Starting phenix.real_space_refine on Thu Feb 5 14:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmc_62427/02_2026/9kmc_62427.map" } resolution = 2.97 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= 0.059 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 5633 2.51 5 N 1520 2.21 5 O 1731 1.98 5 H 8499 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 17434 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2030 Classifications: {'peptide': 133} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3344 Classifications: {'peptide': 208} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3216 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 183} Chain: "D" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2199 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3281 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "F" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3179 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 199} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.15 Number of scatterers: 17434 At special positions: 0 Unit cell: (111.019, 94.449, 155.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1731 8.00 N 1520 7.00 C 5633 6.00 H 8499 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 125 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 3 " NAG-ASN " NAG C 301 " - " ASN C 159 " " NAG G 1 " - " ASN B 43 " " NAG H 1 " - " ASN B 71 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 71 " " NAG K 1 " - " ASN C 84 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 26 sheets defined 11.2% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'D' and resid 27 through 49 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 94 removed outlier: 4.787A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.668A pdb=" N LEU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.549A pdb=" N GLY D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 153 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.710A pdb=" N SER E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.859A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.576A pdb=" N ALA F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 38 removed outlier: 6.720A pdb=" N SER B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 77 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.568A pdb=" N THR B 105 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 120 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS B 110 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL B 118 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B 112 " --> pdb=" O TRP B 116 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 136 through 143 removed outlier: 4.413A pdb=" N LEU B 138 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER B 151 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL B 140 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 149 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.706A pdb=" N GLU B 205 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.545A pdb=" N LEU C 106 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER C 113 " --> pdb=" O TRP C 74 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 153 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 64 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.572A pdb=" N THR C 127 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 166 removed outlier: 4.359A pdb=" N LEU C 160 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN C 173 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU C 162 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU C 171 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS C 164 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLN C 169 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 170 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.524A pdb=" N ARG C 224 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 64 through 67 removed outlier: 7.006A pdb=" N PHE D 64 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU D 130 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N MET D 66 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.629A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.056A pdb=" N TYR E 108 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 126 through 130 removed outlier: 6.043A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'E' and resid 200 through 201 removed outlier: 4.235A pdb=" N TYR E 200 " --> pdb=" O ALA E 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.522A pdb=" N TRP F 34 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AC7, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.518A pdb=" N SER F 113 " --> pdb=" O ASN F 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 143 through 149 removed outlier: 3.517A pdb=" N VAL F 204 " --> pdb=" O VAL F 195 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 828 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: 3.72 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8493 1.03 - 1.23: 151 1.23 - 1.43: 3794 1.43 - 1.62: 5160 1.62 - 1.82: 66 Bond restraints: 17664 Sorted by residual: bond pdb=" CA HIS B 164 " pdb=" C HIS B 164 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 1.01e+00 bond pdb=" CG PRO B 212 " pdb=" CD PRO B 212 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.82e-01 bond pdb=" CB GLN B 207 " pdb=" CG GLN B 207 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.77e-01 bond pdb=" C LEU C 186 " pdb=" N VAL C 187 " ideal model delta sigma weight residual 1.329 1.313 0.016 1.96e-02 2.60e+03 6.36e-01 bond pdb=" CG LEU F 103 " pdb=" CD1 LEU F 103 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.55e-01 ... (remaining 17659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 31596 2.04 - 4.08: 168 4.08 - 6.12: 6 6.12 - 8.15: 0 8.15 - 10.19: 3 Bond angle restraints: 31773 Sorted by residual: angle pdb=" N VAL B 79 " pdb=" CA VAL B 79 " pdb=" C VAL B 79 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" C3 NAG H 2 " pdb=" C4 NAG H 2 " pdb=" O4 NAG H 2 " ideal model delta sigma weight residual 107.29 117.48 -10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C5 NAG H 2 " pdb=" C4 NAG H 2 " pdb=" O4 NAG H 2 " ideal model delta sigma weight residual 111.70 121.76 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C3 NAG H 2 " pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " ideal model delta sigma weight residual 109.38 118.69 -9.31 3.00e+00 1.11e-01 9.63e+00 angle pdb=" N ASN C 180 " pdb=" CA ASN C 180 " pdb=" C ASN C 180 " ideal model delta sigma weight residual 110.97 113.53 -2.56 1.09e+00 8.42e-01 5.53e+00 ... (remaining 31768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 7797 17.42 - 34.85: 628 34.85 - 52.27: 163 52.27 - 69.69: 46 69.69 - 87.11: 18 Dihedral angle restraints: 8652 sinusoidal: 4775 harmonic: 3877 Sorted by residual: dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual -86.00 -128.52 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CB CYS B 74 " pdb=" SG CYS B 74 " pdb=" SG CYS B 86 " pdb=" CB CYS B 86 " ideal model delta sinusoidal sigma weight residual 93.00 52.79 40.21 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.22 39.78 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 8649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.363: 1410 0.363 - 0.726: 0 0.726 - 1.089: 0 1.089 - 1.451: 0 1.451 - 1.814: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C4 NAG H 2 " pdb=" C3 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" O4 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.53 -0.72 -1.81 2.00e-01 2.50e+01 8.23e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 84 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1408 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 27 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C THR D 27 " -0.044 2.00e-02 2.50e+03 pdb=" O THR D 27 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 28 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 228 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO C 229 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 229 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 229 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 27 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 28 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.021 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1371 2.22 - 2.82: 36190 2.82 - 3.41: 43093 3.41 - 4.01: 60851 4.01 - 4.60: 92225 Nonbonded interactions: 233730 Sorted by model distance: nonbonded pdb=" O GLN D 42 " pdb="HD21 ASN D 46 " model vdw 1.626 2.450 nonbonded pdb=" H MET A 39 " pdb=" HG2 MET A 39 " model vdw 1.861 2.270 nonbonded pdb=" H VAL B 79 " pdb=" H SER B 80 " model vdw 1.903 2.100 nonbonded pdb=" HG3 ARG D 58 " pdb="HH11 ARG D 58 " model vdw 1.906 2.270 nonbonded pdb=" HD2 ARG B 107 " pdb="HH11 ARG B 107 " model vdw 1.913 2.270 ... (remaining 233725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.240 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.034 9194 Z= 0.158 Angle : 0.589 10.193 12540 Z= 0.291 Chirality : 0.064 1.814 1411 Planarity : 0.004 0.049 1571 Dihedral : 14.527 87.113 3548 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.71 % Allowed : 11.43 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.26), residues: 1088 helix: 2.35 (0.52), residues: 94 sheet: 0.12 (0.26), residues: 428 loop : -0.18 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.018 0.001 PHE D 137 TRP 0.012 0.001 TRP D 141 HIS 0.005 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9165) covalent geometry : angle 0.55840 (12468) SS BOND : bond 0.00217 ( 15) SS BOND : angle 1.06477 ( 30) hydrogen bonds : bond 0.21209 ( 307) hydrogen bonds : angle 8.87134 ( 828) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 3.81957 ( 18) link_BETA1-6 : bond 0.00417 ( 2) link_BETA1-6 : angle 1.67984 ( 6) link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 2.86281 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8082 (m) cc_final: 0.7740 (t) REVERT: A 169 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7783 (mtpm) REVERT: A 179 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8170 (tm-30) REVERT: B 60 GLN cc_start: 0.7425 (pt0) cc_final: 0.6857 (pt0) REVERT: B 80 SER cc_start: 0.8021 (t) cc_final: 0.7603 (m) REVERT: C 139 ARG cc_start: 0.7040 (mmp80) cc_final: 0.6483 (pmm-80) REVERT: D 124 MET cc_start: 0.7007 (tpp) cc_final: 0.6727 (tpp) REVERT: F 24 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7257 (tmm-80) REVERT: F 171 THR cc_start: 0.7520 (p) cc_final: 0.7253 (t) outliers start: 7 outliers final: 5 residues processed: 204 average time/residue: 1.0072 time to fit residues: 221.4282 Evaluate side-chains 199 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN D 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.200039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129945 restraints weight = 27135.223| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.76 r_work: 0.3178 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9194 Z= 0.213 Angle : 0.622 8.379 12540 Z= 0.315 Chirality : 0.043 0.290 1411 Planarity : 0.005 0.061 1571 Dihedral : 5.813 44.100 1475 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.52 % Allowed : 13.04 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.26), residues: 1088 helix: 2.31 (0.54), residues: 88 sheet: 0.27 (0.25), residues: 433 loop : -0.18 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 107 TYR 0.013 0.002 TYR C 125 PHE 0.020 0.002 PHE D 137 TRP 0.012 0.001 TRP D 141 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9165) covalent geometry : angle 0.59846 (12468) SS BOND : bond 0.00461 ( 15) SS BOND : angle 1.33684 ( 30) hydrogen bonds : bond 0.04877 ( 307) hydrogen bonds : angle 6.56843 ( 828) link_BETA1-4 : bond 0.00317 ( 6) link_BETA1-4 : angle 3.17750 ( 18) link_BETA1-6 : bond 0.00420 ( 2) link_BETA1-6 : angle 1.66603 ( 6) link_NAG-ASN : bond 0.00447 ( 6) link_NAG-ASN : angle 2.78855 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7953 (m) cc_final: 0.7564 (t) REVERT: A 179 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8153 (tm-30) REVERT: B 80 SER cc_start: 0.8172 (t) cc_final: 0.7749 (m) REVERT: B 162 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: B 180 GLU cc_start: 0.7429 (tt0) cc_final: 0.7102 (tm-30) REVERT: C 139 ARG cc_start: 0.7081 (mmp80) cc_final: 0.6520 (pmm-80) REVERT: D 124 MET cc_start: 0.7103 (tpp) cc_final: 0.6843 (tpp) REVERT: E 107 ASP cc_start: 0.7993 (p0) cc_final: 0.7787 (p0) REVERT: F 24 ARG cc_start: 0.7422 (ttp-170) cc_final: 0.7020 (tmm-80) outliers start: 15 outliers final: 11 residues processed: 212 average time/residue: 1.1471 time to fit residues: 261.0265 Evaluate side-chains 211 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 180 ASN D 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.200333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.131060 restraints weight = 27164.647| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.72 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9194 Z= 0.179 Angle : 0.595 8.224 12540 Z= 0.298 Chirality : 0.043 0.280 1411 Planarity : 0.005 0.057 1571 Dihedral : 5.724 44.374 1469 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.53 % Allowed : 13.85 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.26), residues: 1088 helix: 2.34 (0.54), residues: 88 sheet: 0.31 (0.25), residues: 434 loop : -0.20 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.019 0.002 PHE D 137 TRP 0.013 0.001 TRP D 141 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9165) covalent geometry : angle 0.57069 (12468) SS BOND : bond 0.00432 ( 15) SS BOND : angle 1.33051 ( 30) hydrogen bonds : bond 0.04244 ( 307) hydrogen bonds : angle 6.05818 ( 828) link_BETA1-4 : bond 0.00222 ( 6) link_BETA1-4 : angle 3.02164 ( 18) link_BETA1-6 : bond 0.00454 ( 2) link_BETA1-6 : angle 1.75321 ( 6) link_NAG-ASN : bond 0.00362 ( 6) link_NAG-ASN : angle 2.81859 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7909 (m) cc_final: 0.7519 (t) REVERT: A 179 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8164 (tm-30) REVERT: B 80 SER cc_start: 0.8175 (t) cc_final: 0.7790 (m) REVERT: B 162 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: B 180 GLU cc_start: 0.7436 (tt0) cc_final: 0.7153 (tm-30) REVERT: C 139 ARG cc_start: 0.7152 (mmp80) cc_final: 0.6609 (pmm-80) REVERT: C 158 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7341 (mm-30) REVERT: D 124 MET cc_start: 0.7022 (tpp) cc_final: 0.6751 (tpp) REVERT: F 24 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.6958 (tmm-80) REVERT: F 146 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6616 (tm-30) outliers start: 25 outliers final: 18 residues processed: 211 average time/residue: 1.0489 time to fit residues: 238.6036 Evaluate side-chains 212 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 146 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN D 46 ASN F 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.200348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132215 restraints weight = 27323.966| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.63 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9194 Z= 0.169 Angle : 0.588 8.058 12540 Z= 0.294 Chirality : 0.042 0.277 1411 Planarity : 0.005 0.059 1571 Dihedral : 5.516 34.283 1466 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.22 % Allowed : 14.86 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.26), residues: 1088 helix: 1.97 (0.53), residues: 94 sheet: 0.33 (0.25), residues: 434 loop : -0.18 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.019 0.002 PHE D 137 TRP 0.012 0.001 TRP D 141 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9165) covalent geometry : angle 0.56392 (12468) SS BOND : bond 0.00416 ( 15) SS BOND : angle 1.24259 ( 30) hydrogen bonds : bond 0.03873 ( 307) hydrogen bonds : angle 5.77944 ( 828) link_BETA1-4 : bond 0.00241 ( 6) link_BETA1-4 : angle 3.01641 ( 18) link_BETA1-6 : bond 0.00327 ( 2) link_BETA1-6 : angle 1.78806 ( 6) link_NAG-ASN : bond 0.00374 ( 6) link_NAG-ASN : angle 2.78281 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7907 (m) cc_final: 0.7526 (t) REVERT: A 179 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8163 (tm-30) REVERT: B 80 SER cc_start: 0.8171 (t) cc_final: 0.7816 (m) REVERT: B 162 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 180 GLU cc_start: 0.7381 (tt0) cc_final: 0.7157 (tm-30) REVERT: C 139 ARG cc_start: 0.7175 (mmp80) cc_final: 0.6648 (pmm-80) REVERT: C 158 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7320 (mm-30) REVERT: D 124 MET cc_start: 0.7027 (tpp) cc_final: 0.6757 (tpp) REVERT: F 24 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6965 (tmm-80) REVERT: F 146 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6982 (tm-30) outliers start: 22 outliers final: 17 residues processed: 209 average time/residue: 1.1128 time to fit residues: 250.4171 Evaluate side-chains 211 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 146 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN D 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.200191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131992 restraints weight = 27044.681| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.62 r_work: 0.3191 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9194 Z= 0.175 Angle : 0.587 8.018 12540 Z= 0.294 Chirality : 0.042 0.277 1411 Planarity : 0.005 0.060 1571 Dihedral : 5.547 34.527 1466 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 15.57 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.26), residues: 1088 helix: 1.97 (0.53), residues: 94 sheet: 0.34 (0.25), residues: 434 loop : -0.20 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.019 0.002 PHE D 137 TRP 0.012 0.001 TRP D 141 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9165) covalent geometry : angle 0.56323 (12468) SS BOND : bond 0.00392 ( 15) SS BOND : angle 1.22853 ( 30) hydrogen bonds : bond 0.03845 ( 307) hydrogen bonds : angle 5.68880 ( 828) link_BETA1-4 : bond 0.00240 ( 6) link_BETA1-4 : angle 3.01059 ( 18) link_BETA1-6 : bond 0.00427 ( 2) link_BETA1-6 : angle 1.81198 ( 6) link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 2.79958 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7912 (m) cc_final: 0.7531 (t) REVERT: A 179 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8117 (tm-30) REVERT: B 33 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7400 (mm-40) REVERT: B 80 SER cc_start: 0.8181 (t) cc_final: 0.7825 (m) REVERT: B 162 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: B 180 GLU cc_start: 0.7385 (tt0) cc_final: 0.7176 (tm-30) REVERT: C 139 ARG cc_start: 0.7197 (mmp80) cc_final: 0.6670 (pmm-80) REVERT: C 158 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7350 (mm-30) REVERT: D 124 MET cc_start: 0.7057 (tpp) cc_final: 0.6788 (tpp) REVERT: E 89 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7023 (mp0) REVERT: F 24 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6953 (tmm-80) outliers start: 25 outliers final: 21 residues processed: 205 average time/residue: 1.0128 time to fit residues: 224.1125 Evaluate side-chains 214 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN D 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.201918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.133923 restraints weight = 27069.142| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.62 r_work: 0.3216 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9194 Z= 0.108 Angle : 0.556 7.605 12540 Z= 0.276 Chirality : 0.042 0.263 1411 Planarity : 0.005 0.060 1571 Dihedral : 5.393 36.775 1466 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.12 % Allowed : 15.67 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1088 helix: 2.15 (0.53), residues: 94 sheet: 0.39 (0.25), residues: 431 loop : -0.09 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.011 0.001 TYR C 125 PHE 0.018 0.001 PHE D 137 TRP 0.013 0.001 TRP D 141 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9165) covalent geometry : angle 0.53385 (12468) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.05111 ( 30) hydrogen bonds : bond 0.03445 ( 307) hydrogen bonds : angle 5.46335 ( 828) link_BETA1-4 : bond 0.00263 ( 6) link_BETA1-4 : angle 2.83271 ( 18) link_BETA1-6 : bond 0.00281 ( 2) link_BETA1-6 : angle 1.76072 ( 6) link_NAG-ASN : bond 0.00294 ( 6) link_NAG-ASN : angle 2.62194 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7957 (m) cc_final: 0.7586 (t) REVERT: A 179 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8131 (tm-30) REVERT: B 33 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7424 (mm-40) REVERT: B 80 SER cc_start: 0.8190 (t) cc_final: 0.7841 (m) REVERT: B 180 GLU cc_start: 0.7321 (tt0) cc_final: 0.7104 (tm-30) REVERT: C 139 ARG cc_start: 0.7224 (mmp80) cc_final: 0.6698 (pmm-80) REVERT: C 158 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7346 (mm-30) REVERT: D 124 MET cc_start: 0.6814 (tpp) cc_final: 0.6540 (tpp) REVERT: E 89 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7053 (mp0) REVERT: F 24 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.6937 (tmm-80) outliers start: 21 outliers final: 17 residues processed: 200 average time/residue: 1.0643 time to fit residues: 229.6264 Evaluate side-chains 202 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 60 GLN D 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.201788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133717 restraints weight = 27221.162| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.63 r_work: 0.3214 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9194 Z= 0.119 Angle : 0.551 7.571 12540 Z= 0.274 Chirality : 0.041 0.267 1411 Planarity : 0.005 0.062 1571 Dihedral : 5.336 36.947 1466 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.22 % Allowed : 15.57 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1088 helix: 2.22 (0.52), residues: 94 sheet: 0.38 (0.25), residues: 430 loop : -0.09 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.012 0.001 TYR C 125 PHE 0.019 0.001 PHE D 137 TRP 0.012 0.001 TRP D 141 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9165) covalent geometry : angle 0.52829 (12468) SS BOND : bond 0.00353 ( 15) SS BOND : angle 1.06485 ( 30) hydrogen bonds : bond 0.03435 ( 307) hydrogen bonds : angle 5.35075 ( 828) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 2.84337 ( 18) link_BETA1-6 : bond 0.00330 ( 2) link_BETA1-6 : angle 1.73362 ( 6) link_NAG-ASN : bond 0.00332 ( 6) link_NAG-ASN : angle 2.65077 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7967 (m) cc_final: 0.7600 (t) REVERT: A 179 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8133 (tm-30) REVERT: B 33 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7403 (mm-40) REVERT: B 80 SER cc_start: 0.8194 (t) cc_final: 0.7841 (m) REVERT: B 162 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: B 180 GLU cc_start: 0.7325 (tt0) cc_final: 0.7091 (tm-30) REVERT: C 139 ARG cc_start: 0.7210 (mmp80) cc_final: 0.6697 (pmm-80) REVERT: C 158 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7349 (mm-30) REVERT: D 124 MET cc_start: 0.6858 (tpp) cc_final: 0.6598 (tpp) REVERT: E 89 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7049 (mp0) REVERT: F 24 ARG cc_start: 0.7362 (ttp-170) cc_final: 0.6933 (tmm-80) outliers start: 22 outliers final: 19 residues processed: 199 average time/residue: 1.0791 time to fit residues: 231.4871 Evaluate side-chains 203 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.201012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132570 restraints weight = 27143.572| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.64 r_work: 0.3209 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9194 Z= 0.157 Angle : 0.573 7.738 12540 Z= 0.284 Chirality : 0.042 0.275 1411 Planarity : 0.005 0.064 1571 Dihedral : 5.449 36.075 1466 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.43 % Allowed : 15.57 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.33 (0.26), residues: 1088 helix: 2.20 (0.53), residues: 94 sheet: 0.33 (0.25), residues: 430 loop : -0.13 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.020 0.002 PHE D 137 TRP 0.011 0.001 TRP D 141 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9165) covalent geometry : angle 0.54936 (12468) SS BOND : bond 0.00393 ( 15) SS BOND : angle 1.18772 ( 30) hydrogen bonds : bond 0.03577 ( 307) hydrogen bonds : angle 5.34410 ( 828) link_BETA1-4 : bond 0.00255 ( 6) link_BETA1-4 : angle 2.90660 ( 18) link_BETA1-6 : bond 0.00413 ( 2) link_BETA1-6 : angle 1.76451 ( 6) link_NAG-ASN : bond 0.00374 ( 6) link_NAG-ASN : angle 2.75129 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7965 (m) cc_final: 0.7597 (t) REVERT: A 179 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8148 (tm-30) REVERT: B 33 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7415 (mm-40) REVERT: B 80 SER cc_start: 0.8197 (t) cc_final: 0.7842 (m) REVERT: B 162 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: B 180 GLU cc_start: 0.7345 (tt0) cc_final: 0.7133 (tm-30) REVERT: C 139 ARG cc_start: 0.7232 (mmp80) cc_final: 0.6707 (pmm-80) REVERT: C 158 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7356 (mm-30) REVERT: D 124 MET cc_start: 0.7038 (tpp) cc_final: 0.6779 (tpp) REVERT: E 89 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7026 (mp0) REVERT: F 24 ARG cc_start: 0.7357 (ttp-170) cc_final: 0.6928 (tmm-80) outliers start: 24 outliers final: 19 residues processed: 201 average time/residue: 1.0506 time to fit residues: 227.6720 Evaluate side-chains 202 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.200815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.132328 restraints weight = 27075.942| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.64 r_work: 0.3208 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 9194 Z= 0.166 Angle : 0.615 17.100 12540 Z= 0.305 Chirality : 0.042 0.273 1411 Planarity : 0.005 0.063 1571 Dihedral : 5.483 36.077 1466 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.22 % Allowed : 16.48 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1088 helix: 2.24 (0.52), residues: 94 sheet: 0.29 (0.25), residues: 434 loop : -0.10 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.013 0.001 TYR E 182 PHE 0.021 0.002 PHE A 36 TRP 0.011 0.001 TRP D 141 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9165) covalent geometry : angle 0.58221 (12468) SS BOND : bond 0.00888 ( 15) SS BOND : angle 2.68395 ( 30) hydrogen bonds : bond 0.03576 ( 307) hydrogen bonds : angle 5.31161 ( 828) link_BETA1-4 : bond 0.00254 ( 6) link_BETA1-4 : angle 2.90517 ( 18) link_BETA1-6 : bond 0.00421 ( 2) link_BETA1-6 : angle 1.77341 ( 6) link_NAG-ASN : bond 0.00356 ( 6) link_NAG-ASN : angle 2.74151 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7965 (m) cc_final: 0.7597 (t) REVERT: A 179 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8144 (tm-30) REVERT: B 33 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7375 (mm-40) REVERT: B 80 SER cc_start: 0.8202 (t) cc_final: 0.7843 (m) REVERT: B 162 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 180 GLU cc_start: 0.7335 (tt0) cc_final: 0.7133 (tm-30) REVERT: C 139 ARG cc_start: 0.7238 (mmp80) cc_final: 0.6711 (pmm-80) REVERT: C 158 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7351 (mm-30) REVERT: D 124 MET cc_start: 0.7039 (tpp) cc_final: 0.6775 (tpp) REVERT: E 89 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7007 (mp0) REVERT: F 24 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.6929 (tmm-80) REVERT: F 53 LEU cc_start: 0.8562 (tm) cc_final: 0.8318 (tm) outliers start: 22 outliers final: 18 residues processed: 194 average time/residue: 1.0194 time to fit residues: 214.1758 Evaluate side-chains 200 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.200858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.132425 restraints weight = 26919.670| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.64 r_work: 0.3208 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9194 Z= 0.160 Angle : 0.604 13.100 12540 Z= 0.299 Chirality : 0.042 0.271 1411 Planarity : 0.005 0.060 1571 Dihedral : 5.521 36.751 1466 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.12 % Allowed : 16.38 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1088 helix: 2.26 (0.52), residues: 94 sheet: 0.30 (0.25), residues: 434 loop : -0.12 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 58 TYR 0.013 0.001 TYR C 125 PHE 0.022 0.002 PHE A 36 TRP 0.013 0.001 TRP C 74 HIS 0.007 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9165) covalent geometry : angle 0.57608 (12468) SS BOND : bond 0.00662 ( 15) SS BOND : angle 2.04727 ( 30) hydrogen bonds : bond 0.03562 ( 307) hydrogen bonds : angle 5.27992 ( 828) link_BETA1-4 : bond 0.00267 ( 6) link_BETA1-4 : angle 2.89462 ( 18) link_BETA1-6 : bond 0.00416 ( 2) link_BETA1-6 : angle 1.78439 ( 6) link_NAG-ASN : bond 0.00350 ( 6) link_NAG-ASN : angle 2.74482 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.7973 (m) cc_final: 0.7615 (t) REVERT: A 179 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8152 (tm-30) REVERT: B 33 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7368 (mm-40) REVERT: B 80 SER cc_start: 0.8203 (t) cc_final: 0.7869 (m) REVERT: B 180 GLU cc_start: 0.7349 (tt0) cc_final: 0.7142 (tm-30) REVERT: C 139 ARG cc_start: 0.7222 (mmp80) cc_final: 0.6698 (pmm-80) REVERT: C 158 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7355 (mm-30) REVERT: D 124 MET cc_start: 0.7050 (tpp) cc_final: 0.6782 (tpp) REVERT: E 89 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7070 (mp0) REVERT: F 24 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6951 (tmm-80) outliers start: 21 outliers final: 19 residues processed: 198 average time/residue: 1.0543 time to fit residues: 225.3648 Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 46 TRP Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 99 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.202246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133833 restraints weight = 27264.774| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.66 r_work: 0.3228 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9194 Z= 0.115 Angle : 0.571 11.374 12540 Z= 0.284 Chirality : 0.042 0.261 1411 Planarity : 0.005 0.074 1571 Dihedral : 5.408 38.439 1466 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.72 % Allowed : 16.99 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.40 (0.26), residues: 1088 helix: 2.37 (0.52), residues: 94 sheet: 0.39 (0.25), residues: 430 loop : -0.11 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 58 TYR 0.011 0.001 TYR C 125 PHE 0.021 0.001 PHE A 36 TRP 0.013 0.001 TRP D 141 HIS 0.006 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9165) covalent geometry : angle 0.54632 (12468) SS BOND : bond 0.00597 ( 15) SS BOND : angle 1.67288 ( 30) hydrogen bonds : bond 0.03298 ( 307) hydrogen bonds : angle 5.17480 ( 828) link_BETA1-4 : bond 0.00259 ( 6) link_BETA1-4 : angle 2.77141 ( 18) link_BETA1-6 : bond 0.00306 ( 2) link_BETA1-6 : angle 1.75315 ( 6) link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 2.61556 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7820.02 seconds wall clock time: 133 minutes 1.83 seconds (7981.83 seconds total)