Starting phenix.real_space_refine on Wed Feb 4 12:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.map" model { file = "/net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9me6_48185/02_2026/9me6_48185.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.205 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 47 5.16 5 C 6599 2.51 5 N 1724 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1195 Classifications: {'peptide': 158} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 147} Chain: "H" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1623 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1649 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Chain: "I" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1586 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194} Chain: "M" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1528 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1486 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 186} Chain: "N" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1388 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.59, per 1000 atoms: 0.25 Number of scatterers: 10516 At special positions: 0 Unit cell: (76.432, 124.764, 196.7, 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 47 16.00 O 2146 8.00 N 1724 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 199 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.04 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 Links applied ALPHA1-3 " MAN B 3 " - " MAN B 4 " ALPHA1-4 " NAG B 2 " - " MAN B 3 " ALPHA1-6 " MAN B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN L 90 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 549.7 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 34 sheets defined 6.9% alpha, 49.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.860A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'L' and resid 120 through 126 removed outlier: 3.556A pdb=" N SER L 126 " --> pdb=" O GLU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 186 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.835A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 90 Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.692A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 166 through 170 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.678A pdb=" N ALA N 82 " --> pdb=" O ALA N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.892A pdb=" N ALA A 2 " --> pdb=" O HIS A 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 45 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.318A pdb=" N GLY A 16 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN A 147 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 127 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 150 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 125 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 60 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU A 58 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR A 134 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL A 56 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 4.092A pdb=" N GLY A 73 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.609A pdb=" N VAL A 154 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.364A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.940A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 156 through 159 removed outlier: 3.526A pdb=" N THR H 156 " --> pdb=" O ALA H 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 6.541A pdb=" N THR L 68 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN L 27 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N SER L 66 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N VAL L 29 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N SER L 64 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.572A pdb=" N VAL L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR L 48 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP L 34 " --> pdb=" O MET L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.750A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 115 through 117 removed outlier: 3.690A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 152 through 153 Processing sheet with id=AB6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.514A pdb=" N ALA I 92 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR I 33 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.514A pdb=" N ALA I 92 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N CYS I 96 " --> pdb=" O TRP I 107 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP I 107 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG I 98 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.723A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR I 179 " --> pdb=" O GLY I 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.723A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR I 179 " --> pdb=" O GLY I 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 155 through 158 Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.538A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.538A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.871A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.329A pdb=" N TRP M 148 " --> pdb=" O ARG M 155 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN M 145 " --> pdb=" O ARG M 197 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.757A pdb=" N ILE J 34 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.732A pdb=" N TYR J 114 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 132 through 136 removed outlier: 3.951A pdb=" N GLY J 151 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR J 187 " --> pdb=" O GLY J 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 132 through 136 removed outlier: 3.951A pdb=" N GLY J 151 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR J 187 " --> pdb=" O GLY J 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.617A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS N 106 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA N 13 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLN N 36 " --> pdb=" O ILE N 45 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE N 45 " --> pdb=" O GLN N 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.617A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS N 106 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA N 13 " --> pdb=" O LYS N 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR N 96 " --> pdb=" O GLN N 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 113 through 117 removed outlier: 3.860A pdb=" N VAL N 132 " --> pdb=" O PHE N 117 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR N 172 " --> pdb=" O ASN N 137 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1113 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: 1.81 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3330 1.35 - 1.47: 2928 1.47 - 1.60: 4449 1.60 - 1.72: 0 1.72 - 1.85: 68 Bond restraints: 10775 Sorted by residual: bond pdb=" C1 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C1 MAN B 3 " pdb=" C2 MAN B 3 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" N MET I 139 " pdb=" CA MET I 139 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.44e+00 bond pdb=" C PRO M 119 " pdb=" N PRO M 120 " ideal model delta sigma weight residual 1.332 1.364 -0.033 1.30e-02 5.92e+03 6.36e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.73e+00 ... (remaining 10770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14334 1.66 - 3.32: 294 3.32 - 4.97: 49 4.97 - 6.63: 11 6.63 - 8.29: 5 Bond angle restraints: 14693 Sorted by residual: angle pdb=" N PRO M 120 " pdb=" CA PRO M 120 " pdb=" CB PRO M 120 " ideal model delta sigma weight residual 103.31 106.34 -3.03 8.90e-01 1.26e+00 1.16e+01 angle pdb=" CA CYS A 44 " pdb=" C CYS A 44 " pdb=" O CYS A 44 " ideal model delta sigma weight residual 121.40 117.65 3.75 1.11e+00 8.12e-01 1.14e+01 angle pdb=" C SER L 49 " pdb=" N ALA L 50 " pdb=" CA ALA L 50 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.51e+00 angle pdb=" C GLN L 89 " pdb=" N ASN L 90 " pdb=" CA ASN L 90 " ideal model delta sigma weight residual 122.49 118.23 4.26 1.55e+00 4.16e-01 7.56e+00 angle pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sigma weight residual 107.29 115.53 -8.24 3.00e+00 1.11e-01 7.54e+00 ... (remaining 14688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5680 17.17 - 34.34: 567 34.34 - 51.51: 150 51.51 - 68.68: 38 68.68 - 85.85: 13 Dihedral angle restraints: 6448 sinusoidal: 2476 harmonic: 3972 Sorted by residual: dihedral pdb=" CA SER H 195 " pdb=" C SER H 195 " pdb=" N GLU H 196 " pdb=" CA GLU H 196 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TYR J 60 " pdb=" C TYR J 60 " pdb=" N ASN J 61 " pdb=" CA ASN J 61 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN N 136 " pdb=" C ASN N 136 " pdb=" N ASN N 137 " pdb=" CA ASN N 137 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1303 0.051 - 0.103: 295 0.103 - 0.154: 63 0.154 - 0.206: 0 0.206 - 0.257: 1 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE N 47 " pdb=" N ILE N 47 " pdb=" C ILE N 47 " pdb=" CB ILE N 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO H 194 " pdb=" N PRO H 194 " pdb=" C PRO H 194 " pdb=" CB PRO H 194 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1659 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 90 " -0.026 2.00e-02 2.50e+03 2.46e-02 7.59e+00 pdb=" CG ASN L 90 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN L 90 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN L 90 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 90 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 91 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 204 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO H 205 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 205 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 205 " -0.028 5.00e-02 4.00e+02 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 997 2.75 - 3.28: 9491 3.28 - 3.82: 16963 3.82 - 4.36: 20432 4.36 - 4.90: 36057 Nonbonded interactions: 83940 Sorted by model distance: nonbonded pdb=" ND2 ASN I 55 " pdb=" OD1 ASP I 57 " model vdw 2.208 3.120 nonbonded pdb=" OE1 GLN L 3 " pdb=" OG1 THR L 5 " model vdw 2.213 3.040 nonbonded pdb=" N GLN N 1 " pdb=" OE1 GLN N 1 " model vdw 2.233 3.120 nonbonded pdb=" N GLU L 1 " pdb=" OE1 GLU L 1 " model vdw 2.236 3.120 nonbonded pdb=" O SER J 85 " pdb=" OG SER J 85 " model vdw 2.241 3.040 ... (remaining 83935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10791 Z= 0.184 Angle : 0.640 9.594 14730 Z= 0.329 Chirality : 0.045 0.257 1662 Planarity : 0.005 0.054 1870 Dihedral : 15.551 85.851 3883 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.29 % Allowed : 19.04 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1357 helix: -0.86 (0.73), residues: 44 sheet: 0.96 (0.21), residues: 624 loop : -0.57 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 98 TYR 0.020 0.002 TYR I 33 PHE 0.013 0.001 PHE L 86 TRP 0.014 0.002 TRP N 90 HIS 0.003 0.001 HIS L 197 Details of bonding type rmsd covalent geometry : bond 0.00412 (10775) covalent geometry : angle 0.62401 (14693) SS BOND : bond 0.00666 ( 11) SS BOND : angle 1.31632 ( 22) hydrogen bonds : bond 0.21010 ( 400) hydrogen bonds : angle 9.31109 ( 1113) link_ALPHA1-3 : bond 0.00875 ( 1) link_ALPHA1-3 : angle 4.62212 ( 3) link_ALPHA1-4 : bond 0.00525 ( 1) link_ALPHA1-4 : angle 5.73080 ( 3) link_ALPHA1-6 : bond 0.01821 ( 1) link_ALPHA1-6 : angle 1.91423 ( 3) link_BETA1-4 : bond 0.00367 ( 1) link_BETA1-4 : angle 5.12376 ( 3) link_NAG-ASN : bond 0.00326 ( 1) link_NAG-ASN : angle 3.07759 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: I 62 GLN cc_start: 0.8317 (tp40) cc_final: 0.8112 (tp40) outliers start: 39 outliers final: 36 residues processed: 204 average time/residue: 0.1145 time to fit residues: 31.8289 Evaluate side-chains 202 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 5 GLN L 31 ASN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.153354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.108134 restraints weight = 11588.043| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.59 r_work: 0.2516 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10791 Z= 0.160 Angle : 0.639 9.461 14730 Z= 0.330 Chirality : 0.046 0.244 1662 Planarity : 0.005 0.053 1870 Dihedral : 7.083 55.462 1626 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.62 % Allowed : 17.02 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1357 helix: -0.84 (0.72), residues: 44 sheet: 1.00 (0.21), residues: 629 loop : -0.55 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.021 0.002 TYR I 33 PHE 0.011 0.002 PHE L 86 TRP 0.016 0.001 TRP N 90 HIS 0.004 0.001 HIS L 197 Details of bonding type rmsd covalent geometry : bond 0.00372 (10775) covalent geometry : angle 0.62673 (14693) SS BOND : bond 0.00654 ( 11) SS BOND : angle 1.16538 ( 22) hydrogen bonds : bond 0.04028 ( 400) hydrogen bonds : angle 6.39426 ( 1113) link_ALPHA1-3 : bond 0.00825 ( 1) link_ALPHA1-3 : angle 3.74781 ( 3) link_ALPHA1-4 : bond 0.00790 ( 1) link_ALPHA1-4 : angle 4.64680 ( 3) link_ALPHA1-6 : bond 0.02199 ( 1) link_ALPHA1-6 : angle 2.04369 ( 3) link_BETA1-4 : bond 0.00000 ( 1) link_BETA1-4 : angle 3.79436 ( 3) link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 4.09674 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 163 LEU cc_start: 0.8320 (mp) cc_final: 0.8038 (mp) REVERT: J 142 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6400 (p0) outliers start: 43 outliers final: 26 residues processed: 207 average time/residue: 0.1152 time to fit residues: 32.4630 Evaluate side-chains 198 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 30 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 31 ASN I 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.152969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.107267 restraints weight = 11597.040| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.65 r_work: 0.2511 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10791 Z= 0.171 Angle : 0.627 9.024 14730 Z= 0.323 Chirality : 0.046 0.259 1662 Planarity : 0.005 0.055 1870 Dihedral : 6.562 52.377 1591 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.62 % Allowed : 17.02 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1357 helix: -0.45 (0.74), residues: 43 sheet: 1.05 (0.21), residues: 625 loop : -0.58 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.024 0.002 TYR I 33 PHE 0.013 0.002 PHE L 86 TRP 0.016 0.001 TRP N 90 HIS 0.004 0.001 HIS N 33 Details of bonding type rmsd covalent geometry : bond 0.00404 (10775) covalent geometry : angle 0.61556 (14693) SS BOND : bond 0.00657 ( 11) SS BOND : angle 1.21873 ( 22) hydrogen bonds : bond 0.03866 ( 400) hydrogen bonds : angle 5.89811 ( 1113) link_ALPHA1-3 : bond 0.00745 ( 1) link_ALPHA1-3 : angle 3.89901 ( 3) link_ALPHA1-4 : bond 0.00876 ( 1) link_ALPHA1-4 : angle 4.61784 ( 3) link_ALPHA1-6 : bond 0.02210 ( 1) link_ALPHA1-6 : angle 2.08141 ( 3) link_BETA1-4 : bond 0.00008 ( 1) link_BETA1-4 : angle 3.35490 ( 3) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 3.10749 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7744 (mtpt) REVERT: J 43 THR cc_start: 0.8437 (m) cc_final: 0.8005 (t) outliers start: 43 outliers final: 36 residues processed: 208 average time/residue: 0.1121 time to fit residues: 32.4299 Evaluate side-chains 210 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 53 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 31 ASN I 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.152481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.106221 restraints weight = 11583.149| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.64 r_work: 0.2489 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10791 Z= 0.198 Angle : 0.643 9.312 14730 Z= 0.331 Chirality : 0.047 0.294 1662 Planarity : 0.005 0.055 1870 Dihedral : 6.526 55.626 1588 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.55 % Allowed : 16.76 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1357 helix: -0.33 (0.75), residues: 43 sheet: 1.04 (0.20), residues: 625 loop : -0.65 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.025 0.002 TYR I 33 PHE 0.014 0.002 PHE L 86 TRP 0.016 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00471 (10775) covalent geometry : angle 0.63195 (14693) SS BOND : bond 0.00665 ( 11) SS BOND : angle 1.31616 ( 22) hydrogen bonds : bond 0.03678 ( 400) hydrogen bonds : angle 5.76783 ( 1113) link_ALPHA1-3 : bond 0.00740 ( 1) link_ALPHA1-3 : angle 4.21029 ( 3) link_ALPHA1-4 : bond 0.00815 ( 1) link_ALPHA1-4 : angle 4.68588 ( 3) link_ALPHA1-6 : bond 0.02272 ( 1) link_ALPHA1-6 : angle 1.96814 ( 3) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 3.42881 ( 3) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 2.95378 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 62 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8955 (m) REVERT: H 63 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7712 (mtpt) REVERT: H 152 PRO cc_start: 0.7850 (Cg_endo) cc_final: 0.7645 (Cg_exo) REVERT: M 6 GLN cc_start: 0.8656 (mt0) cc_final: 0.8241 (mt0) REVERT: J 43 THR cc_start: 0.8457 (m) cc_final: 0.8035 (t) outliers start: 54 outliers final: 43 residues processed: 212 average time/residue: 0.1075 time to fit residues: 32.0200 Evaluate side-chains 217 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 121 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 31 ASN I 55 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.153634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.103979 restraints weight = 11534.068| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.58 r_work: 0.2530 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10791 Z= 0.141 Angle : 0.592 8.240 14730 Z= 0.304 Chirality : 0.045 0.248 1662 Planarity : 0.004 0.056 1870 Dihedral : 6.187 56.015 1588 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.88 % Allowed : 17.44 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1357 helix: -0.17 (0.77), residues: 43 sheet: 1.12 (0.20), residues: 625 loop : -0.56 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 100 TYR 0.020 0.002 TYR I 33 PHE 0.012 0.001 PHE L 86 TRP 0.016 0.001 TRP N 90 HIS 0.003 0.001 HIS N 33 Details of bonding type rmsd covalent geometry : bond 0.00329 (10775) covalent geometry : angle 0.58083 (14693) SS BOND : bond 0.00562 ( 11) SS BOND : angle 1.12663 ( 22) hydrogen bonds : bond 0.03272 ( 400) hydrogen bonds : angle 5.51663 ( 1113) link_ALPHA1-3 : bond 0.00802 ( 1) link_ALPHA1-3 : angle 3.66777 ( 3) link_ALPHA1-4 : bond 0.00755 ( 1) link_ALPHA1-4 : angle 4.42503 ( 3) link_ALPHA1-6 : bond 0.02264 ( 1) link_ALPHA1-6 : angle 2.15855 ( 3) link_BETA1-4 : bond 0.00014 ( 1) link_BETA1-4 : angle 3.52407 ( 3) link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 2.63959 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: H 40 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8251 (mtp-110) REVERT: H 63 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7736 (mtpt) REVERT: L 3 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6829 (tm130) REVERT: I 3 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: J 43 THR cc_start: 0.8489 (m) cc_final: 0.8035 (t) outliers start: 46 outliers final: 37 residues processed: 204 average time/residue: 0.1191 time to fit residues: 33.3880 Evaluate side-chains 216 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 31 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.152268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.109917 restraints weight = 11573.970| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.64 r_work: 0.2492 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2328 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10791 Z= 0.215 Angle : 0.657 9.541 14730 Z= 0.336 Chirality : 0.047 0.306 1662 Planarity : 0.005 0.070 1870 Dihedral : 6.520 59.643 1588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 16.93 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1357 helix: -0.15 (0.77), residues: 43 sheet: 1.07 (0.20), residues: 620 loop : -0.66 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.027 0.002 TYR I 33 PHE 0.015 0.002 PHE L 86 TRP 0.016 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00513 (10775) covalent geometry : angle 0.64559 (14693) SS BOND : bond 0.00739 ( 11) SS BOND : angle 1.44949 ( 22) hydrogen bonds : bond 0.03678 ( 400) hydrogen bonds : angle 5.61799 ( 1113) link_ALPHA1-3 : bond 0.00735 ( 1) link_ALPHA1-3 : angle 4.34261 ( 3) link_ALPHA1-4 : bond 0.00740 ( 1) link_ALPHA1-4 : angle 4.69283 ( 3) link_ALPHA1-6 : bond 0.02231 ( 1) link_ALPHA1-6 : angle 1.79866 ( 3) link_BETA1-4 : bond 0.00508 ( 1) link_BETA1-4 : angle 3.28750 ( 3) link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 2.63262 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: A 62 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8961 (m) REVERT: H 40 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8279 (mtp-110) REVERT: H 63 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7207 (ttmt) REVERT: M 6 GLN cc_start: 0.8694 (mt0) cc_final: 0.8310 (mt0) REVERT: J 43 THR cc_start: 0.8441 (m) cc_final: 0.7990 (t) outliers start: 55 outliers final: 47 residues processed: 210 average time/residue: 0.1187 time to fit residues: 34.4563 Evaluate side-chains 220 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN L 31 ASN I 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.152392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.106029 restraints weight = 11563.589| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.65 r_work: 0.2482 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2333 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10791 Z= 0.207 Angle : 0.650 9.393 14730 Z= 0.332 Chirality : 0.047 0.308 1662 Planarity : 0.005 0.059 1870 Dihedral : 6.522 55.832 1588 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.14 % Allowed : 16.93 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1357 helix: -0.15 (0.77), residues: 43 sheet: 1.07 (0.20), residues: 619 loop : -0.66 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.025 0.002 TYR I 33 PHE 0.015 0.002 PHE L 86 TRP 0.016 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00493 (10775) covalent geometry : angle 0.63837 (14693) SS BOND : bond 0.00679 ( 11) SS BOND : angle 1.42275 ( 22) hydrogen bonds : bond 0.03578 ( 400) hydrogen bonds : angle 5.57781 ( 1113) link_ALPHA1-3 : bond 0.00646 ( 1) link_ALPHA1-3 : angle 4.40115 ( 3) link_ALPHA1-4 : bond 0.00679 ( 1) link_ALPHA1-4 : angle 4.74505 ( 3) link_ALPHA1-6 : bond 0.02154 ( 1) link_ALPHA1-6 : angle 2.02509 ( 3) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 3.58832 ( 3) link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 2.44839 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: H 40 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (mtp-110) REVERT: H 63 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7190 (ttmt) REVERT: I 3 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: M 6 GLN cc_start: 0.8680 (mt0) cc_final: 0.8301 (mt0) REVERT: J 43 THR cc_start: 0.8458 (m) cc_final: 0.8009 (t) outliers start: 61 outliers final: 52 residues processed: 215 average time/residue: 0.1125 time to fit residues: 33.2989 Evaluate side-chains 227 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 163 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 0.0370 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 77 ASN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.152446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.108085 restraints weight = 11477.491| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.73 r_work: 0.2481 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2323 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10791 Z= 0.201 Angle : 0.654 9.450 14730 Z= 0.334 Chirality : 0.047 0.305 1662 Planarity : 0.005 0.057 1870 Dihedral : 6.566 53.622 1588 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.22 % Allowed : 17.02 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1357 helix: -0.11 (0.78), residues: 43 sheet: 1.07 (0.20), residues: 614 loop : -0.64 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 11 TYR 0.025 0.002 TYR I 33 PHE 0.014 0.002 PHE L 86 TRP 0.017 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00481 (10775) covalent geometry : angle 0.64083 (14693) SS BOND : bond 0.00760 ( 11) SS BOND : angle 1.78383 ( 22) hydrogen bonds : bond 0.03502 ( 400) hydrogen bonds : angle 5.55854 ( 1113) link_ALPHA1-3 : bond 0.00649 ( 1) link_ALPHA1-3 : angle 4.35731 ( 3) link_ALPHA1-4 : bond 0.00714 ( 1) link_ALPHA1-4 : angle 4.72347 ( 3) link_ALPHA1-6 : bond 0.02137 ( 1) link_ALPHA1-6 : angle 2.00493 ( 3) link_BETA1-4 : bond 0.00404 ( 1) link_BETA1-4 : angle 3.42639 ( 3) link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 2.46816 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: H 40 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8247 (mtp-110) REVERT: H 63 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7203 (ttmt) REVERT: I 3 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7851 (mm-40) REVERT: J 43 THR cc_start: 0.8453 (m) cc_final: 0.8008 (t) outliers start: 62 outliers final: 55 residues processed: 213 average time/residue: 0.1204 time to fit residues: 34.8665 Evaluate side-chains 229 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 154 GLU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 77 ASN L 31 ASN I 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.151827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.104972 restraints weight = 11552.784| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.65 r_work: 0.2487 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10791 Z= 0.250 Angle : 0.703 10.783 14730 Z= 0.358 Chirality : 0.049 0.349 1662 Planarity : 0.005 0.060 1870 Dihedral : 6.797 58.573 1588 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.39 % Allowed : 16.85 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1357 helix: -0.06 (0.79), residues: 42 sheet: 1.07 (0.20), residues: 604 loop : -0.75 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 11 TYR 0.028 0.003 TYR I 33 PHE 0.016 0.002 PHE L 86 TRP 0.016 0.002 TRP N 90 HIS 0.005 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00598 (10775) covalent geometry : angle 0.68908 (14693) SS BOND : bond 0.00905 ( 11) SS BOND : angle 2.22420 ( 22) hydrogen bonds : bond 0.03804 ( 400) hydrogen bonds : angle 5.65636 ( 1113) link_ALPHA1-3 : bond 0.00557 ( 1) link_ALPHA1-3 : angle 4.69893 ( 3) link_ALPHA1-4 : bond 0.00666 ( 1) link_ALPHA1-4 : angle 4.83945 ( 3) link_ALPHA1-6 : bond 0.02197 ( 1) link_ALPHA1-6 : angle 1.59202 ( 3) link_BETA1-4 : bond 0.00610 ( 1) link_BETA1-4 : angle 3.40587 ( 3) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 2.58072 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: H 40 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8217 (mtp-110) REVERT: H 63 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7220 (ttmt) REVERT: I 3 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: J 43 THR cc_start: 0.8445 (m) cc_final: 0.8012 (t) outliers start: 64 outliers final: 59 residues processed: 214 average time/residue: 0.1097 time to fit residues: 32.2627 Evaluate side-chains 233 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 81 optimal weight: 0.4980 chunk 124 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 70 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 77 ASN L 27 GLN L 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.152917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.106576 restraints weight = 11434.135| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.72 r_work: 0.2483 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2332 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10791 Z= 0.172 Angle : 0.637 9.670 14730 Z= 0.326 Chirality : 0.046 0.284 1662 Planarity : 0.005 0.056 1870 Dihedral : 6.504 55.514 1588 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.80 % Allowed : 17.44 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1357 helix: 0.06 (0.79), residues: 42 sheet: 1.13 (0.20), residues: 611 loop : -0.68 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.022 0.002 TYR I 33 PHE 0.013 0.002 PHE L 86 TRP 0.018 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00408 (10775) covalent geometry : angle 0.62453 (14693) SS BOND : bond 0.00700 ( 11) SS BOND : angle 1.75034 ( 22) hydrogen bonds : bond 0.03367 ( 400) hydrogen bonds : angle 5.49629 ( 1113) link_ALPHA1-3 : bond 0.00634 ( 1) link_ALPHA1-3 : angle 4.19934 ( 3) link_ALPHA1-4 : bond 0.00781 ( 1) link_ALPHA1-4 : angle 4.68573 ( 3) link_ALPHA1-6 : bond 0.02096 ( 1) link_ALPHA1-6 : angle 2.06461 ( 3) link_BETA1-4 : bond 0.00155 ( 1) link_BETA1-4 : angle 3.53254 ( 3) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 2.46357 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: A 62 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (m) REVERT: H 40 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8223 (mtp-110) REVERT: H 63 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7172 (ttmt) REVERT: I 3 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7739 (mm-40) REVERT: J 43 THR cc_start: 0.8459 (m) cc_final: 0.8016 (t) outliers start: 57 outliers final: 52 residues processed: 211 average time/residue: 0.0915 time to fit residues: 27.1198 Evaluate side-chains 226 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 98 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 77 ASN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.106580 restraints weight = 11519.194| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.70 r_work: 0.2507 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10791 Z= 0.195 Angle : 0.655 9.851 14730 Z= 0.334 Chirality : 0.047 0.301 1662 Planarity : 0.005 0.058 1870 Dihedral : 6.508 51.995 1588 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.80 % Allowed : 17.27 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1357 helix: 0.10 (0.79), residues: 42 sheet: 1.11 (0.20), residues: 611 loop : -0.70 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100 TYR 0.025 0.002 TYR I 33 PHE 0.014 0.002 PHE L 86 TRP 0.017 0.002 TRP N 90 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00465 (10775) covalent geometry : angle 0.64214 (14693) SS BOND : bond 0.00772 ( 11) SS BOND : angle 1.91536 ( 22) hydrogen bonds : bond 0.03494 ( 400) hydrogen bonds : angle 5.50689 ( 1113) link_ALPHA1-3 : bond 0.00595 ( 1) link_ALPHA1-3 : angle 4.38401 ( 3) link_ALPHA1-4 : bond 0.00745 ( 1) link_ALPHA1-4 : angle 4.61252 ( 3) link_ALPHA1-6 : bond 0.02157 ( 1) link_ALPHA1-6 : angle 1.84239 ( 3) link_BETA1-4 : bond 0.00407 ( 1) link_BETA1-4 : angle 3.36735 ( 3) link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 2.47645 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3321.42 seconds wall clock time: 57 minutes 36.15 seconds (3456.15 seconds total)