Starting phenix.real_space_refine on Tue Nov 18 08:35:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3r_10095/11_2025/6s3r_10095.map" } resolution = 3.5 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 8592 2.51 5 N 1970 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12855 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1510 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "E" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "F" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1907 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "K" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain breaks: 1 Time building chain proxies: 3.54, per 1000 atoms: 0.28 Number of scatterers: 12855 At special positions: 0 Unit cell: (107.682, 98.64, 120.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 2176 8.00 N 1970 7.00 C 8592 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: 1.12 Conformation dependent library (CDL) restraints added in 659.6 milliseconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.556A pdb=" N PHE A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.610A pdb=" N GLY A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 118 through 122 removed outlier: 4.156A pdb=" N LEU A 121 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 118 through 122' Processing helix chain 'A' and resid 129 through 144 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.556A pdb=" N LEU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 211 Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.943A pdb=" N ILE A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Proline residue: A 224 - end of helix Processing helix chain 'A' and resid 235 through 248 removed outlier: 4.354A pdb=" N GLY A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 90 through 105 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 129 through 144 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 173 through 211 removed outlier: 3.881A pdb=" N ALA B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.777A pdb=" N ILE B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Proline residue: B 224 - end of helix Processing helix chain 'B' and resid 235 through 248 removed outlier: 4.006A pdb=" N GLY B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.520A pdb=" N ILE C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 118 through 122 removed outlier: 4.250A pdb=" N LEU C 121 " --> pdb=" O GLN C 118 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 129 through 146 Proline residue: C 137 - end of helix removed outlier: 3.725A pdb=" N GLN C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 170 through 211 removed outlier: 3.704A pdb=" N LEU C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Proline residue: C 176 - end of helix Proline residue: C 196 - end of helix Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.730A pdb=" N ILE C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Proline residue: C 224 - end of helix Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.133A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 65 Proline residue: D 59 - end of helix removed outlier: 3.824A pdb=" N MET D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.727A pdb=" N ILE D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 105 removed outlier: 3.718A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.143A pdb=" N LEU D 121 " --> pdb=" O GLN D 118 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 122' Processing helix chain 'D' and resid 129 through 146 Proline residue: D 137 - end of helix removed outlier: 3.710A pdb=" N GLN D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 170 through 211 removed outlier: 3.749A pdb=" N LEU D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Proline residue: D 176 - end of helix Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.742A pdb=" N ILE D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Proline residue: D 224 - end of helix Processing helix chain 'D' and resid 235 through 248 removed outlier: 4.007A pdb=" N GLY D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 removed outlier: 3.576A pdb=" N ILE E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 91 through 116 removed outlier: 3.592A pdb=" N GLY E 95 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Proline residue: E 107 - end of helix Processing helix chain 'E' and resid 118 through 122 removed outlier: 4.059A pdb=" N LEU E 121 " --> pdb=" O GLN E 118 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 122' Processing helix chain 'E' and resid 129 through 146 Proline residue: E 137 - end of helix removed outlier: 3.812A pdb=" N GLN E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 173 through 211 removed outlier: 3.843A pdb=" N ALA E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Proline residue: E 196 - end of helix Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.661A pdb=" N ILE E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Proline residue: E 224 - end of helix removed outlier: 3.592A pdb=" N VAL E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 248 removed outlier: 3.858A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.805A pdb=" N PHE F 24 " --> pdb=" O MET F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'F' and resid 73 through 111 removed outlier: 4.115A pdb=" N PHE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE F 99 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 144 Processing helix chain 'F' and resid 145 through 161 removed outlier: 4.321A pdb=" N LEU F 151 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 177 through 211 removed outlier: 4.289A pdb=" N TRP F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) Proline residue: F 192 - end of helix removed outlier: 3.844A pdb=" N ALA F 196 " --> pdb=" O PRO F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 260 removed outlier: 3.553A pdb=" N VAL F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 237 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Proline residue: F 245 - end of helix removed outlier: 3.515A pdb=" N SER F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 Proline residue: G 27 - end of helix removed outlier: 3.654A pdb=" N THR G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 66 Processing helix chain 'G' and resid 66 through 88 Proline residue: G 85 - end of helix Processing helix chain 'H' and resid 2 through 42 Proline residue: H 27 - end of helix removed outlier: 3.655A pdb=" N THR H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 66 Processing helix chain 'H' and resid 66 through 88 Proline residue: H 85 - end of helix Processing helix chain 'I' and resid 2 through 42 Proline residue: I 27 - end of helix removed outlier: 3.654A pdb=" N THR I 42 " --> pdb=" O PHE I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 66 Processing helix chain 'I' and resid 66 through 88 Proline residue: I 85 - end of helix Processing helix chain 'J' and resid 2 through 42 Proline residue: J 27 - end of helix removed outlier: 3.656A pdb=" N THR J 42 " --> pdb=" O PHE J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 66 Processing helix chain 'J' and resid 66 through 88 Proline residue: J 85 - end of helix Processing helix chain 'K' and resid 3 through 35 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 53 through 66 Processing helix chain 'K' and resid 66 through 89 removed outlier: 3.601A pdb=" N LEU K 70 " --> pdb=" O GLY K 66 " (cutoff:3.500A) Proline residue: K 85 - end of helix removed outlier: 3.907A pdb=" N GLY K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.47 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: 3839 1.34 - 1.46: 2590 1.46 - 1.58: 6459 1.58 - 1.70: 0 1.70 - 1.81: 229 Bond restraints: 13117 Sorted by residual: bond pdb=" CA ASN F 177 " pdb=" C ASN F 177 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.41e-02 5.03e+03 5.98e+00 bond pdb=" CA ILE G 84 " pdb=" CB ILE G 84 " ideal model delta sigma weight residual 1.537 1.525 0.012 5.00e-03 4.00e+04 5.80e+00 bond pdb=" CA ILE I 84 " pdb=" CB ILE I 84 " ideal model delta sigma weight residual 1.537 1.525 0.012 5.00e-03 4.00e+04 5.49e+00 bond pdb=" CA ILE J 84 " pdb=" CB ILE J 84 " ideal model delta sigma weight residual 1.537 1.525 0.011 5.00e-03 4.00e+04 5.20e+00 bond pdb=" CA ILE H 84 " pdb=" CB ILE H 84 " ideal model delta sigma weight residual 1.537 1.526 0.011 5.00e-03 4.00e+04 5.10e+00 ... (remaining 13112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16968 1.77 - 3.53: 692 3.53 - 5.30: 164 5.30 - 7.06: 39 7.06 - 8.83: 8 Bond angle restraints: 17871 Sorted by residual: angle pdb=" C ILE K 84 " pdb=" CA ILE K 84 " pdb=" CB ILE K 84 " ideal model delta sigma weight residual 113.70 109.64 4.06 9.50e-01 1.11e+00 1.82e+01 angle pdb=" C PRO A 88 " pdb=" N SER A 89 " pdb=" CA SER A 89 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" N ASP E 234 " pdb=" CA ASP E 234 " pdb=" CB ASP E 234 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" C VAL F 118 " pdb=" N ASP F 119 " pdb=" CA ASP F 119 " ideal model delta sigma weight residual 121.80 130.63 -8.83 2.44e+00 1.68e-01 1.31e+01 angle pdb=" C PRO F 34 " pdb=" N VAL F 35 " pdb=" CA VAL F 35 " ideal model delta sigma weight residual 123.08 119.69 3.39 1.01e+00 9.80e-01 1.12e+01 ... (remaining 17866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6959 17.23 - 34.45: 753 34.45 - 51.68: 147 51.68 - 68.91: 23 68.91 - 86.14: 18 Dihedral angle restraints: 7900 sinusoidal: 3052 harmonic: 4848 Sorted by residual: dihedral pdb=" CA THR B 87 " pdb=" C THR B 87 " pdb=" N PRO B 88 " pdb=" CA PRO B 88 " ideal model delta harmonic sigma weight residual 180.00 119.23 60.77 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA THR A 87 " pdb=" C THR A 87 " pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta harmonic sigma weight residual 180.00 119.46 60.54 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N PRO C 88 " pdb=" CA PRO C 88 " ideal model delta harmonic sigma weight residual 180.00 120.51 59.49 0 5.00e+00 4.00e-02 1.42e+02 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1656 0.046 - 0.093: 487 0.093 - 0.139: 134 0.139 - 0.185: 7 0.185 - 0.232: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA GLU J 75 " pdb=" N GLU J 75 " pdb=" C GLU J 75 " pdb=" CB GLU J 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLU G 75 " pdb=" N GLU G 75 " pdb=" C GLU G 75 " pdb=" CB GLU G 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU I 75 " pdb=" N GLU I 75 " pdb=" C GLU I 75 " pdb=" CB GLU I 75 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2285 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 119 " -0.065 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO F 120 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO F 120 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 120 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 87 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 88 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " -0.061 5.00e-02 4.00e+02 9.34e-02 1.39e+01 pdb=" N PRO D 88 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.051 5.00e-02 4.00e+02 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 99 2.61 - 3.18: 12476 3.18 - 3.75: 20709 3.75 - 4.33: 27378 4.33 - 4.90: 45488 Nonbonded interactions: 106150 Sorted by model distance: nonbonded pdb=" O LEU J 78 " pdb=" OG1 THR J 82 " model vdw 2.035 3.040 nonbonded pdb=" O LEU G 78 " pdb=" OG1 THR G 82 " model vdw 2.035 3.040 nonbonded pdb=" O LEU I 78 " pdb=" OG1 THR I 82 " model vdw 2.035 3.040 nonbonded pdb=" O LEU H 78 " pdb=" OG1 THR H 82 " model vdw 2.035 3.040 nonbonded pdb=" O VAL C 62 " pdb=" OG1 THR C 66 " model vdw 2.163 3.040 ... (remaining 106145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 55 through 250) selection = (chain 'C' and resid 55 through 250) selection = (chain 'D' and resid 55 through 250) selection = (chain 'E' and resid 55 through 250) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.770 Find NCS groups from input model: 0.180 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: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.006 0.049 13117 Z= 0.254 Angle : 0.886 8.831 17871 Z= 0.467 Chirality : 0.046 0.232 2288 Planarity : 0.007 0.100 2149 Dihedral : 15.344 86.137 4726 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.39 % Favored : 90.82 % Rotamer: Outliers : 2.22 % Allowed : 5.42 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.19 % 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: -3.03 (0.18), residues: 1645 helix: -1.31 (0.13), residues: 1302 sheet: None (None), residues: 0 loop : -4.26 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 70 TYR 0.012 0.002 TYR J 76 PHE 0.029 0.002 PHE F 132 TRP 0.020 0.002 TRP J 68 HIS 0.005 0.002 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00581 (13117) covalent geometry : angle 0.88629 (17871) hydrogen bonds : bond 0.12794 ( 931) hydrogen bonds : angle 5.97394 ( 2793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 376 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7914 (tttt) REVERT: A 211 MET cc_start: 0.7489 (mmm) cc_final: 0.7261 (mmm) REVERT: A 220 ILE cc_start: 0.8731 (tt) cc_final: 0.8497 (tt) REVERT: B 170 PRO cc_start: 0.5769 (Cg_endo) cc_final: 0.5496 (Cg_exo) REVERT: C 182 GLU cc_start: 0.7463 (tp30) cc_final: 0.7180 (tp30) REVERT: D 96 MET cc_start: 0.7659 (tpt) cc_final: 0.7163 (ttm) REVERT: D 98 LEU cc_start: 0.8623 (tp) cc_final: 0.8277 (tt) REVERT: D 182 GLU cc_start: 0.7414 (tp30) cc_final: 0.7190 (tp30) REVERT: E 209 MET cc_start: 0.3688 (ppp) cc_final: 0.2756 (ppp) REVERT: F 117 MET cc_start: 0.5891 (pmm) cc_final: 0.5481 (pmm) REVERT: F 219 ILE cc_start: 0.8821 (mm) cc_final: 0.8611 (mm) REVERT: H 29 LEU cc_start: 0.8355 (tt) cc_final: 0.8151 (tt) REVERT: H 34 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7361 (tp) REVERT: J 23 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (mm) REVERT: K 58 MET cc_start: 0.8273 (tpp) cc_final: 0.8056 (tpp) REVERT: K 71 LYS cc_start: 0.6237 (tttp) cc_final: 0.5460 (mptt) outliers start: 32 outliers final: 5 residues processed: 393 average time/residue: 0.1095 time to fit residues: 63.9685 Evaluate side-chains 302 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 295 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 37 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0170 chunk 149 optimal weight: 3.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN C 113 ASN E 118 GLN F 11 GLN F 97 HIS F 109 GLN ** F 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN H 39 GLN J 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153032 restraints weight = 15392.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154857 restraints weight = 11207.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155803 restraints weight = 8568.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155990 restraints weight = 7347.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156066 restraints weight = 7075.695| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13117 Z= 0.171 Angle : 0.808 13.549 17871 Z= 0.400 Chirality : 0.046 0.293 2288 Planarity : 0.006 0.084 2149 Dihedral : 6.774 59.181 1739 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.98 % Rotamer: Outliers : 2.64 % Allowed : 13.62 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: -0.96 (0.21), residues: 1645 helix: 0.20 (0.14), residues: 1331 sheet: None (None), residues: 0 loop : -4.12 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 25 TYR 0.019 0.002 TYR B 120 PHE 0.025 0.002 PHE D 109 TRP 0.024 0.002 TRP G 68 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00372 (13117) covalent geometry : angle 0.80832 (17871) hydrogen bonds : bond 0.04586 ( 931) hydrogen bonds : angle 4.57204 ( 2793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7939 (p0) cc_final: 0.7543 (t0) REVERT: A 139 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7918 (tttm) REVERT: A 220 ILE cc_start: 0.8642 (tt) cc_final: 0.8432 (tt) REVERT: C 71 ILE cc_start: 0.8916 (mt) cc_final: 0.8690 (mm) REVERT: C 105 MET cc_start: 0.7935 (mmm) cc_final: 0.7554 (mmm) REVERT: C 139 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8484 (mtpt) REVERT: C 192 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7095 (mpp) REVERT: D 109 PHE cc_start: 0.7674 (m-80) cc_final: 0.7132 (m-80) REVERT: D 173 ILE cc_start: 0.7493 (tt) cc_final: 0.6869 (mt) REVERT: D 211 MET cc_start: 0.7104 (mmm) cc_final: 0.6450 (mtm) REVERT: E 142 MET cc_start: 0.8443 (mtp) cc_final: 0.8215 (mtm) REVERT: E 209 MET cc_start: 0.4080 (ppp) cc_final: 0.1356 (tpp) REVERT: I 23 ILE cc_start: 0.8931 (mm) cc_final: 0.8691 (mt) REVERT: K 58 MET cc_start: 0.8109 (tpp) cc_final: 0.7834 (tpp) REVERT: K 71 LYS cc_start: 0.6184 (tttp) cc_final: 0.5403 (mptt) outliers start: 38 outliers final: 14 residues processed: 331 average time/residue: 0.0980 time to fit residues: 49.9909 Evaluate side-chains 298 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 144 optimal weight: 0.0470 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN G 39 GLN I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.174885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149779 restraints weight = 15625.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152682 restraints weight = 10418.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154580 restraints weight = 7980.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155458 restraints weight = 6739.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156431 restraints weight = 6128.324| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13117 Z= 0.153 Angle : 0.760 13.187 17871 Z= 0.372 Chirality : 0.043 0.217 2288 Planarity : 0.006 0.086 2149 Dihedral : 6.244 58.091 1725 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.46 % Rotamer: Outliers : 2.57 % Allowed : 16.75 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: -0.15 (0.21), residues: 1645 helix: 0.90 (0.15), residues: 1293 sheet: None (None), residues: 0 loop : -3.91 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 111 TYR 0.029 0.002 TYR A 120 PHE 0.032 0.002 PHE B 247 TRP 0.022 0.002 TRP G 68 HIS 0.005 0.002 HIS F 147 Details of bonding type rmsd covalent geometry : bond 0.00323 (13117) covalent geometry : angle 0.75983 (17871) hydrogen bonds : bond 0.04139 ( 931) hydrogen bonds : angle 4.34715 ( 2793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7860 (tttm) REVERT: A 220 ILE cc_start: 0.8550 (tt) cc_final: 0.8344 (tt) REVERT: B 70 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7806 (ptp-170) REVERT: B 175 VAL cc_start: 0.9315 (t) cc_final: 0.9033 (t) REVERT: C 71 ILE cc_start: 0.8890 (mt) cc_final: 0.8615 (mm) REVERT: C 192 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7054 (mpp) REVERT: D 100 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7774 (tt) REVERT: D 109 PHE cc_start: 0.7676 (m-80) cc_final: 0.7312 (m-80) REVERT: D 209 MET cc_start: 0.8137 (mmm) cc_final: 0.7930 (mmm) REVERT: D 211 MET cc_start: 0.6902 (mmm) cc_final: 0.6600 (mtm) REVERT: E 105 MET cc_start: 0.7359 (mmm) cc_final: 0.6531 (mmm) REVERT: E 142 MET cc_start: 0.8400 (mtp) cc_final: 0.8162 (mtm) REVERT: E 209 MET cc_start: 0.4106 (ppp) cc_final: 0.1720 (tpp) REVERT: F 94 MET cc_start: 0.8454 (mpp) cc_final: 0.8115 (mpp) REVERT: I 23 ILE cc_start: 0.8877 (mm) cc_final: 0.8512 (mt) REVERT: I 52 LEU cc_start: 0.8447 (tp) cc_final: 0.8242 (tp) REVERT: K 58 MET cc_start: 0.8012 (tpp) cc_final: 0.7805 (tpp) REVERT: K 71 LYS cc_start: 0.6094 (tttp) cc_final: 0.5387 (mptt) outliers start: 37 outliers final: 16 residues processed: 315 average time/residue: 0.1007 time to fit residues: 48.4918 Evaluate side-chains 292 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149486 restraints weight = 15520.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150704 restraints weight = 11594.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151315 restraints weight = 9661.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152018 restraints weight = 8576.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152096 restraints weight = 7452.956| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13117 Z= 0.183 Angle : 0.766 12.466 17871 Z= 0.376 Chirality : 0.044 0.229 2288 Planarity : 0.006 0.087 2149 Dihedral : 6.175 59.070 1723 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 4.31 % Allowed : 18.42 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % 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: 0.00 (0.22), residues: 1645 helix: 0.94 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -3.97 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 111 TYR 0.008 0.001 TYR C 120 PHE 0.020 0.002 PHE C 154 TRP 0.016 0.002 TRP H 68 HIS 0.003 0.002 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00440 (13117) covalent geometry : angle 0.76618 (17871) hydrogen bonds : bond 0.04233 ( 931) hydrogen bonds : angle 4.31175 ( 2793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7945 (tttt) REVERT: A 220 ILE cc_start: 0.8592 (tt) cc_final: 0.8382 (tt) REVERT: B 70 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7736 (ptp-170) REVERT: B 175 VAL cc_start: 0.9334 (t) cc_final: 0.9043 (t) REVERT: B 247 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: C 92 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6065 (mt) REVERT: C 192 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: D 109 PHE cc_start: 0.7766 (m-80) cc_final: 0.7420 (m-80) REVERT: D 229 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7916 (mm) REVERT: E 105 MET cc_start: 0.7397 (mmm) cc_final: 0.6600 (mmm) REVERT: E 209 MET cc_start: 0.4486 (ppp) cc_final: 0.3245 (tpp) REVERT: F 251 LEU cc_start: 0.7900 (mt) cc_final: 0.7681 (mt) REVERT: G 1 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6582 (ttt) REVERT: H 37 MET cc_start: 0.6234 (ttt) cc_final: 0.5444 (mtt) REVERT: I 23 ILE cc_start: 0.8852 (mm) cc_final: 0.8508 (mt) REVERT: K 58 MET cc_start: 0.7934 (tpp) cc_final: 0.7687 (tpp) REVERT: K 71 LYS cc_start: 0.6178 (tttp) cc_final: 0.5424 (mptt) outliers start: 62 outliers final: 32 residues processed: 329 average time/residue: 0.0973 time to fit residues: 49.6001 Evaluate side-chains 320 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 31 CYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 101 optimal weight: 0.0980 chunk 69 optimal weight: 0.0010 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 188 GLN F 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151451 restraints weight = 15507.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152937 restraints weight = 11809.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154387 restraints weight = 8782.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155093 restraints weight = 7430.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155261 restraints weight = 6841.733| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13117 Z= 0.138 Angle : 0.739 14.909 17871 Z= 0.359 Chirality : 0.042 0.199 2288 Planarity : 0.006 0.083 2149 Dihedral : 5.917 59.287 1723 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 3.20 % Allowed : 21.26 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.34 (0.22), residues: 1645 helix: 1.26 (0.15), residues: 1298 sheet: None (None), residues: 0 loop : -3.94 (0.28), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 111 TYR 0.009 0.001 TYR D 120 PHE 0.018 0.002 PHE C 154 TRP 0.021 0.001 TRP H 68 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00290 (13117) covalent geometry : angle 0.73896 (17871) hydrogen bonds : bond 0.03824 ( 931) hydrogen bonds : angle 4.15901 ( 2793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7834 (tttm) REVERT: B 70 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7659 (ptp-170) REVERT: B 247 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: C 92 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.5944 (mt) REVERT: C 192 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7159 (mpp) REVERT: D 100 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7830 (tt) REVERT: D 109 PHE cc_start: 0.7777 (m-80) cc_final: 0.7408 (m-80) REVERT: E 105 MET cc_start: 0.7288 (mmm) cc_final: 0.6563 (mmm) REVERT: E 209 MET cc_start: 0.4333 (ppp) cc_final: 0.2665 (tpp) REVERT: F 94 MET cc_start: 0.8474 (mpp) cc_final: 0.8226 (mpp) REVERT: F 117 MET cc_start: 0.5043 (pmm) cc_final: 0.4754 (pmm) REVERT: G 1 MET cc_start: 0.7025 (ttt) cc_final: 0.6698 (ttt) REVERT: H 37 MET cc_start: 0.6292 (ttt) cc_final: 0.5583 (mtt) REVERT: I 72 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7481 (mt) REVERT: K 58 MET cc_start: 0.7824 (tpp) cc_final: 0.7575 (tpp) outliers start: 46 outliers final: 24 residues processed: 327 average time/residue: 0.0964 time to fit residues: 48.7105 Evaluate side-chains 312 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 91 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN I 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144462 restraints weight = 15549.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145442 restraints weight = 10170.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145804 restraints weight = 8540.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146426 restraints weight = 7963.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146553 restraints weight = 7474.776| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13117 Z= 0.238 Angle : 0.833 14.929 17871 Z= 0.403 Chirality : 0.047 0.259 2288 Planarity : 0.006 0.095 2149 Dihedral : 6.250 59.557 1723 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 4.24 % Allowed : 21.89 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % 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: 0.05 (0.21), residues: 1645 helix: 1.06 (0.15), residues: 1294 sheet: None (None), residues: 0 loop : -3.98 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 111 TYR 0.013 0.002 TYR D 120 PHE 0.021 0.002 PHE G 10 TRP 0.016 0.002 TRP I 68 HIS 0.005 0.002 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00581 (13117) covalent geometry : angle 0.83254 (17871) hydrogen bonds : bond 0.04546 ( 931) hydrogen bonds : angle 4.35907 ( 2793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8035 (tttm) REVERT: B 70 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7752 (ptp-170) REVERT: C 92 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6218 (mt) REVERT: C 192 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: D 100 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8214 (tt) REVERT: D 109 PHE cc_start: 0.7784 (m-80) cc_final: 0.7342 (m-80) REVERT: D 173 ILE cc_start: 0.7598 (tt) cc_final: 0.6981 (mt) REVERT: D 229 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7949 (mm) REVERT: E 90 ASN cc_start: 0.7649 (p0) cc_final: 0.7267 (p0) REVERT: E 105 MET cc_start: 0.7456 (mmm) cc_final: 0.6712 (mmm) REVERT: E 109 PHE cc_start: 0.7125 (m-80) cc_final: 0.6919 (m-80) REVERT: E 156 ARG cc_start: 0.8154 (tmm160) cc_final: 0.7942 (ptt90) REVERT: E 209 MET cc_start: 0.5513 (ppp) cc_final: 0.4676 (tpp) REVERT: G 34 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7508 (tt) REVERT: H 34 LEU cc_start: 0.7873 (mt) cc_final: 0.7493 (tt) REVERT: H 37 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5695 (mtt) outliers start: 61 outliers final: 35 residues processed: 336 average time/residue: 0.0961 time to fit residues: 50.0508 Evaluate side-chains 329 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147773 restraints weight = 15467.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150432 restraints weight = 10503.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152174 restraints weight = 8166.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153100 restraints weight = 6953.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153882 restraints weight = 6326.085| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13117 Z= 0.154 Angle : 0.768 13.845 17871 Z= 0.371 Chirality : 0.043 0.222 2288 Planarity : 0.006 0.088 2149 Dihedral : 5.987 58.247 1723 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 3.27 % Allowed : 23.07 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1645 helix: 1.25 (0.15), residues: 1303 sheet: None (None), residues: 0 loop : -3.84 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 70 TYR 0.016 0.001 TYR H 76 PHE 0.021 0.002 PHE A 247 TRP 0.017 0.002 TRP H 68 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00349 (13117) covalent geometry : angle 0.76760 (17871) hydrogen bonds : bond 0.04017 ( 931) hydrogen bonds : angle 4.20188 ( 2793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7922 (tttm) REVERT: B 70 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7680 (ptp-170) REVERT: C 69 THR cc_start: 0.9419 (p) cc_final: 0.9206 (m) REVERT: C 92 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.5972 (mt) REVERT: C 192 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: D 100 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8104 (tt) REVERT: D 109 PHE cc_start: 0.7738 (m-80) cc_final: 0.7339 (m-80) REVERT: D 173 ILE cc_start: 0.7501 (tt) cc_final: 0.6852 (mt) REVERT: D 201 ASP cc_start: 0.8102 (t0) cc_final: 0.7875 (t0) REVERT: D 229 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7889 (mm) REVERT: E 105 MET cc_start: 0.7321 (mmm) cc_final: 0.6638 (mmm) REVERT: E 109 PHE cc_start: 0.7099 (m-80) cc_final: 0.6842 (m-80) REVERT: E 156 ARG cc_start: 0.8055 (tmm160) cc_final: 0.7853 (ptt90) REVERT: E 209 MET cc_start: 0.5447 (ppp) cc_final: 0.4693 (tpp) REVERT: H 34 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7509 (tt) REVERT: H 37 MET cc_start: 0.6088 (ttt) cc_final: 0.5797 (mtt) REVERT: K 58 MET cc_start: 0.8118 (tpp) cc_final: 0.7871 (tpp) outliers start: 47 outliers final: 25 residues processed: 320 average time/residue: 0.0975 time to fit residues: 48.0147 Evaluate side-chains 316 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** 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 = 0.4039 r_free = 0.4039 target = 0.178726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154866 restraints weight = 15089.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155398 restraints weight = 10874.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155819 restraints weight = 9215.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156745 restraints weight = 8562.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156890 restraints weight = 7401.975| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13117 Z= 0.144 Angle : 0.772 16.449 17871 Z= 0.369 Chirality : 0.043 0.221 2288 Planarity : 0.006 0.086 2149 Dihedral : 5.827 58.046 1723 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 2.92 % Allowed : 24.67 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1645 helix: 1.35 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -3.74 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 111 TYR 0.013 0.001 TYR H 76 PHE 0.034 0.002 PHE A 247 TRP 0.018 0.002 TRP I 68 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00318 (13117) covalent geometry : angle 0.77246 (17871) hydrogen bonds : bond 0.03850 ( 931) hydrogen bonds : angle 4.12976 ( 2793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 120 TYR cc_start: 0.6290 (t80) cc_final: 0.6039 (t80) REVERT: A 139 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7868 (tttm) REVERT: A 211 MET cc_start: 0.6526 (mmm) cc_final: 0.6253 (mmp) REVERT: B 70 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7741 (ptp-170) REVERT: B 80 GLN cc_start: 0.7799 (mt0) cc_final: 0.7578 (mt0) REVERT: C 69 THR cc_start: 0.9432 (p) cc_final: 0.9198 (m) REVERT: C 92 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6046 (mt) REVERT: C 192 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7236 (mpp) REVERT: D 100 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8072 (tt) REVERT: D 109 PHE cc_start: 0.7701 (m-80) cc_final: 0.7313 (m-80) REVERT: D 139 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7868 (ttmm) REVERT: D 173 ILE cc_start: 0.7534 (tt) cc_final: 0.6901 (mt) REVERT: D 201 ASP cc_start: 0.8105 (t0) cc_final: 0.7836 (t0) REVERT: D 211 MET cc_start: 0.7189 (mmm) cc_final: 0.6495 (mtm) REVERT: D 214 MET cc_start: 0.7013 (tpp) cc_final: 0.6782 (mmm) REVERT: E 105 MET cc_start: 0.7143 (mmm) cc_final: 0.6474 (mmm) REVERT: E 109 PHE cc_start: 0.7051 (m-80) cc_final: 0.6771 (m-80) REVERT: E 209 MET cc_start: 0.5698 (ppp) cc_final: 0.5248 (tpp) REVERT: E 247 PHE cc_start: 0.8355 (t80) cc_final: 0.8098 (t80) REVERT: F 252 GLN cc_start: 0.7697 (tp40) cc_final: 0.7483 (tp-100) REVERT: H 34 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7511 (tt) REVERT: H 37 MET cc_start: 0.6132 (ttt) cc_final: 0.5788 (mtt) outliers start: 42 outliers final: 22 residues processed: 318 average time/residue: 0.0971 time to fit residues: 47.5985 Evaluate side-chains 310 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 31 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 109 GLN ** 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 = 0.4033 r_free = 0.4033 target = 0.177888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152503 restraints weight = 15283.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155139 restraints weight = 10320.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156948 restraints weight = 8068.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157855 restraints weight = 6906.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158729 restraints weight = 6299.125| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13117 Z= 0.154 Angle : 0.782 15.098 17871 Z= 0.373 Chirality : 0.044 0.450 2288 Planarity : 0.006 0.088 2149 Dihedral : 5.818 56.820 1723 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 2.50 % Allowed : 25.09 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % 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 (0.22), residues: 1645 helix: 1.35 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -3.64 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 70 TYR 0.016 0.001 TYR H 76 PHE 0.029 0.002 PHE A 247 TRP 0.019 0.002 TRP I 68 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00353 (13117) covalent geometry : angle 0.78203 (17871) hydrogen bonds : bond 0.03900 ( 931) hydrogen bonds : angle 4.12621 ( 2793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7873 (tttm) REVERT: A 211 MET cc_start: 0.6466 (mmm) cc_final: 0.6226 (mmp) REVERT: B 70 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: B 80 GLN cc_start: 0.7813 (mt0) cc_final: 0.7579 (mt0) REVERT: C 69 THR cc_start: 0.9396 (p) cc_final: 0.9179 (m) REVERT: C 92 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.5958 (mt) REVERT: C 109 PHE cc_start: 0.7274 (m-80) cc_final: 0.7064 (m-80) REVERT: C 192 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7200 (mpp) REVERT: D 100 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8054 (tt) REVERT: D 109 PHE cc_start: 0.7713 (m-80) cc_final: 0.7349 (m-80) REVERT: D 139 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7852 (ttmm) REVERT: D 173 ILE cc_start: 0.7494 (tt) cc_final: 0.6858 (mt) REVERT: D 214 MET cc_start: 0.6940 (tpp) cc_final: 0.6669 (mmt) REVERT: D 229 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7831 (mm) REVERT: E 105 MET cc_start: 0.7178 (mmm) cc_final: 0.6485 (mmm) REVERT: E 109 PHE cc_start: 0.7090 (m-80) cc_final: 0.6796 (m-80) REVERT: E 209 MET cc_start: 0.5917 (ppp) cc_final: 0.5544 (tpp) REVERT: E 247 PHE cc_start: 0.8314 (t80) cc_final: 0.8080 (t80) REVERT: F 252 GLN cc_start: 0.7682 (tp40) cc_final: 0.7467 (tp-100) REVERT: H 34 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7524 (tt) outliers start: 36 outliers final: 24 residues processed: 304 average time/residue: 0.1005 time to fit residues: 47.0712 Evaluate side-chains 313 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 PHE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain K residue 72 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7076 > 50: distance: 4 - 26: 32.654 distance: 23 - 26: 34.372 distance: 27 - 28: 35.882 distance: 27 - 30: 29.104 distance: 28 - 29: 55.838 distance: 28 - 34: 31.614 distance: 30 - 31: 46.939 distance: 31 - 32: 25.166 distance: 31 - 33: 41.489 distance: 34 - 35: 27.424 distance: 35 - 36: 8.087 distance: 36 - 37: 23.653 distance: 36 - 38: 6.391 distance: 38 - 39: 34.713 distance: 39 - 40: 52.997 distance: 39 - 42: 7.763 distance: 40 - 41: 34.166 distance: 40 - 46: 8.086 distance: 42 - 43: 22.789 distance: 43 - 44: 18.597 distance: 43 - 45: 29.687 distance: 46 - 47: 22.506 distance: 47 - 48: 48.911 distance: 47 - 50: 40.551 distance: 48 - 49: 15.367 distance: 48 - 55: 42.828 distance: 50 - 51: 46.578 distance: 51 - 52: 41.051 distance: 52 - 53: 29.599 distance: 52 - 54: 40.171 distance: 55 - 56: 18.618 distance: 56 - 57: 41.266 distance: 56 - 59: 12.332 distance: 57 - 58: 33.438 distance: 57 - 64: 24.124 distance: 59 - 60: 45.845 distance: 60 - 61: 17.504 distance: 61 - 62: 43.466 distance: 61 - 63: 9.850 distance: 65 - 66: 40.647 distance: 65 - 68: 6.248 distance: 66 - 67: 40.560 distance: 66 - 71: 59.051 distance: 68 - 69: 19.529 distance: 68 - 70: 29.295 distance: 71 - 72: 55.135 distance: 71 - 77: 39.352 distance: 72 - 73: 22.971 distance: 72 - 75: 33.775 distance: 73 - 74: 27.178 distance: 73 - 78: 21.627 distance: 75 - 76: 16.733 distance: 76 - 77: 41.162 distance: 78 - 79: 46.274 distance: 79 - 80: 13.601 distance: 79 - 82: 14.864 distance: 80 - 81: 6.272 distance: 80 - 84: 6.070 distance: 84 - 85: 36.546 distance: 85 - 86: 4.518 distance: 85 - 88: 23.470 distance: 86 - 87: 40.438 distance: 86 - 92: 5.461 distance: 88 - 89: 45.378 distance: 89 - 90: 38.578 distance: 89 - 91: 40.574 distance: 92 - 93: 12.897 distance: 93 - 94: 13.160 distance: 93 - 96: 6.101 distance: 94 - 95: 11.203 distance: 94 - 101: 22.408 distance: 95 - 123: 23.089 distance: 96 - 97: 46.853 distance: 97 - 98: 16.008 distance: 98 - 99: 17.364 distance: 98 - 100: 19.099