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.859A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.924A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.984A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.531A pdb=" N ARG M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 3.538A pdb=" N ARG M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.543A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 37 through 49 removed outlier: 3.796A 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 80 through 91 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.593A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.127A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 161 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.946A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.985A 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 'C' and resid 164 through 170 Processing sheet with id=AA6, first strand: chain 'G' and resid 73 through 74 Processing sheet with id=AA7, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.551A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 36 through 41 removed outlier: 5.463A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB1, first strand: chain 'S' and resid 31 through 33 removed outlier: 5.951A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 572 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4199 1.34 - 1.45: 6672 1.45 - 1.57: 8377 1.57 - 1.69: 951 1.69 - 1.81: 52 Bond restraints: 20251 Sorted by residual: bond pdb=" P 2MG 11207 " pdb=" O5' 2MG 11207 " ideal model delta sigma weight residual 1.593 1.710 -0.117 1.50e-02 4.44e+03 6.03e+01 bond pdb=" C VAL M 16 " pdb=" O VAL M 16 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.13e-02 7.83e+03 2.07e+01 bond pdb=" C HIS M 14 " pdb=" O HIS M 14 " ideal model delta sigma weight residual 1.234 1.278 -0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" CA ALA M 18 " pdb=" CB ALA M 18 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.57e-02 4.06e+03 1.23e+01 bond pdb=" N HIS J 56 " pdb=" CA HIS J 56 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.09e-02 8.42e+03 1.12e+01 ... (remaining 20246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 29024 2.27 - 4.54: 578 4.54 - 6.81: 43 6.81 - 9.08: 7 9.08 - 11.34: 4 Bond angle restraints: 29656 Sorted by residual: angle pdb=" N ILE M 17 " pdb=" CA ILE M 17 " pdb=" C ILE M 17 " ideal model delta sigma weight residual 110.62 103.46 7.16 1.02e+00 9.61e-01 4.93e+01 angle pdb=" CA GLY M 6 " pdb=" C GLY M 6 " pdb=" O GLY M 6 " ideal model delta sigma weight residual 122.23 117.87 4.36 6.90e-01 2.10e+00 4.00e+01 angle pdb=" N THR B 72 " pdb=" CA THR B 72 " pdb=" C THR B 72 " ideal model delta sigma weight residual 114.31 106.36 7.95 1.29e+00 6.01e-01 3.80e+01 angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 124.74 -5.94 1.10e+00 8.26e-01 2.92e+01 angle pdb=" CA VAL B 47 " pdb=" C VAL B 47 " pdb=" N PRO B 48 " ideal model delta sigma weight residual 120.83 117.60 3.23 6.10e-01 2.69e+00 2.81e+01 ... (remaining 29651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 11767 35.11 - 70.23: 1032 70.23 - 105.34: 143 105.34 - 140.45: 4 140.45 - 175.56: 2 Dihedral angle restraints: 12948 sinusoidal: 9796 harmonic: 3152 Sorted by residual: dihedral pdb=" C4' U 11183 " pdb=" C3' U 11183 " pdb=" C2' U 11183 " pdb=" C1' U 11183 " ideal model delta sinusoidal sigma weight residual -35.00 21.37 -56.37 1 8.00e+00 1.56e-02 6.69e+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 47.56 -175.56 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C5' U 11183 " pdb=" C4' U 11183 " pdb=" C3' U 11183 " pdb=" O3' U 11183 " ideal model delta sinusoidal sigma weight residual 147.00 94.27 52.73 1 8.00e+00 1.56e-02 5.92e+01 ... (remaining 12945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3621 0.113 - 0.226: 76 0.226 - 0.340: 5 0.340 - 0.453: 3 0.453 - 0.566: 4 Chirality restraints: 3709 Sorted by residual: chirality pdb=" P A 2 16 " pdb=" OP1 A 2 16 " pdb=" OP2 A 2 16 " pdb=" O5' A 2 16 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P C 3 28 " pdb=" OP1 C 3 28 " pdb=" OP2 C 3 28 " pdb=" O5' C 3 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.56e+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 2.94 -0.53 2.00e-01 2.50e+01 7.11e+00 ... (remaining 3706 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.029 2.00e-02 2.50e+03 3.38e-02 3.72e+01 pdb=" N9 2MG 1 966 " 0.016 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.017 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.022 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " -0.000 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.017 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.018 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.030 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.048 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.026 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.016 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.017 2.00e-02 2.50e+03 2.05e-02 1.37e+01 pdb=" N9 2MG 11207 " -0.005 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.009 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.014 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.001 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.010 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.010 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.019 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.031 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.015 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.006 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 15 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C ALA M 15 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA M 15 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL M 16 " 0.016 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 159 2.51 - 3.11: 14396 3.11 - 3.71: 35059 3.71 - 4.30: 49735 4.30 - 4.90: 69919 Nonbonded interactions: 169268 Sorted by model distance: nonbonded pdb=" OD2 ASP B 205 " pdb="ZN ZN B 301 " model vdw 1.916 2.230 nonbonded pdb=" OD1 ASP B 204 " pdb="ZN ZN B 301 " model vdw 2.020 2.230 nonbonded pdb=" O2' U 11183 " pdb=" OP1 G 11184 " model vdw 2.032 3.040 nonbonded pdb=" O GLU C 125 " pdb=" NH1 ARG C 127 " model vdw 2.051 3.120 nonbonded pdb=" O2' A 11256 " pdb=" O6 G 11278 " model vdw 2.104 3.040 ... (remaining 169263 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 20252 Z= 0.294 Angle : 0.763 11.344 29656 Z= 0.577 Chirality : 0.055 0.566 3709 Planarity : 0.006 0.104 2007 Dihedral : 21.314 175.563 10908 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % 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: -0.39 (0.24), residues: 1086 helix: 0.29 (0.22), residues: 479 sheet: -0.27 (0.38), residues: 182 loop : -0.74 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 124 TYR 0.017 0.002 TYR N 20 PHE 0.024 0.002 PHE B 90 TRP 0.007 0.001 TRP B 23 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.29 (20251) covalent geometry : angle 0.76253 / 0.58 (29656) hydrogen bonds : bond 0.21181 / 22.61 ( 779) hydrogen bonds : angle 7.71368 / 9.92 ( 1820) metal coordination : bond 0.17285 / 8.64 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 HIS cc_start: 0.5745 (t-90) cc_final: 0.5512 (t-170) REVERT: C 168 TYR cc_start: 0.7350 (t80) cc_final: 0.7034 (t80) REVERT: N 86 GLU cc_start: 0.7325 (pt0) cc_final: 0.7115 (pt0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1294 time to fit residues: 29.6937 Evaluate side-chains 113 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN J 58 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.031583 restraints weight = 146900.522| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.00 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20252 Z= 0.226 Angle : 0.639 12.357 29656 Z= 0.358 Chirality : 0.044 0.437 3709 Planarity : 0.005 0.039 2007 Dihedral : 21.912 179.380 8693 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.85 % Allowed : 9.91 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1086 helix: 0.89 (0.22), residues: 495 sheet: -0.02 (0.39), residues: 182 loop : -0.54 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 79 TYR 0.023 0.002 TYR C 193 PHE 0.015 0.002 PHE I 127 TRP 0.013 0.002 TRP C 201 HIS 0.009 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.23 (20251) covalent geometry : angle 0.63935 / 0.36 (29656) hydrogen bonds : bond 0.08261 / 8.76 ( 779) hydrogen bonds : angle 4.47008 / 5.94 ( 1820) metal coordination : bond 0.02221 / 1.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.6994 (t-100) cc_final: 0.6466 (t-100) REVERT: G 31 MET cc_start: 0.9088 (ttp) cc_final: 0.8779 (ttp) REVERT: G 116 MET cc_start: 0.8675 (tpp) cc_final: 0.8413 (tpt) REVERT: I 46 MET cc_start: 0.8971 (mpp) cc_final: 0.8324 (mpp) REVERT: I 124 ARG cc_start: 0.9337 (ttm110) cc_final: 0.8768 (ttp80) REVERT: J 30 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9122 (mmmt) REVERT: N 54 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8017 (t70) REVERT: S 20 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8858 (tm-30) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.1436 time to fit residues: 29.7652 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 136 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.032185 restraints weight = 146680.906| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.92 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20252 Z= 0.155 Angle : 0.550 12.822 29656 Z= 0.315 Chirality : 0.038 0.327 3709 Planarity : 0.004 0.049 2007 Dihedral : 21.808 179.315 8693 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.96 % Allowed : 10.13 % Favored : 87.91 % 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: 0.52 (0.26), residues: 1086 helix: 1.08 (0.23), residues: 493 sheet: 0.16 (0.39), residues: 173 loop : -0.32 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 79 TYR 0.028 0.002 TYR C 193 PHE 0.014 0.001 PHE B 90 TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (20251) covalent geometry : angle 0.54975 / 0.32 (29656) hydrogen bonds : bond 0.06658 / 7.00 ( 779) hydrogen bonds : angle 4.09358 / 5.49 ( 1820) metal coordination : bond 0.00467 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.7497 (mtp) cc_final: 0.7295 (mmm) REVERT: B 96 TRP cc_start: 0.7243 (t-100) cc_final: 0.6741 (t-100) REVERT: G 31 MET cc_start: 0.9067 (ttp) cc_final: 0.8759 (ttp) REVERT: I 46 MET cc_start: 0.8922 (mpp) cc_final: 0.8630 (mtm) REVERT: I 57 MET cc_start: 0.9068 (mmp) cc_final: 0.8853 (mmp) REVERT: I 62 ASP cc_start: 0.8433 (m-30) cc_final: 0.8212 (p0) REVERT: I 120 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8213 (ttpt) REVERT: I 124 ARG cc_start: 0.9345 (ttm110) cc_final: 0.8699 (ttp80) REVERT: M 11 ASP cc_start: 0.7559 (p0) cc_final: 0.7358 (p0) REVERT: M 50 GLU cc_start: 0.8313 (tp30) cc_final: 0.8107 (tp30) REVERT: M 62 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8919 (ptpt) REVERT: M 114 LYS cc_start: 0.9283 (ptmm) cc_final: 0.8775 (ptmm) REVERT: N 33 ASP cc_start: 0.8458 (t0) cc_final: 0.8068 (t70) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 0.1129 time to fit residues: 25.1539 Evaluate side-chains 125 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 134 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 overall best weight: 3.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.044114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.031911 restraints weight = 148233.820| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.03 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20252 Z= 0.199 Angle : 0.561 8.333 29656 Z= 0.316 Chirality : 0.040 0.321 3709 Planarity : 0.004 0.051 2007 Dihedral : 21.703 179.767 8693 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.85 % Allowed : 13.62 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1086 helix: 1.13 (0.23), residues: 495 sheet: 0.16 (0.39), residues: 173 loop : -0.30 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 79 TYR 0.025 0.002 TYR C 193 PHE 0.026 0.002 PHE I 127 TRP 0.013 0.001 TRP C 201 HIS 0.009 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (20251) covalent geometry : angle 0.56144 / 0.32 (29656) hydrogen bonds : bond 0.06474 / 6.68 ( 779) hydrogen bonds : angle 4.04282 / 5.44 ( 1820) metal coordination : bond 0.00217 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.6245 (ptp) cc_final: 0.5840 (ptp) REVERT: B 96 TRP cc_start: 0.7283 (t-100) cc_final: 0.6799 (t-100) REVERT: I 120 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8208 (ttpt) REVERT: I 124 ARG cc_start: 0.9397 (ttm110) cc_final: 0.8785 (ttp80) REVERT: I 127 PHE cc_start: 0.9192 (t80) cc_final: 0.8974 (t80) REVERT: J 19 ASP cc_start: 0.8720 (m-30) cc_final: 0.8498 (m-30) REVERT: J 30 LYS cc_start: 0.9356 (mmmt) cc_final: 0.8990 (mmmt) REVERT: M 50 GLU cc_start: 0.8364 (tp30) cc_final: 0.8131 (tp30) REVERT: M 114 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8749 (ptmm) REVERT: N 33 ASP cc_start: 0.8472 (t0) cc_final: 0.8073 (t70) REVERT: N 89 MET cc_start: 0.8775 (mpp) cc_final: 0.8517 (mpp) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.1351 time to fit residues: 26.4706 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 30 optimal weight: 20.0000 chunk 58 optimal weight: 0.0970 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 0.0070 chunk 54 optimal weight: 9.9990 overall best weight: 4.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.043785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.031660 restraints weight = 147446.007| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.81 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 20252 Z= 0.233 Angle : 0.587 8.675 29656 Z= 0.325 Chirality : 0.041 0.212 3709 Planarity : 0.004 0.053 2007 Dihedral : 21.706 179.625 8693 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.29 % Allowed : 13.40 % Favored : 84.31 % 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: 0.52 (0.26), residues: 1086 helix: 1.12 (0.23), residues: 493 sheet: 0.08 (0.39), residues: 173 loop : -0.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 79 TYR 0.028 0.002 TYR C 193 PHE 0.022 0.002 PHE I 127 TRP 0.012 0.001 TRP C 201 HIS 0.011 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.23 (20251) covalent geometry : angle 0.58716 / 0.32 (29656) hydrogen bonds : bond 0.06626 / 6.80 ( 779) hydrogen bonds : angle 4.02519 / 5.41 ( 1820) metal coordination : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7371 (t-100) cc_final: 0.6880 (t-100) REVERT: G 31 MET cc_start: 0.9095 (ttp) cc_final: 0.8800 (ttp) REVERT: I 57 MET cc_start: 0.9050 (mmp) cc_final: 0.8757 (mmp) REVERT: I 120 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8166 (ttpt) REVERT: I 124 ARG cc_start: 0.9408 (ttm110) cc_final: 0.8840 (ttp80) REVERT: I 127 PHE cc_start: 0.9158 (t80) cc_final: 0.8652 (t80) REVERT: J 19 ASP cc_start: 0.8774 (m-30) cc_final: 0.8476 (m-30) REVERT: J 30 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9022 (mmmt) REVERT: M 114 LYS cc_start: 0.9253 (ptmm) cc_final: 0.8759 (ptmm) REVERT: N 33 ASP cc_start: 0.8532 (t0) cc_final: 0.8199 (t70) REVERT: N 89 MET cc_start: 0.8791 (mpp) cc_final: 0.8584 (mpp) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.1370 time to fit residues: 28.1896 Evaluate side-chains 124 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 69 optimal weight: 0.1980 chunk 17 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.044335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.032127 restraints weight = 145338.332| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.85 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20252 Z= 0.149 Angle : 0.520 10.087 29656 Z= 0.296 Chirality : 0.036 0.176 3709 Planarity : 0.004 0.057 2007 Dihedral : 21.684 179.537 8693 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.18 % Allowed : 14.60 % Favored : 83.22 % 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: 0.69 (0.26), residues: 1086 helix: 1.24 (0.24), residues: 493 sheet: 0.26 (0.40), residues: 175 loop : -0.30 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 79 TYR 0.011 0.002 TYR C 168 PHE 0.018 0.001 PHE I 127 TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20251) covalent geometry : angle 0.52031 / 0.30 (29656) hydrogen bonds : bond 0.05799 / 5.92 ( 779) hydrogen bonds : angle 3.81852 / 5.11 ( 1820) metal coordination : bond 0.00157 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7420 (t-100) cc_final: 0.6932 (t-100) REVERT: G 31 MET cc_start: 0.9102 (ttp) cc_final: 0.8846 (ttp) REVERT: I 57 MET cc_start: 0.8996 (mmp) cc_final: 0.8713 (mmm) REVERT: I 120 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8175 (ttpt) REVERT: I 124 ARG cc_start: 0.9384 (ttm110) cc_final: 0.8807 (ttp80) REVERT: I 127 PHE cc_start: 0.9184 (t80) cc_final: 0.8717 (t80) REVERT: J 19 ASP cc_start: 0.8774 (m-30) cc_final: 0.8463 (m-30) REVERT: J 30 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9060 (mmmt) REVERT: M 114 LYS cc_start: 0.9245 (ptmm) cc_final: 0.8790 (ptmm) REVERT: N 33 ASP cc_start: 0.8460 (t0) cc_final: 0.8040 (t70) REVERT: N 89 MET cc_start: 0.8818 (mpp) cc_final: 0.8564 (mpp) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.1339 time to fit residues: 27.5930 Evaluate side-chains 127 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 26 optimal weight: 20.0000 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.043167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.030843 restraints weight = 149900.681| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.07 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 20252 Z= 0.325 Angle : 0.695 8.558 29656 Z= 0.372 Chirality : 0.047 0.322 3709 Planarity : 0.005 0.051 2007 Dihedral : 21.725 179.791 8693 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.61 % 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 (0.26), residues: 1086 helix: 0.91 (0.23), residues: 499 sheet: -0.09 (0.40), residues: 173 loop : -0.54 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 79 TYR 0.015 0.002 TYR I 90 PHE 0.023 0.002 PHE C 130 TRP 0.010 0.002 TRP B 104 HIS 0.016 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.33 (20251) covalent geometry : angle 0.69527 / 0.37 (29656) hydrogen bonds : bond 0.07564 / 7.78 ( 779) hydrogen bonds : angle 4.12431 / 5.50 ( 1820) metal coordination : bond 0.00379 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7349 (t-100) cc_final: 0.6927 (t-100) REVERT: B 168 HIS cc_start: 0.7753 (t70) cc_final: 0.7491 (t70) REVERT: I 57 MET cc_start: 0.9110 (mmp) cc_final: 0.8849 (mmm) REVERT: I 120 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (tttm) REVERT: I 124 ARG cc_start: 0.9415 (ttm110) cc_final: 0.8851 (ttp80) REVERT: I 127 PHE cc_start: 0.9165 (t80) cc_final: 0.8893 (t80) REVERT: J 30 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9051 (mmmt) REVERT: M 62 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8782 (mttp) REVERT: M 114 LYS cc_start: 0.9242 (ptmm) cc_final: 0.8775 (ptmm) REVERT: N 33 ASP cc_start: 0.8579 (t0) cc_final: 0.8252 (t70) REVERT: N 89 MET cc_start: 0.8889 (mpp) cc_final: 0.8554 (mpp) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.1375 time to fit residues: 26.2447 Evaluate side-chains 120 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.043829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.031582 restraints weight = 147280.444| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.02 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20252 Z= 0.190 Angle : 0.572 10.046 29656 Z= 0.320 Chirality : 0.039 0.306 3709 Planarity : 0.004 0.055 2007 Dihedral : 21.716 179.458 8693 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.51 % Allowed : 17.21 % Favored : 80.28 % 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: 0.55 (0.26), residues: 1086 helix: 1.22 (0.24), residues: 490 sheet: 0.01 (0.40), residues: 175 loop : -0.39 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 79 TYR 0.010 0.002 TYR C 168 PHE 0.013 0.002 PHE C 130 TRP 0.013 0.001 TRP C 201 HIS 0.007 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (20251) covalent geometry : angle 0.57235 / 0.32 (29656) hydrogen bonds : bond 0.06221 / 6.35 ( 779) hydrogen bonds : angle 3.93994 / 5.24 ( 1820) metal coordination : bond 0.00230 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7422 (t-100) cc_final: 0.6987 (t-100) REVERT: B 168 HIS cc_start: 0.7787 (t70) cc_final: 0.7511 (t70) REVERT: C 168 TYR cc_start: 0.8212 (t80) cc_final: 0.7984 (t80) REVERT: G 31 MET cc_start: 0.9093 (ttp) cc_final: 0.8815 (ttp) REVERT: I 57 MET cc_start: 0.9065 (mmp) cc_final: 0.8786 (mmm) REVERT: I 112 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8427 (mm-30) REVERT: I 120 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: I 124 ARG cc_start: 0.9375 (ttm110) cc_final: 0.8792 (ttp80) REVERT: I 127 PHE cc_start: 0.9190 (t80) cc_final: 0.8934 (t80) REVERT: J 19 ASP cc_start: 0.8846 (m-30) cc_final: 0.8513 (m-30) REVERT: J 30 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9088 (mmmt) REVERT: M 62 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8781 (mttp) REVERT: M 114 LYS cc_start: 0.9230 (ptmm) cc_final: 0.8785 (ptmm) REVERT: N 33 ASP cc_start: 0.8565 (t0) cc_final: 0.8227 (t70) REVERT: N 89 MET cc_start: 0.8863 (mpp) cc_final: 0.8520 (mpp) outliers start: 23 outliers final: 17 residues processed: 119 average time/residue: 0.1397 time to fit residues: 26.0066 Evaluate side-chains 120 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 153 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.044687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.032459 restraints weight = 145497.373| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.88 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 : 0.002 0.053 20252 Z= 0.125 Angle : 0.531 13.064 29656 Z= 0.298 Chirality : 0.035 0.280 3709 Planarity : 0.004 0.056 2007 Dihedral : 21.647 179.627 8693 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.29 % Allowed : 17.32 % Favored : 80.39 % 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: 0.86 (0.27), residues: 1086 helix: 1.41 (0.24), residues: 493 sheet: 0.30 (0.40), residues: 173 loop : -0.22 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 79 TYR 0.010 0.001 TYR C 168 PHE 0.012 0.001 PHE I 127 TRP 0.015 0.001 TRP C 201 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (20251) covalent geometry : angle 0.53059 / 0.30 (29656) hydrogen bonds : bond 0.05406 / 5.54 ( 779) hydrogen bonds : angle 3.76600 / 4.99 ( 1820) metal coordination : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7462 (t-100) cc_final: 0.7022 (t-100) REVERT: C 168 TYR cc_start: 0.8168 (t80) cc_final: 0.7878 (t80) REVERT: C 181 ASP cc_start: 0.8234 (p0) cc_final: 0.7877 (p0) REVERT: G 31 MET cc_start: 0.9028 (ttp) cc_final: 0.8731 (ttp) REVERT: I 57 MET cc_start: 0.8962 (mmp) cc_final: 0.8648 (mmm) REVERT: I 112 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8355 (mm-30) REVERT: I 120 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8246 (mtpt) REVERT: I 124 ARG cc_start: 0.9358 (ttm110) cc_final: 0.8769 (ttp80) REVERT: I 127 PHE cc_start: 0.9161 (t80) cc_final: 0.8699 (t80) REVERT: J 30 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9186 (mmmt) REVERT: M 114 LYS cc_start: 0.9224 (ptmm) cc_final: 0.8785 (ptmm) REVERT: N 33 ASP cc_start: 0.8501 (t0) cc_final: 0.8079 (t70) REVERT: N 89 MET cc_start: 0.8815 (mpp) cc_final: 0.8445 (mpp) REVERT: S 29 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8040 (tmtt) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.1435 time to fit residues: 29.2966 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 0.0170 chunk 123 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.044462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.032186 restraints weight = 145792.275| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.03 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20252 Z= 0.145 Angle : 0.551 12.545 29656 Z= 0.305 Chirality : 0.036 0.366 3709 Planarity : 0.004 0.056 2007 Dihedral : 21.611 179.896 8693 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.53 % Allowed : 18.63 % Favored : 79.85 % 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: 0.86 (0.26), residues: 1086 helix: 1.41 (0.24), residues: 495 sheet: 0.36 (0.40), residues: 175 loop : -0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 95 TYR 0.013 0.002 TYR C 42 PHE 0.013 0.001 PHE I 127 TRP 0.012 0.001 TRP C 201 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (20251) covalent geometry : angle 0.55078 / 0.30 (29656) hydrogen bonds : bond 0.05510 / 5.64 ( 779) hydrogen bonds : angle 3.83020 / 5.07 ( 1820) metal coordination : bond 0.00109 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7462 (t-100) cc_final: 0.7009 (t-100) REVERT: C 168 TYR cc_start: 0.8216 (t80) cc_final: 0.7920 (t80) REVERT: G 31 MET cc_start: 0.9036 (ttp) cc_final: 0.8702 (ttp) REVERT: I 57 MET cc_start: 0.9007 (mmp) cc_final: 0.8699 (mmm) REVERT: I 88 MET cc_start: 0.9051 (mmm) cc_final: 0.8752 (tpt) REVERT: I 120 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: I 124 ARG cc_start: 0.9367 (ttm110) cc_final: 0.8757 (ttp80) REVERT: I 127 PHE cc_start: 0.9165 (t80) cc_final: 0.8893 (t80) REVERT: J 30 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9208 (mmmt) REVERT: M 114 LYS cc_start: 0.9223 (ptmm) cc_final: 0.8782 (ptmm) REVERT: N 33 ASP cc_start: 0.8486 (t0) cc_final: 0.8070 (t70) REVERT: N 89 MET cc_start: 0.8834 (mpp) cc_final: 0.8457 (mpp) REVERT: S 66 MET cc_start: 0.8906 (mtp) cc_final: 0.8647 (mtp) outliers start: 14 outliers final: 11 residues processed: 119 average time/residue: 0.1384 time to fit residues: 25.8946 Evaluate side-chains 119 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 82 LYS Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 69 optimal weight: 0.0770 chunk 24 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.032262 restraints weight = 144810.886| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.82 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20252 Z= 0.145 Angle : 0.548 12.858 29656 Z= 0.303 Chirality : 0.036 0.394 3709 Planarity : 0.004 0.055 2007 Dihedral : 21.598 179.813 8693 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.63 % Allowed : 18.63 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1086 helix: 1.37 (0.24), residues: 495 sheet: 0.44 (0.40), residues: 175 loop : -0.25 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 79 TYR 0.011 0.002 TYR C 42 PHE 0.012 0.001 PHE I 127 TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (20251) covalent geometry : angle 0.54805 / 0.30 (29656) hydrogen bonds : bond 0.05442 / 5.58 ( 779) hydrogen bonds : angle 3.80312 / 5.04 ( 1820) metal coordination : bond 0.00141 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.91 seconds wall clock time: 78 minutes 20.98 seconds (4700.98 seconds total)