Starting phenix.real_space_refine on Sat Jul 4 07:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9i_51965/07_2026/9h9i_51965_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9i_51965/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9h9i_51965/07_2026/9h9i_51965_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9i_51965/07_2026/9h9i_51965_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h9i_51965/07_2026/9h9i_51965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9i_51965/07_2026/9h9i_51965.map" } 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-dev-6108/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: 3.91, per 1000 atoms: 0.21 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: 1.70 Conformation dependent library (CDL) restraints added in 478.1 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: 2.87 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: 4.26 Time building geometry restraints manager: 2.29 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: 29218 2.27 - 4.54: 385 4.54 - 6.81: 42 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: 3613 0.113 - 0.226: 84 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 22.320 Find NCS groups from input model: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- 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= 0.275 Angle : 0.642 11.344 29656 Z= 0.441 Chirality : 0.045 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 0.00367 / 0.27 (20251) covalent geometry : angle 0.64188 / 0.44 (29656) hydrogen bonds : bond 0.21181 / 20.77 ( 779) hydrogen bonds : angle 7.71368 / 9.58 ( 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 : 0.445 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: 0.1432 time to fit residues: 32.2101 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 : 0.351 ------------------------------------------------------------------------------- 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: 30.0000 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: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.043943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.031506 restraints weight = 147339.024| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.09 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20252 Z= 0.232 Angle : 0.597 7.908 29656 Z= 0.348 Chirality : 0.041 0.313 3709 Planarity : 0.005 0.040 2007 Dihedral : 21.986 179.377 8693 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.74 % Allowed : 9.80 % Favored : 88.45 % 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: 0.26 (0.25), residues: 1086 helix: 0.91 (0.22), residues: 495 sheet: -0.02 (0.39), residues: 182 loop : -0.53 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 79 TYR 0.024 0.002 TYR C 193 PHE 0.019 0.002 PHE I 127 TRP 0.013 0.002 TRP C 201 HIS 0.008 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.23 (20251) covalent geometry : angle 0.59733 / 0.35 (29656) hydrogen bonds : bond 0.08384 / 8.22 ( 779) hydrogen bonds : angle 4.48645 / 5.75 ( 1820) metal coordination : bond 0.00934 / 0.47 ( 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: 16 poor density : 130 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7008 (t-100) cc_final: 0.6485 (t-100) REVERT: G 31 MET cc_start: 0.9151 (ttp) cc_final: 0.8852 (ttp) REVERT: G 116 MET cc_start: 0.8678 (tpp) cc_final: 0.8418 (tpt) REVERT: I 46 MET cc_start: 0.8982 (mpp) cc_final: 0.8533 (mpp) REVERT: J 30 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9101 (mmmt) REVERT: N 54 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8015 (t70) REVERT: S 20 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8861 (tm-30) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.1478 time to fit residues: 30.5767 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 20 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.043658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.031355 restraints weight = 148621.785| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.00 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20252 Z= 0.239 Angle : 0.573 9.241 29656 Z= 0.333 Chirality : 0.040 0.298 3709 Planarity : 0.005 0.046 2007 Dihedral : 21.948 179.663 8693 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.96 % Allowed : 10.78 % Favored : 87.25 % 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: 0.85 (0.23), residues: 498 sheet: -0.05 (0.39), residues: 173 loop : -0.46 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 79 TYR 0.030 0.003 TYR C 193 PHE 0.014 0.002 PHE B 90 TRP 0.014 0.002 TRP C 201 HIS 0.010 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.24 (20251) covalent geometry : angle 0.57260 / 0.33 (29656) hydrogen bonds : bond 0.07279 / 7.02 ( 779) hydrogen bonds : angle 4.18669 / 5.44 ( 1820) metal coordination : bond 0.00370 / 0.19 ( 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 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7291 (t-100) cc_final: 0.6822 (t-100) REVERT: G 31 MET cc_start: 0.9104 (ttp) cc_final: 0.8786 (ttp) REVERT: I 27 LYS cc_start: 0.9166 (ptpp) cc_final: 0.8835 (ptpp) REVERT: I 46 MET cc_start: 0.8939 (mpp) cc_final: 0.8586 (mpp) REVERT: I 120 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8209 (mtpt) REVERT: I 124 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8150 (ttp80) REVERT: J 30 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9115 (mmmt) REVERT: N 33 ASP cc_start: 0.8485 (t0) cc_final: 0.8097 (t70) REVERT: N 89 MET cc_start: 0.8924 (mpp) cc_final: 0.8683 (mpp) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.1437 time to fit residues: 30.3534 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 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 152 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.043655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.031454 restraints weight = 148799.342| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.02 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 20252 Z= 0.235 Angle : 0.556 8.773 29656 Z= 0.326 Chirality : 0.040 0.297 3709 Planarity : 0.004 0.050 2007 Dihedral : 21.899 179.711 8693 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.61 % Allowed : 12.64 % Favored : 84.75 % 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 (0.26), residues: 1086 helix: 1.03 (0.23), residues: 495 sheet: -0.08 (0.38), residues: 175 loop : -0.40 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 79 TYR 0.012 0.002 TYR I 38 PHE 0.012 0.002 PHE C 130 TRP 0.013 0.001 TRP C 201 HIS 0.010 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.24 (20251) covalent geometry : angle 0.55644 / 0.33 (29656) hydrogen bonds : bond 0.06676 / 6.33 ( 779) hydrogen bonds : angle 4.07625 / 5.26 ( 1820) metal coordination : bond 0.00226 / 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 140 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7376 (t-100) cc_final: 0.6921 (t-100) REVERT: C 152 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: I 57 MET cc_start: 0.9061 (mmp) cc_final: 0.8780 (mmp) REVERT: I 120 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: I 124 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8051 (ttp80) REVERT: J 19 ASP cc_start: 0.8744 (m-30) cc_final: 0.8494 (m-30) REVERT: J 30 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9139 (mmmt) REVERT: M 62 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8875 (mttp) REVERT: N 33 ASP cc_start: 0.8546 (t0) cc_final: 0.8222 (t70) REVERT: N 89 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8597 (mpp) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 0.1480 time to fit residues: 30.6068 Evaluate side-chains 126 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 152 GLU 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 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 N residue 89 MET 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: 10.0000 chunk 58 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN B 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.043178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.030979 restraints weight = 150054.046| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.00 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 20252 Z= 0.312 Angle : 0.612 8.679 29656 Z= 0.351 Chirality : 0.042 0.276 3709 Planarity : 0.005 0.048 2007 Dihedral : 21.902 179.807 8693 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.51 % Allowed : 14.49 % Favored : 83.01 % 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: 0.16 (0.25), residues: 1086 helix: 0.86 (0.23), residues: 499 sheet: -0.15 (0.39), residues: 173 loop : -0.59 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 79 TYR 0.014 0.002 TYR I 38 PHE 0.023 0.002 PHE C 130 TRP 0.012 0.002 TRP C 201 HIS 0.013 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.31 (20251) covalent geometry : angle 0.61172 / 0.35 (29656) hydrogen bonds : bond 0.07356 / 6.97 ( 779) hydrogen bonds : angle 4.15700 / 5.38 ( 1820) metal coordination : bond 0.00060 / 0.03 ( 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 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7359 (t-100) cc_final: 0.6946 (t-100) REVERT: C 152 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: C 168 TYR cc_start: 0.8202 (t80) cc_final: 0.7905 (t80) REVERT: G 31 MET cc_start: 0.9109 (ttp) cc_final: 0.8823 (ttp) REVERT: I 57 MET cc_start: 0.9048 (mmp) cc_final: 0.8801 (mmm) REVERT: I 120 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: I 124 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8155 (ttp80) REVERT: J 30 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9119 (mmmt) REVERT: M 62 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8782 (mttp) REVERT: N 89 MET cc_start: 0.8777 (mpp) cc_final: 0.8533 (mpp) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 0.1452 time to fit residues: 28.9482 Evaluate side-chains 120 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 56 ASP 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 34 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 45 VAL 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: 0.5980 chunk 17 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.044231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.032003 restraints weight = 145822.510| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.96 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20252 Z= 0.140 Angle : 0.502 8.723 29656 Z= 0.293 Chirality : 0.036 0.258 3709 Planarity : 0.004 0.052 2007 Dihedral : 21.838 179.577 8693 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.18 % Allowed : 16.01 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1086 helix: 1.17 (0.24), residues: 498 sheet: 0.13 (0.39), residues: 177 loop : -0.51 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 79 TYR 0.010 0.002 TYR M 86 PHE 0.010 0.001 PHE C 130 TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (20251) covalent geometry : angle 0.50180 / 0.29 (29656) hydrogen bonds : bond 0.05703 / 5.39 ( 779) hydrogen bonds : angle 3.81418 / 4.94 ( 1820) metal coordination : bond 0.00088 / 0.04 ( 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 146 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7435 (t-100) cc_final: 0.6978 (t-100) REVERT: C 152 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: C 168 TYR cc_start: 0.8184 (t80) cc_final: 0.7916 (t80) REVERT: G 31 MET cc_start: 0.9105 (ttp) cc_final: 0.8836 (ttp) REVERT: I 27 LYS cc_start: 0.9229 (ptpp) cc_final: 0.8965 (ptpp) REVERT: I 57 MET cc_start: 0.8991 (mmp) cc_final: 0.8688 (mmm) REVERT: I 120 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: J 19 ASP cc_start: 0.8780 (m-30) cc_final: 0.8456 (m-30) REVERT: J 30 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9133 (mmmt) REVERT: M 62 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8826 (mttp) REVERT: N 33 ASP cc_start: 0.8583 (t0) cc_final: 0.8144 (t70) REVERT: N 89 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8543 (mpp) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.1488 time to fit residues: 31.1432 Evaluate side-chains 129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 GLU 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 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 M residue 83 LEU Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 26 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 overall best weight: 2.1504 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.044282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.032048 restraints weight = 147216.114| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.93 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20252 Z= 0.144 Angle : 0.510 9.884 29656 Z= 0.295 Chirality : 0.036 0.248 3709 Planarity : 0.004 0.051 2007 Dihedral : 21.762 179.972 8693 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.85 % Allowed : 17.21 % Favored : 80.94 % 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: 0.59 (0.26), residues: 1086 helix: 1.23 (0.24), residues: 498 sheet: 0.31 (0.40), residues: 177 loop : -0.53 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 79 TYR 0.012 0.002 TYR J 65 PHE 0.022 0.001 PHE I 127 TRP 0.012 0.001 TRP C 201 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (20251) covalent geometry : angle 0.51032 / 0.29 (29656) hydrogen bonds : bond 0.05582 / 5.24 ( 779) hydrogen bonds : angle 3.79530 / 4.85 ( 1820) metal coordination : bond 0.00126 / 0.06 ( 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 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.506 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: B 96 TRP cc_start: 0.7431 (t-100) cc_final: 0.6981 (t-100) REVERT: B 168 HIS cc_start: 0.7745 (t70) cc_final: 0.7472 (t70) REVERT: C 152 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: I 57 MET cc_start: 0.8981 (mmp) cc_final: 0.8670 (mmm) REVERT: I 120 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: I 124 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7950 (ttp80) REVERT: J 19 ASP cc_start: 0.8794 (m-30) cc_final: 0.8487 (m-30) REVERT: J 30 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9121 (mmmt) REVERT: M 81 MET cc_start: 0.9230 (mmt) cc_final: 0.9002 (mmm) REVERT: N 33 ASP cc_start: 0.8471 (t0) cc_final: 0.8056 (t70) REVERT: N 89 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8404 (mpp) outliers start: 17 outliers final: 13 residues processed: 125 average time/residue: 0.1520 time to fit residues: 29.4878 Evaluate side-chains 129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 43 VAL 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 69 THR 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 N residue 89 MET Chi-restraints excluded: chain S residue 55 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.043773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.031569 restraints weight = 148086.094| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.03 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20252 Z= 0.227 Angle : 0.550 9.834 29656 Z= 0.316 Chirality : 0.038 0.249 3709 Planarity : 0.004 0.051 2007 Dihedral : 21.730 179.947 8693 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.51 % Allowed : 18.30 % Favored : 79.19 % 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: 0.57 (0.26), residues: 1086 helix: 1.29 (0.24), residues: 491 sheet: 0.25 (0.40), residues: 175 loop : -0.57 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 79 TYR 0.012 0.002 TYR J 65 PHE 0.014 0.001 PHE C 130 TRP 0.010 0.001 TRP C 201 HIS 0.009 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 (20251) covalent geometry : angle 0.55035 / 0.32 (29656) hydrogen bonds : bond 0.06094 / 5.72 ( 779) hydrogen bonds : angle 3.94172 / 5.05 ( 1820) metal coordination : bond 0.00259 / 0.13 ( 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 136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7499 (t-100) cc_final: 0.7069 (t-100) REVERT: B 168 HIS cc_start: 0.7791 (t70) cc_final: 0.7513 (t70) REVERT: C 152 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: C 168 TYR cc_start: 0.8244 (t80) cc_final: 0.7964 (t80) REVERT: I 57 MET cc_start: 0.9042 (mmp) cc_final: 0.8743 (mmm) REVERT: I 120 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8171 (mtpt) REVERT: I 124 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8074 (ttp80) REVERT: J 30 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9132 (mmmt) REVERT: J 87 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9226 (pp) REVERT: M 62 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8792 (mttp) REVERT: M 72 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8564 (pp20) REVERT: M 81 MET cc_start: 0.9282 (mmt) cc_final: 0.9075 (mmm) REVERT: N 33 ASP cc_start: 0.8545 (t0) cc_final: 0.8329 (t70) REVERT: N 89 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8444 (mpp) REVERT: S 5 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9258 (mm) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.1522 time to fit residues: 29.2944 Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 GLU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 43 VAL 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 25 ILE Chi-restraints excluded: chain J residue 46 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 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 Chi-restraints excluded: chain N residue 89 MET Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 55 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.032707 restraints weight = 144209.892| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.85 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20252 Z= 0.110 Angle : 0.504 10.804 29656 Z= 0.290 Chirality : 0.034 0.226 3709 Planarity : 0.004 0.046 2007 Dihedral : 21.724 179.733 8693 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.29 % Allowed : 18.30 % Favored : 79.41 % 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: 0.83 (0.26), residues: 1086 helix: 1.39 (0.24), residues: 496 sheet: 0.52 (0.41), residues: 175 loop : -0.38 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 45 TYR 0.015 0.002 TYR J 65 PHE 0.009 0.001 PHE C 130 TRP 0.014 0.001 TRP C 201 HIS 0.003 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (20251) covalent geometry : angle 0.50436 / 0.29 (29656) hydrogen bonds : bond 0.05145 / 4.83 ( 779) hydrogen bonds : angle 3.74747 / 4.78 ( 1820) metal coordination : bond 0.00077 / 0.04 ( 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 150 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7479 (t-100) cc_final: 0.7058 (t-100) REVERT: C 152 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: C 168 TYR cc_start: 0.8197 (t80) cc_final: 0.7996 (t80) REVERT: G 116 MET cc_start: 0.8729 (tpt) cc_final: 0.8476 (tpt) REVERT: I 57 MET cc_start: 0.8985 (mmp) cc_final: 0.8702 (mmm) REVERT: I 112 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8354 (mm-30) REVERT: I 120 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8241 (ttpt) REVERT: I 124 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7974 (ttp80) REVERT: J 87 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9257 (pp) REVERT: N 33 ASP cc_start: 0.8444 (t0) cc_final: 0.8029 (t70) REVERT: N 89 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8486 (mpp) REVERT: N 101 TRP cc_start: 0.8713 (p90) cc_final: 0.8500 (p90) REVERT: S 29 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7999 (tmtt) outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 0.1552 time to fit residues: 32.7647 Evaluate side-chains 130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 GLU 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 25 ILE Chi-restraints excluded: chain J residue 46 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 M residue 83 LEU Chi-restraints excluded: chain N residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 GLN I 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.044233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032032 restraints weight = 144900.060| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.84 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20252 Z= 0.169 Angle : 0.541 11.689 29656 Z= 0.308 Chirality : 0.036 0.228 3709 Planarity : 0.004 0.049 2007 Dihedral : 21.659 179.837 8693 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.63 % Allowed : 19.72 % Favored : 78.65 % 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: 0.78 (0.26), residues: 1086 helix: 1.39 (0.24), residues: 491 sheet: 0.48 (0.40), residues: 175 loop : -0.44 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 95 TYR 0.014 0.002 TYR J 65 PHE 0.026 0.001 PHE I 127 TRP 0.010 0.001 TRP B 104 HIS 0.006 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (20251) covalent geometry : angle 0.54074 / 0.31 (29656) hydrogen bonds : bond 0.05450 / 5.11 ( 779) hydrogen bonds : angle 3.82839 / 4.86 ( 1820) metal coordination : bond 0.00157 / 0.08 ( 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 130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.7509 (t-100) cc_final: 0.7077 (t-100) REVERT: C 152 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 168 TYR cc_start: 0.8267 (t80) cc_final: 0.7996 (t80) REVERT: I 27 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8832 (ptpp) REVERT: I 57 MET cc_start: 0.8995 (mmp) cc_final: 0.8728 (mmm) REVERT: I 62 ASP cc_start: 0.7770 (m-30) cc_final: 0.7159 (m-30) REVERT: I 88 MET cc_start: 0.9022 (mmm) cc_final: 0.8596 (tpt) REVERT: I 120 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8218 (ttpt) REVERT: I 124 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8071 (ttp80) REVERT: J 87 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9363 (pp) REVERT: M 62 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8887 (mttp) REVERT: M 81 MET cc_start: 0.9064 (mmm) cc_final: 0.8854 (tpt) REVERT: N 33 ASP cc_start: 0.8428 (t0) cc_final: 0.8017 (t70) REVERT: N 89 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8394 (mpp) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.1466 time to fit residues: 27.7106 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 152 GLU 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 46 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 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 Chi-restraints excluded: chain N residue 89 MET 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: 10.0000 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 0.0770 chunk 24 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 15 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 = 0.3351 r_free = 0.3351 target = 0.043420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.031324 restraints weight = 147209.410| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.79 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 20252 Z= 0.255 Angle : 0.591 12.367 29656 Z= 0.336 Chirality : 0.039 0.246 3709 Planarity : 0.005 0.050 2007 Dihedral : 21.693 179.947 8693 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.53 % Allowed : 19.61 % Favored : 78.87 % 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: 0.61 (0.26), residues: 1086 helix: 1.28 (0.24), residues: 490 sheet: 0.53 (0.41), residues: 165 loop : -0.61 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 79 TYR 0.018 0.002 TYR I 90 PHE 0.016 0.002 PHE C 130 TRP 0.011 0.001 TRP B 104 HIS 0.010 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.26 (20251) covalent geometry : angle 0.59145 / 0.34 (29656) hydrogen bonds : bond 0.06450 / 6.00 ( 779) hydrogen bonds : angle 3.96962 / 5.08 ( 1820) metal coordination : bond 0.00300 / 0.15 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.47 seconds wall clock time: 79 minutes 40.80 seconds (4780.80 seconds total)