Starting phenix.real_space_refine on Tue Jul 29 15:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_13427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_13427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_13427.map" model { file = "/net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_13427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phr_13427/07_2025/7phr_13427.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: 9.41, per 1000 atoms: 0.82 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: 3.01 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.76 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: 5.26 Time building geometry restraints manager: 3.62 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: 232.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.210 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 272.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP H 167 HIS 0.006 0.001 HIS H 70 PHE 0.016 0.002 PHE e 65 TYR 0.025 0.002 TYR B 251 ARG 0.007 0.001 ARG B 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 6) link_NAG-ASN : angle 1.69300 ( 18) hydrogen bonds : bond 0.12418 ( 565) hydrogen bonds : angle 6.33402 ( 1638) SS BOND : bond 0.00557 ( 17) SS BOND : angle 1.44726 ( 34) covalent geometry : bond 0.00568 (11778) covalent geometry : angle 0.77433 (15989) *********************** 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 : 1.540 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: 0.4465 time to fit residues: 95.7064 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 : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.0170 chunk 65 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 D 68 HIS E 38 GLN L 84 HIS e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151928 restraints weight = 12213.380| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.67 r_work: 0.3244 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1048 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= 0.127 Angle : 0.472 5.137 16041 Z= 0.251 Chirality : 0.041 0.153 1774 Planarity : 0.004 0.035 2045 Dihedral : 5.046 53.300 1701 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.88 % Allowed : 6.36 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1421 helix: 2.78 (0.26), residues: 343 sheet: -0.03 (0.25), residues: 418 loop : -0.84 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 167 HIS 0.002 0.001 HIS H 70 PHE 0.009 0.001 PHE L 30 TYR 0.016 0.001 TYR B 251 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 6) link_NAG-ASN : angle 1.59641 ( 18) hydrogen bonds : bond 0.03519 ( 565) hydrogen bonds : angle 4.56259 ( 1638) SS BOND : bond 0.00315 ( 17) SS BOND : angle 0.92846 ( 34) covalent geometry : bond 0.00297 (11778) covalent geometry : angle 0.46763 (15989) *********************** 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 166 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.243 Fit side-chains REVERT: A 126 LYS cc_start: 0.7261 (mptt) cc_final: 0.6826 (mmtt) REVERT: B 10 LYS cc_start: 0.8404 (tttt) cc_final: 0.7924 (tptp) REVERT: H 264 GLU cc_start: 0.7245 (pp20) cc_final: 0.6873 (pm20) REVERT: L 83 ASN cc_start: 0.7899 (t0) cc_final: 0.7617 (m-40) REVERT: e 99 ASN cc_start: 0.7362 (m-40) cc_final: 0.6598 (p0) outliers start: 11 outliers final: 9 residues processed: 157 average time/residue: 0.2536 time to fit residues: 55.9992 Evaluate side-chains 146 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 31 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 128 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153293 restraints weight = 12402.514| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.45 r_work: 0.3225 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11801 Z= 0.179 Angle : 0.502 8.595 16041 Z= 0.264 Chirality : 0.042 0.205 1774 Planarity : 0.004 0.048 2045 Dihedral : 4.929 55.676 1701 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.61 % Allowed : 7.72 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1421 helix: 2.76 (0.26), residues: 343 sheet: 0.08 (0.26), residues: 417 loop : -0.79 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 167 HIS 0.003 0.001 HIS H 74 PHE 0.014 0.002 PHE L 30 TYR 0.017 0.002 TYR E 14 ARG 0.006 0.001 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 6) link_NAG-ASN : angle 1.79698 ( 18) hydrogen bonds : bond 0.03605 ( 565) hydrogen bonds : angle 4.48418 ( 1638) SS BOND : bond 0.00423 ( 17) SS BOND : angle 1.78819 ( 34) covalent geometry : bond 0.00431 (11778) covalent geometry : angle 0.49242 (15989) *********************** 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 168 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8501 (tttt) cc_final: 0.8041 (tptp) REVERT: B 117 ASN cc_start: 0.8493 (t0) cc_final: 0.7680 (m-40) REVERT: B 241 ARG cc_start: 0.8847 (ttm-80) cc_final: 0.8482 (ttm170) REVERT: H 264 GLU cc_start: 0.7237 (pp20) cc_final: 0.7031 (pm20) REVERT: P 3 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: e 99 ASN cc_start: 0.7375 (m-40) cc_final: 0.6593 (p0) outliers start: 20 outliers final: 18 residues processed: 157 average time/residue: 0.2597 time to fit residues: 57.5639 Evaluate side-chains 160 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 23 SER 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 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 37 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 e 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153322 restraints weight = 12324.755| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.42 r_work: 0.3223 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11801 Z= 0.177 Angle : 0.493 5.936 16041 Z= 0.259 Chirality : 0.042 0.166 1774 Planarity : 0.004 0.039 2045 Dihedral : 4.851 55.956 1701 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 9.57 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1421 helix: 2.78 (0.26), residues: 343 sheet: 0.09 (0.26), residues: 422 loop : -0.71 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 167 HIS 0.003 0.001 HIS e 39 PHE 0.012 0.001 PHE L 30 TYR 0.016 0.002 TYR E 14 ARG 0.006 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 2.00806 ( 18) hydrogen bonds : bond 0.03490 ( 565) hydrogen bonds : angle 4.39306 ( 1638) SS BOND : bond 0.00363 ( 17) SS BOND : angle 1.29404 ( 34) covalent geometry : bond 0.00424 (11778) covalent geometry : angle 0.48586 (15989) *********************** 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 178 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8489 (tttt) cc_final: 0.7971 (tptp) REVERT: B 117 ASN cc_start: 0.8475 (t0) cc_final: 0.7652 (m-40) REVERT: B 241 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8489 (ttm170) REVERT: C 81 MET cc_start: 0.8232 (mmm) cc_final: 0.7963 (mmm) REVERT: H 232 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7555 (pt0) REVERT: L 83 ASN cc_start: 0.7818 (t0) cc_final: 0.7320 (m-40) REVERT: P 3 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: e 99 ASN cc_start: 0.7412 (m-40) cc_final: 0.6550 (p0) outliers start: 24 outliers final: 20 residues processed: 164 average time/residue: 0.2598 time to fit residues: 59.4638 Evaluate side-chains 163 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain B residue 23 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.182745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150576 restraints weight = 12284.201| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.57 r_work: 0.3443 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11801 Z= 0.146 Angle : 0.475 5.660 16041 Z= 0.250 Chirality : 0.041 0.195 1774 Planarity : 0.004 0.036 2045 Dihedral : 4.825 55.264 1701 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.01 % Allowed : 10.38 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1421 helix: 2.84 (0.26), residues: 343 sheet: 0.17 (0.26), residues: 421 loop : -0.66 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 175 HIS 0.004 0.001 HIS e 39 PHE 0.011 0.001 PHE L 30 TYR 0.015 0.001 TYR B 100 ARG 0.006 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 2.00665 ( 18) hydrogen bonds : bond 0.03299 ( 565) hydrogen bonds : angle 4.29302 ( 1638) SS BOND : bond 0.00304 ( 17) SS BOND : angle 1.33415 ( 34) covalent geometry : bond 0.00350 (11778) covalent geometry : angle 0.46720 (15989) *********************** 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 172 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 2.591 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8489 (tttt) cc_final: 0.8044 (tptt) REVERT: B 117 ASN cc_start: 0.8569 (t0) cc_final: 0.7812 (m-40) REVERT: B 241 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8656 (ttm170) REVERT: E 98 GLU cc_start: 0.8054 (tp30) cc_final: 0.7696 (tp30) REVERT: H 76 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8411 (t) REVERT: P 3 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: e 99 ASN cc_start: 0.7394 (m-40) cc_final: 0.6588 (p0) outliers start: 25 outliers final: 20 residues processed: 160 average time/residue: 0.3261 time to fit residues: 75.7523 Evaluate side-chains 163 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 A residue 183 CYS 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 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 128 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.185220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151293 restraints weight = 12386.192| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.65 r_work: 0.3226 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11801 Z= 0.145 Angle : 0.475 5.684 16041 Z= 0.249 Chirality : 0.041 0.182 1774 Planarity : 0.004 0.037 2045 Dihedral : 4.800 55.092 1701 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 10.86 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1421 helix: 2.91 (0.26), residues: 343 sheet: 0.15 (0.25), residues: 434 loop : -0.63 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.004 0.001 HIS e 39 PHE 0.011 0.001 PHE L 30 TYR 0.015 0.001 TYR B 100 ARG 0.008 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 6) link_NAG-ASN : angle 2.02525 ( 18) hydrogen bonds : bond 0.03267 ( 565) hydrogen bonds : angle 4.22239 ( 1638) SS BOND : bond 0.00322 ( 17) SS BOND : angle 1.25795 ( 34) covalent geometry : bond 0.00348 (11778) covalent geometry : angle 0.46779 (15989) *********************** 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 173 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8507 (tttt) cc_final: 0.7861 (tptt) REVERT: B 117 ASN cc_start: 0.8445 (t0) cc_final: 0.7636 (m-40) REVERT: B 241 ARG cc_start: 0.8912 (ttm-80) cc_final: 0.8573 (ttm170) REVERT: C 81 MET cc_start: 0.8375 (mmm) cc_final: 0.8000 (mmm) REVERT: E 98 GLU cc_start: 0.7930 (tp30) cc_final: 0.7557 (tp30) REVERT: H 76 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8383 (t) REVERT: L 83 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7830 (m-40) REVERT: P 3 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: e 99 ASN cc_start: 0.7394 (m-40) cc_final: 0.6552 (p0) outliers start: 28 outliers final: 23 residues processed: 160 average time/residue: 0.2528 time to fit residues: 57.3521 Evaluate side-chains 166 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 A residue 183 CYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 LEU 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 L residue 83 ASN 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 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.184685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152734 restraints weight = 12543.321| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.58 r_work: 0.3436 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11801 Z= 0.161 Angle : 0.488 6.393 16041 Z= 0.254 Chirality : 0.041 0.178 1774 Planarity : 0.004 0.037 2045 Dihedral : 4.832 55.257 1701 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.57 % Allowed : 10.78 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1421 helix: 2.88 (0.26), residues: 343 sheet: 0.16 (0.25), residues: 433 loop : -0.62 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.004 0.001 HIS e 39 PHE 0.012 0.001 PHE L 30 TYR 0.014 0.001 TYR B 100 ARG 0.008 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 6) link_NAG-ASN : angle 2.11231 ( 18) hydrogen bonds : bond 0.03313 ( 565) hydrogen bonds : angle 4.24173 ( 1638) SS BOND : bond 0.00336 ( 17) SS BOND : angle 1.21784 ( 34) covalent geometry : bond 0.00389 (11778) covalent geometry : angle 0.48021 (15989) *********************** 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: 32 poor density : 145 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7910 (mp0) cc_final: 0.7682 (mp0) REVERT: A 248 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7652 (mm) REVERT: B 10 LYS cc_start: 0.8496 (tttt) cc_final: 0.8039 (tptt) REVERT: B 117 ASN cc_start: 0.8588 (t0) cc_final: 0.7792 (m-40) REVERT: B 241 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8715 (ttm170) REVERT: C 81 MET cc_start: 0.8392 (mmm) cc_final: 0.8059 (mmm) REVERT: E 98 GLU cc_start: 0.8089 (tp30) cc_final: 0.7743 (tp30) REVERT: H 76 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8423 (t) REVERT: P 3 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: e 99 ASN cc_start: 0.7347 (m-40) cc_final: 0.6593 (p0) outliers start: 32 outliers final: 26 residues processed: 162 average time/residue: 0.2448 time to fit residues: 56.2866 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 : 1.255 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 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 30 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 0.0010 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.184127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150781 restraints weight = 12435.734| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.59 r_work: 0.3473 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11801 Z= 0.117 Angle : 0.456 6.018 16041 Z= 0.238 Chirality : 0.040 0.162 1774 Planarity : 0.003 0.034 2045 Dihedral : 4.705 54.210 1701 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.41 % Allowed : 11.02 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1421 helix: 2.99 (0.26), residues: 345 sheet: 0.23 (0.25), residues: 436 loop : -0.58 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 PHE 0.009 0.001 PHE L 30 TYR 0.015 0.001 TYR B 100 ARG 0.008 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 6) link_NAG-ASN : angle 1.82785 ( 18) hydrogen bonds : bond 0.03085 ( 565) hydrogen bonds : angle 4.08177 ( 1638) SS BOND : bond 0.00230 ( 17) SS BOND : angle 1.04620 ( 34) covalent geometry : bond 0.00279 (11778) covalent geometry : angle 0.45030 (15989) *********************** 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 179 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7599 (mm) REVERT: B 10 LYS cc_start: 0.8464 (tttt) cc_final: 0.8010 (tptt) REVERT: B 117 ASN cc_start: 0.8479 (t0) cc_final: 0.7762 (m-40) REVERT: B 241 ARG cc_start: 0.8923 (ttm-80) cc_final: 0.8625 (ttm170) REVERT: C 81 MET cc_start: 0.8379 (mmm) cc_final: 0.8017 (mmm) REVERT: E 98 GLU cc_start: 0.8072 (tp30) cc_final: 0.7732 (tp30) REVERT: H 76 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8384 (t) REVERT: H 232 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7597 (pt0) REVERT: P 3 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: e 73 TYR cc_start: 0.8745 (m-80) cc_final: 0.8501 (m-80) REVERT: e 99 ASN cc_start: 0.7373 (m-40) cc_final: 0.6595 (p0) outliers start: 30 outliers final: 22 residues processed: 164 average time/residue: 0.2578 time to fit residues: 59.5620 Evaluate side-chains 168 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 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 30 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 96 VAL 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 52 SER 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 73 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 99 GLN A 113 GLN A 189 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 = 0.3990 r_free = 0.3990 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142544 restraints weight = 12547.291| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.86 r_work: 0.3134 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 11801 Z= 0.319 Angle : 0.623 8.187 16041 Z= 0.321 Chirality : 0.046 0.222 1774 Planarity : 0.004 0.041 2045 Dihedral : 5.322 58.970 1701 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.17 % Allowed : 11.75 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1421 helix: 2.42 (0.26), residues: 343 sheet: -0.01 (0.25), residues: 412 loop : -0.83 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 175 HIS 0.005 0.001 HIS e 39 PHE 0.019 0.002 PHE L 30 TYR 0.023 0.002 TYR C 112 ARG 0.007 0.001 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 2.81097 ( 18) hydrogen bonds : bond 0.03964 ( 565) hydrogen bonds : angle 4.62641 ( 1638) SS BOND : bond 0.00620 ( 17) SS BOND : angle 1.68908 ( 34) covalent geometry : bond 0.00772 (11778) covalent geometry : angle 0.61214 (15989) *********************** 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 172 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7097 (mm) REVERT: B 10 LYS cc_start: 0.8594 (tttt) cc_final: 0.7822 (tptt) REVERT: C 15 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6801 (mm-40) REVERT: C 81 MET cc_start: 0.8428 (mmm) cc_final: 0.8041 (mmm) REVERT: E 98 GLU cc_start: 0.8005 (tp30) cc_final: 0.7634 (tp30) REVERT: H 76 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8510 (t) REVERT: P 3 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: e 99 ASN cc_start: 0.7557 (m-40) cc_final: 0.6498 (p0) outliers start: 27 outliers final: 22 residues processed: 163 average time/residue: 0.2622 time to fit residues: 60.4068 Evaluate side-chains 166 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 151 ASP Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 248 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 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 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 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS 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 = 0.4055 r_free = 0.4055 target = 0.184324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153357 restraints weight = 12382.447| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.48 r_work: 0.3442 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11801 Z= 0.155 Angle : 0.496 6.971 16041 Z= 0.259 Chirality : 0.041 0.179 1774 Planarity : 0.004 0.037 2045 Dihedral : 4.978 56.154 1701 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.93 % Allowed : 12.31 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1421 helix: 2.71 (0.26), residues: 345 sheet: 0.10 (0.25), residues: 425 loop : -0.72 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 167 HIS 0.005 0.001 HIS e 39 PHE 0.012 0.001 PHE L 30 TYR 0.015 0.001 TYR H 99 ARG 0.009 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 6) link_NAG-ASN : angle 2.22576 ( 18) hydrogen bonds : bond 0.03312 ( 565) hydrogen bonds : angle 4.30381 ( 1638) SS BOND : bond 0.00314 ( 17) SS BOND : angle 1.23645 ( 34) covalent geometry : bond 0.00372 (11778) covalent geometry : angle 0.48806 (15989) ********************** 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 173 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: A 194 GLU cc_start: 0.7919 (mp0) cc_final: 0.7697 (mp0) REVERT: A 248 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7626 (mm) REVERT: B 10 LYS cc_start: 0.8471 (tttt) cc_final: 0.8071 (tptt) REVERT: B 241 ARG cc_start: 0.8960 (ttm-80) cc_final: 0.8660 (ttm170) REVERT: C 81 MET cc_start: 0.8376 (mmm) cc_final: 0.8029 (mmm) REVERT: E 98 GLU cc_start: 0.8151 (tp30) cc_final: 0.7806 (tp30) REVERT: P 3 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: e 99 ASN cc_start: 0.7421 (m-40) cc_final: 0.6552 (p0) outliers start: 24 outliers final: 18 residues processed: 163 average time/residue: 0.2760 time to fit residues: 62.6665 Evaluate side-chains 167 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 183 CYS Chi-restraints excluded: chain A residue 248 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 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 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 52 SER Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 e 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151814 restraints weight = 12251.843| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.47 r_work: 0.3229 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11801 Z= 0.148 Angle : 0.490 7.402 16041 Z= 0.255 Chirality : 0.041 0.174 1774 Planarity : 0.004 0.038 2045 Dihedral : 4.912 55.239 1701 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 12.39 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1421 helix: 2.81 (0.26), residues: 345 sheet: 0.14 (0.25), residues: 434 loop : -0.66 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.005 0.001 HIS e 39 PHE 0.011 0.001 PHE L 30 TYR 0.014 0.001 TYR H 99 ARG 0.009 0.000 ARG D 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 2.09296 ( 18) hydrogen bonds : bond 0.03254 ( 565) hydrogen bonds : angle 4.23589 ( 1638) SS BOND : bond 0.00303 ( 17) SS BOND : angle 1.19343 ( 34) covalent geometry : bond 0.00356 (11778) covalent geometry : angle 0.48215 (15989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7690.39 seconds wall clock time: 134 minutes 44.34 seconds (8084.34 seconds total)