Starting phenix.real_space_refine on Wed Mar 4 06:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phr_13427/03_2026/7phr_13427.map" } resolution = 3.08 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= 0.035 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 61 5.16 5 C 7304 2.51 5 N 1939 2.21 5 O 2207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11511 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1898 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 235} Chain: "B" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2252 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "Z" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "e" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "z" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" 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 Chain: "D" 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 Time building chain proxies: 2.78, per 1000 atoms: 0.24 Number of scatterers: 11511 At special positions: 0 Unit cell: (85.05, 91.35, 194.25, 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 61 16.00 O 2207 8.00 N 1939 7.00 C 7304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 209 " distance=2.02 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 80 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 11 " - pdb=" SG CYS z 11 " distance=2.03 Simple disulfide: pdb=" SG CYS e 27 " - pdb=" SG CYS e 76 " distance=2.03 Simple disulfide: pdb=" SG CYS e 97 " - pdb=" SG CYS e 100 " 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 NAG-ASN " NAG A 301 " - " ASN A 23 " " NAG A 302 " - " ASN A 143 " " NAG A 303 " - " ASN A 177 " " NAG B 301 " - " ASN B 19 " " NAG D 401 " - " ASN D 17 " " NAG D 402 " - " ASN D 53 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 560.3 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 25 sheets defined 26.6% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.987A pdb=" N THR A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.655A pdb=" N ASN A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 217 through 250 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.527A pdb=" N LYS B 118 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 247 through 286 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 89 through 116 Processing helix chain 'D' and resid 57 through 60 Processing helix chain 'D' and resid 79 through 107 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 104 through 132 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 137 through 150 Processing helix chain 'H' and resid 151 through 162 Processing helix chain 'H' and resid 162 through 175 Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'Z' and resid 3 through 6 Processing helix chain 'Z' and resid 7 through 34 removed outlier: 3.974A pdb=" N CYS Z 11 " --> pdb=" O ASP Z 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 Processing helix chain 'e' and resid 104 through 134 Processing helix chain 'z' and resid 7 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 6.488A pdb=" N LEU A 12 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 109 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 14 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 25 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.061A pdb=" N ASN A 170 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.061A pdb=" N ASN A 170 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 15 removed outlier: 6.667A pdb=" N MET B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP B 35 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 39 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 15 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 127 removed outlier: 5.297A pdb=" N THR B 141 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 195 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B 143 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU B 193 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 145 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER B 191 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR B 147 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 189 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 removed outlier: 4.682A pdb=" N TRP B 158 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 4.116A pdb=" N LEU C 21 " --> pdb=" O TYR C 12 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL C 20 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 43 removed outlier: 6.648A pdb=" N TRP C 33 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 79 removed outlier: 3.811A pdb=" N TRP e 37 " --> pdb=" O ILE e 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 87 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.944A pdb=" N VAL D 12 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.573A pdb=" N ILE D 49 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N TYR E 89 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR E 91 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN D 66 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG E 93 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS D 68 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP E 37 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB8, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AB9, first strand: chain 'H' and resid 46 through 47 removed outlier: 6.568A pdb=" N GLY H 26 " --> pdb=" O PHE H 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 35 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA H 24 " --> pdb=" O ARG H 35 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP H 37 " --> pdb=" O PHE H 22 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE H 22 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR H 94 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR H 118 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN H 96 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR H 116 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET H 98 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS H 114 " --> pdb=" O MET H 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY H 100 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY H 112 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP H 102 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 114 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA H 125 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR H 116 " --> pdb=" O TYR H 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 189 through 192 removed outlier: 5.757A pdb=" N PHE H 241 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 189 through 192 removed outlier: 5.757A pdb=" N PHE H 241 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 222 through 223 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE L 62 " --> pdb=" O GLY L 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE L 62 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER L 55 " --> pdb=" O TYR L 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 44 through 45 Processing sheet with id=AC7, first strand: chain 'e' and resid 17 through 19 612 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2886 1.33 - 1.45: 2565 1.45 - 1.58: 6243 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 11778 Sorted by residual: bond pdb=" N ILE C 40 " pdb=" CA ILE C 40 " ideal model delta sigma weight residual 1.459 1.490 -0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" N GLN C 15 " pdb=" CA GLN C 15 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N GLN e 70 " pdb=" CA GLN e 70 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.68e+00 bond pdb=" N ILE e 118 " pdb=" CA ILE e 118 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.87e+00 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14964 1.55 - 3.09: 899 3.09 - 4.64: 113 4.64 - 6.18: 11 6.18 - 7.73: 2 Bond angle restraints: 15989 Sorted by residual: angle pdb=" N ILE C 40 " pdb=" CA ILE C 40 " pdb=" C ILE C 40 " ideal model delta sigma weight residual 113.47 108.91 4.56 1.01e+00 9.80e-01 2.03e+01 angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 122.57 118.56 4.01 9.20e-01 1.18e+00 1.90e+01 angle pdb=" N LEU Z 6 " pdb=" CA LEU Z 6 " pdb=" C LEU Z 6 " ideal model delta sigma weight residual 112.88 107.35 5.53 1.29e+00 6.01e-01 1.84e+01 angle pdb=" C TYR H 113 " pdb=" CA TYR H 113 " pdb=" CB TYR H 113 " ideal model delta sigma weight residual 109.70 101.97 7.73 1.81e+00 3.05e-01 1.82e+01 angle pdb=" N GLY e 120 " pdb=" CA GLY e 120 " pdb=" C GLY e 120 " ideal model delta sigma weight residual 112.50 107.62 4.88 1.16e+00 7.43e-01 1.77e+01 ... (remaining 15984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6553 17.84 - 35.69: 430 35.69 - 53.53: 92 53.53 - 71.38: 19 71.38 - 89.22: 8 Dihedral angle restraints: 7102 sinusoidal: 2899 harmonic: 4203 Sorted by residual: dihedral pdb=" CB CYS E 97 " pdb=" SG CYS E 97 " pdb=" SG CYS E 100 " pdb=" CB CYS E 100 " ideal model delta sinusoidal sigma weight residual 93.00 148.70 -55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 90 " pdb=" CB CYS A 90 " ideal model delta sinusoidal sigma weight residual 93.00 43.16 49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CA VAL E 96 " pdb=" C VAL E 96 " pdb=" N CYS E 97 " pdb=" CA CYS E 97 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 7099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1260 0.046 - 0.092: 352 0.092 - 0.138: 132 0.138 - 0.185: 21 0.185 - 0.231: 9 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA VAL C 11 " pdb=" N VAL C 11 " pdb=" C VAL C 11 " pdb=" CB VAL C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU Z 6 " pdb=" N LEU Z 6 " pdb=" C LEU Z 6 " pdb=" CB LEU Z 6 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1771 not shown) Planarity restraints: 2051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU e 69 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU e 69 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU e 69 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN e 70 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ILE B 233 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 233 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 234 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 111 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C THR B 111 " -0.038 2.00e-02 2.50e+03 pdb=" O THR B 111 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 112 " 0.013 2.00e-02 2.50e+03 ... (remaining 2048 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5261 2.96 - 3.45: 10926 3.45 - 3.93: 19387 3.93 - 4.42: 22068 4.42 - 4.90: 37405 Nonbonded interactions: 95047 Sorted by model distance: nonbonded pdb=" O SER B 170 " pdb=" OG SER B 170 " model vdw 2.475 3.040 nonbonded pdb=" O5 NAG A 303 " pdb=" O6 NAG A 303 " model vdw 2.488 2.432 nonbonded pdb=" O ASP A 129 " pdb=" OD1 ASP A 129 " model vdw 2.508 3.040 nonbonded pdb=" O5 NAG A 301 " pdb=" O6 NAG A 301 " model vdw 2.538 2.432 nonbonded pdb=" N ASP D 10 " pdb=" OD1 ASP D 10 " model vdw 2.540 3.120 ... (remaining 95042 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 'E' and (resid 11 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 133)) selection = (chain 'e' and (resid 11 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 81 or (resid 82 and ( \ name N or name CA or name C or name O or name CB )) or resid 83 through 132 or ( \ resid 133 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'Z' and (resid 6 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'z' } 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.150 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11801 Z= 0.357 Angle : 0.778 7.730 16041 Z= 0.511 Chirality : 0.051 0.231 1774 Planarity : 0.004 0.035 2045 Dihedral : 12.734 89.220 4351 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.08 % Allowed : 0.56 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.08 (0.22), residues: 1421 helix: 2.15 (0.27), residues: 342 sheet: -0.27 (0.25), residues: 415 loop : -1.08 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 45 TYR 0.025 0.002 TYR B 251 PHE 0.016 0.002 PHE e 65 TRP 0.014 0.001 TRP H 167 HIS 0.006 0.001 HIS H 70 Details of bonding type rmsd covalent geometry : bond 0.00568 (11778) covalent geometry : angle 0.77433 (15989) SS BOND : bond 0.00557 ( 17) SS BOND : angle 1.44726 ( 34) hydrogen bonds : bond 0.12418 ( 565) hydrogen bonds : angle 6.33402 ( 1638) link_NAG-ASN : bond 0.00578 ( 6) link_NAG-ASN : angle 1.69300 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.424 Fit side-chains REVERT: A 126 LYS cc_start: 0.7205 (mptt) cc_final: 0.6873 (mmtt) REVERT: B 23 SER cc_start: 0.8489 (m) cc_final: 0.8270 (m) REVERT: B 155 GLU cc_start: 0.7631 (tt0) cc_final: 0.7389 (tt0) REVERT: C 73 LYS cc_start: 0.6775 (mttt) cc_final: 0.6462 (mttt) REVERT: e 99 ASN cc_start: 0.7371 (m-40) cc_final: 0.6823 (p0) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1299 time to fit residues: 28.1672 Evaluate side-chains 133 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN D 68 HIS E 38 GLN e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148916 restraints weight = 12412.294| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.56 r_work: 0.3177 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11801 Z= 0.250 Angle : 0.566 6.110 16041 Z= 0.298 Chirality : 0.044 0.155 1774 Planarity : 0.004 0.046 2045 Dihedral : 5.458 56.178 1701 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 6.76 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1421 helix: 2.44 (0.27), residues: 343 sheet: -0.16 (0.25), residues: 415 loop : -0.95 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 208 TYR 0.022 0.002 TYR E 14 PHE 0.017 0.002 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 59 Details of bonding type rmsd covalent geometry : bond 0.00603 (11778) covalent geometry : angle 0.56035 (15989) SS BOND : bond 0.00526 ( 17) SS BOND : angle 1.11213 ( 34) hydrogen bonds : bond 0.04117 ( 565) hydrogen bonds : angle 4.86879 ( 1638) link_NAG-ASN : bond 0.00327 ( 6) link_NAG-ASN : angle 1.96904 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.450 Fit side-chains REVERT: B 10 LYS cc_start: 0.8550 (tttt) cc_final: 0.7928 (tptp) REVERT: D 51 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7791 (ptp-110) REVERT: H 264 GLU cc_start: 0.7364 (pp20) cc_final: 0.6949 (pm20) REVERT: L 83 ASN cc_start: 0.8000 (t0) cc_final: 0.7671 (m-40) REVERT: e 99 ASN cc_start: 0.7468 (m-40) cc_final: 0.6626 (p0) outliers start: 15 outliers final: 14 residues processed: 160 average time/residue: 0.1167 time to fit residues: 25.8337 Evaluate side-chains 154 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149291 restraints weight = 12436.876| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.71 r_work: 0.3212 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.004 0.050 11801 Z= 0.162 Angle : 0.491 8.891 16041 Z= 0.259 Chirality : 0.042 0.232 1774 Planarity : 0.004 0.035 2045 Dihedral : 5.077 55.706 1701 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.85 % Allowed : 8.37 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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 (0.22), residues: 1421 helix: 2.70 (0.26), residues: 343 sheet: -0.06 (0.25), residues: 416 loop : -0.87 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 44 TYR 0.017 0.001 TYR B 100 PHE 0.011 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.002 0.001 HIS e 59 Details of bonding type rmsd covalent geometry : bond 0.00386 (11778) covalent geometry : angle 0.48111 (15989) SS BOND : bond 0.00346 ( 17) SS BOND : angle 1.76484 ( 34) hydrogen bonds : bond 0.03530 ( 565) hydrogen bonds : angle 4.51150 ( 1638) link_NAG-ASN : bond 0.00205 ( 6) link_NAG-ASN : angle 1.91188 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8605 (tttt) cc_final: 0.8032 (tptp) REVERT: B 241 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.8567 (ttm170) REVERT: D 51 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7748 (ptp-110) REVERT: H 212 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7766 (mm-30) REVERT: H 232 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7689 (pt0) REVERT: H 264 GLU cc_start: 0.7216 (pp20) cc_final: 0.6919 (pm20) REVERT: P 3 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: e 99 ASN cc_start: 0.7458 (m-40) cc_final: 0.6585 (p0) outliers start: 23 outliers final: 17 residues processed: 159 average time/residue: 0.1165 time to fit residues: 26.2351 Evaluate side-chains 156 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 84 HIS e 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.184587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153930 restraints weight = 12404.034| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.45 r_work: 0.3449 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11801 Z= 0.147 Angle : 0.471 5.539 16041 Z= 0.248 Chirality : 0.041 0.164 1774 Planarity : 0.004 0.034 2045 Dihedral : 4.788 55.021 1701 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 10.14 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1421 helix: 2.84 (0.26), residues: 343 sheet: 0.01 (0.25), residues: 423 loop : -0.73 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 35 TYR 0.016 0.001 TYR B 100 PHE 0.011 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.003 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00350 (11778) covalent geometry : angle 0.46392 (15989) SS BOND : bond 0.00303 ( 17) SS BOND : angle 1.14951 ( 34) hydrogen bonds : bond 0.03366 ( 565) hydrogen bonds : angle 4.32567 ( 1638) link_NAG-ASN : bond 0.00236 ( 6) link_NAG-ASN : angle 1.95361 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8488 (tttt) cc_final: 0.8067 (tptt) REVERT: B 117 ASN cc_start: 0.8425 (t0) cc_final: 0.7678 (m-40) REVERT: B 241 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8617 (ttm170) REVERT: D 51 ARG cc_start: 0.8062 (ptp-110) cc_final: 0.7861 (ptp-110) REVERT: H 232 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7709 (pt0) REVERT: L 83 ASN cc_start: 0.7880 (t0) cc_final: 0.7524 (m-40) REVERT: P 3 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: e 99 ASN cc_start: 0.7420 (m-40) cc_final: 0.6608 (p0) outliers start: 23 outliers final: 17 residues processed: 159 average time/residue: 0.1139 time to fit residues: 25.3143 Evaluate side-chains 158 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152907 restraints weight = 12482.058| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.48 r_work: 0.3433 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11801 Z= 0.195 Angle : 0.508 5.430 16041 Z= 0.267 Chirality : 0.042 0.152 1774 Planarity : 0.004 0.041 2045 Dihedral : 4.916 56.323 1701 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.17 % Allowed : 10.86 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.48 (0.22), residues: 1421 helix: 2.73 (0.26), residues: 343 sheet: -0.02 (0.25), residues: 420 loop : -0.75 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.018 0.002 TYR E 14 PHE 0.013 0.002 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00470 (11778) covalent geometry : angle 0.50091 (15989) SS BOND : bond 0.00382 ( 17) SS BOND : angle 1.16289 ( 34) hydrogen bonds : bond 0.03543 ( 565) hydrogen bonds : angle 4.42080 ( 1638) link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.17475 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8507 (tttt) cc_final: 0.8076 (tptt) REVERT: B 117 ASN cc_start: 0.8527 (t0) cc_final: 0.7702 (m-40) REVERT: B 241 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8624 (ttm170) REVERT: C 81 MET cc_start: 0.8155 (mmm) cc_final: 0.7904 (mmm) REVERT: E 98 GLU cc_start: 0.8084 (tp30) cc_final: 0.7743 (tp30) REVERT: H 76 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8483 (t) REVERT: L 83 ASN cc_start: 0.8033 (t0) cc_final: 0.7831 (m-40) REVERT: P 3 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: e 99 ASN cc_start: 0.7352 (m-40) cc_final: 0.6531 (p0) outliers start: 27 outliers final: 22 residues processed: 162 average time/residue: 0.1190 time to fit residues: 27.3029 Evaluate side-chains 169 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 117 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153670 restraints weight = 12380.805| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.49 r_work: 0.3449 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11801 Z= 0.154 Angle : 0.477 5.480 16041 Z= 0.250 Chirality : 0.041 0.160 1774 Planarity : 0.004 0.035 2045 Dihedral : 4.836 55.662 1701 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.49 % Allowed : 11.34 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.60 (0.22), residues: 1421 helix: 2.85 (0.26), residues: 343 sheet: 0.03 (0.25), residues: 436 loop : -0.67 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.016 0.001 TYR B 100 PHE 0.011 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00369 (11778) covalent geometry : angle 0.46958 (15989) SS BOND : bond 0.00311 ( 17) SS BOND : angle 1.18554 ( 34) hydrogen bonds : bond 0.03340 ( 565) hydrogen bonds : angle 4.28334 ( 1638) link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 2.13074 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7872 (mp0) cc_final: 0.7632 (mp0) REVERT: A 248 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7659 (mm) REVERT: B 10 LYS cc_start: 0.8479 (tttt) cc_final: 0.8077 (tptt) REVERT: B 117 ASN cc_start: 0.8487 (t0) cc_final: 0.7708 (m-40) REVERT: B 138 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: B 241 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8638 (ttm170) REVERT: E 98 GLU cc_start: 0.8129 (tp30) cc_final: 0.7781 (tp30) REVERT: H 76 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8426 (t) REVERT: P 3 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: e 99 ASN cc_start: 0.7337 (m-40) cc_final: 0.6491 (p0) outliers start: 31 outliers final: 25 residues processed: 165 average time/residue: 0.1217 time to fit residues: 28.2176 Evaluate side-chains 172 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 83 ASN e 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154932 restraints weight = 12365.435| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.48 r_work: 0.3475 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11801 Z= 0.115 Angle : 0.452 6.291 16041 Z= 0.236 Chirality : 0.040 0.143 1774 Planarity : 0.003 0.034 2045 Dihedral : 4.714 54.577 1701 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.65 % Allowed : 11.18 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.72 (0.22), residues: 1421 helix: 2.96 (0.26), residues: 344 sheet: 0.12 (0.25), residues: 436 loop : -0.63 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.016 0.001 TYR B 100 PHE 0.009 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00270 (11778) covalent geometry : angle 0.44573 (15989) SS BOND : bond 0.00238 ( 17) SS BOND : angle 0.93728 ( 34) hydrogen bonds : bond 0.03119 ( 565) hydrogen bonds : angle 4.12110 ( 1638) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 1.91296 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8533 (mtm110) cc_final: 0.8325 (mtm110) REVERT: A 194 GLU cc_start: 0.7878 (mp0) cc_final: 0.7644 (mp0) REVERT: B 10 LYS cc_start: 0.8489 (tttt) cc_final: 0.8078 (tptt) REVERT: B 117 ASN cc_start: 0.8455 (t0) cc_final: 0.7708 (m-40) REVERT: B 138 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: B 241 ARG cc_start: 0.8909 (ttm-80) cc_final: 0.8623 (ttm170) REVERT: C 81 MET cc_start: 0.8276 (mmm) cc_final: 0.7971 (mmm) REVERT: E 98 GLU cc_start: 0.8084 (tp30) cc_final: 0.7744 (tp30) REVERT: H 76 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8384 (t) REVERT: L 83 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: P 3 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: e 99 ASN cc_start: 0.7319 (m-40) cc_final: 0.6547 (p0) outliers start: 33 outliers final: 17 residues processed: 161 average time/residue: 0.1137 time to fit residues: 26.2200 Evaluate side-chains 161 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 83 ASN Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 83 ASN e 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.152041 restraints weight = 12323.482| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.48 r_work: 0.3224 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11801 Z= 0.172 Angle : 0.491 6.315 16041 Z= 0.255 Chirality : 0.042 0.147 1774 Planarity : 0.004 0.032 2045 Dihedral : 4.822 55.390 1701 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.41 % Allowed : 11.58 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.68 (0.22), residues: 1421 helix: 2.87 (0.26), residues: 343 sheet: 0.11 (0.25), residues: 435 loop : -0.63 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 35 TYR 0.017 0.002 TYR E 14 PHE 0.012 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00414 (11778) covalent geometry : angle 0.48440 (15989) SS BOND : bond 0.00350 ( 17) SS BOND : angle 1.05997 ( 34) hydrogen bonds : bond 0.03355 ( 565) hydrogen bonds : angle 4.23028 ( 1638) link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 2.15575 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 10 LYS cc_start: 0.8541 (tttt) cc_final: 0.7915 (tptt) REVERT: B 117 ASN cc_start: 0.8417 (t0) cc_final: 0.7601 (m-40) REVERT: B 138 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: B 241 ARG cc_start: 0.8894 (ttm-80) cc_final: 0.8561 (ttm170) REVERT: C 81 MET cc_start: 0.8327 (mmm) cc_final: 0.7983 (mmm) REVERT: E 98 GLU cc_start: 0.8058 (tp30) cc_final: 0.7704 (tp30) REVERT: H 76 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (t) REVERT: L 83 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (m-40) REVERT: P 3 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: e 99 ASN cc_start: 0.7370 (m-40) cc_final: 0.6474 (p0) outliers start: 30 outliers final: 23 residues processed: 162 average time/residue: 0.1079 time to fit residues: 25.2172 Evaluate side-chains 169 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 83 ASN Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN L 83 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149566 restraints weight = 12352.093| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.60 r_work: 0.3192 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11801 Z= 0.209 Angle : 0.525 6.428 16041 Z= 0.272 Chirality : 0.043 0.149 1774 Planarity : 0.004 0.033 2045 Dihedral : 4.977 56.459 1701 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.74 % Allowed : 11.58 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1421 helix: 2.74 (0.26), residues: 343 sheet: 0.04 (0.25), residues: 433 loop : -0.67 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 35 TYR 0.021 0.002 TYR E 14 PHE 0.014 0.002 PHE L 30 TRP 0.010 0.001 TRP H 167 HIS 0.005 0.001 HIS L 84 Details of bonding type rmsd covalent geometry : bond 0.00502 (11778) covalent geometry : angle 0.51752 (15989) SS BOND : bond 0.00410 ( 17) SS BOND : angle 1.17206 ( 34) hydrogen bonds : bond 0.03547 ( 565) hydrogen bonds : angle 4.36546 ( 1638) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.29642 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8177 (mtm110) REVERT: A 194 GLU cc_start: 0.8069 (mp0) cc_final: 0.7830 (mp0) REVERT: A 248 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7206 (mm) REVERT: B 10 LYS cc_start: 0.8574 (tttt) cc_final: 0.7966 (tptp) REVERT: B 117 ASN cc_start: 0.8447 (t0) cc_final: 0.7543 (m-40) REVERT: B 138 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: B 241 ARG cc_start: 0.8896 (ttm-80) cc_final: 0.8540 (ttm170) REVERT: C 81 MET cc_start: 0.8341 (mmm) cc_final: 0.8004 (mmm) REVERT: E 98 GLU cc_start: 0.8011 (tp30) cc_final: 0.7648 (tp30) REVERT: H 76 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8475 (t) REVERT: L 83 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (m-40) REVERT: P 3 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: e 99 ASN cc_start: 0.7442 (m-40) cc_final: 0.6467 (p0) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.1120 time to fit residues: 26.7588 Evaluate side-chains 179 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 83 ASN Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain e residue 35 ILE Chi-restraints excluded: chain e residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 118 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN L 83 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151892 restraints weight = 12367.599| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.56 r_work: 0.3216 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11801 Z= 0.136 Angle : 0.475 6.105 16041 Z= 0.247 Chirality : 0.041 0.145 1774 Planarity : 0.004 0.034 2045 Dihedral : 4.832 55.295 1701 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.65 % Allowed : 11.67 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.68 (0.22), residues: 1421 helix: 2.86 (0.26), residues: 345 sheet: 0.10 (0.25), residues: 434 loop : -0.63 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 35 TYR 0.015 0.001 TYR B 100 PHE 0.010 0.001 PHE L 30 TRP 0.010 0.001 TRP H 167 HIS 0.005 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00322 (11778) covalent geometry : angle 0.46851 (15989) SS BOND : bond 0.00283 ( 17) SS BOND : angle 0.97304 ( 34) hydrogen bonds : bond 0.03225 ( 565) hydrogen bonds : angle 4.20421 ( 1638) link_NAG-ASN : bond 0.00174 ( 6) link_NAG-ASN : angle 2.06572 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8237 (mtm110) REVERT: A 194 GLU cc_start: 0.8029 (mp0) cc_final: 0.7795 (mp0) REVERT: A 248 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7341 (mm) REVERT: B 10 LYS cc_start: 0.8536 (tttt) cc_final: 0.7927 (tptt) REVERT: B 117 ASN cc_start: 0.8430 (t0) cc_final: 0.7615 (m-40) REVERT: B 138 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: B 241 ARG cc_start: 0.8906 (ttm-80) cc_final: 0.8574 (ttm170) REVERT: C 81 MET cc_start: 0.8386 (mmm) cc_final: 0.8027 (mmm) REVERT: E 98 GLU cc_start: 0.8030 (tp30) cc_final: 0.7672 (tp30) REVERT: L 83 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: P 3 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: e 99 ASN cc_start: 0.7398 (m-40) cc_final: 0.6476 (p0) outliers start: 33 outliers final: 24 residues processed: 168 average time/residue: 0.1141 time to fit residues: 27.3217 Evaluate side-chains 174 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 83 ASN Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain e residue 75 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN L 83 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151562 restraints weight = 12401.016| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.49 r_work: 0.3206 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11801 Z= 0.175 Angle : 0.503 7.753 16041 Z= 0.260 Chirality : 0.042 0.148 1774 Planarity : 0.004 0.033 2045 Dihedral : 4.895 55.599 1701 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 11.91 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.63 (0.22), residues: 1421 helix: 2.80 (0.26), residues: 344 sheet: 0.07 (0.25), residues: 433 loop : -0.64 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 35 TYR 0.017 0.002 TYR E 14 PHE 0.012 0.001 PHE L 30 TRP 0.011 0.001 TRP H 167 HIS 0.005 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00421 (11778) covalent geometry : angle 0.49665 (15989) SS BOND : bond 0.00354 ( 17) SS BOND : angle 1.05797 ( 34) hydrogen bonds : bond 0.03378 ( 565) hydrogen bonds : angle 4.27393 ( 1638) link_NAG-ASN : bond 0.00183 ( 6) link_NAG-ASN : angle 2.12576 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.94 seconds wall clock time: 56 minutes 40.19 seconds (3400.19 seconds total)