Starting phenix.real_space_refine on Sun Dec 29 21:42:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phr_13427/12_2024/7phr_13427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phr_13427/12_2024/7phr_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_13427/12_2024/7phr_13427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phr_13427/12_2024/7phr_13427.map" model { file = "/net/cci-nas-00/data/ceres_data/7phr_13427/12_2024/7phr_13427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phr_13427/12_2024/7phr_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.42, per 1000 atoms: 0.73 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 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: 1.50 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: 4.33 Time building geometry restraints manager: 3.28 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: 2.750 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- 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 11778 Z= 0.370 Angle : 0.774 7.730 15989 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 *********************** 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 : 1.352 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: 0.3369 time to fit residues: 73.0345 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 : 1.273 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 11778 Z= 0.191 Angle : 0.468 5.137 15989 Z= 0.250 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 *********************** 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 : 1.432 Fit side-chains REVERT: A 126 LYS cc_start: 0.7136 (mptt) cc_final: 0.6823 (mmtt) REVERT: B 10 LYS cc_start: 0.8201 (tttt) cc_final: 0.7866 (tptp) REVERT: H 264 GLU cc_start: 0.7028 (pp20) cc_final: 0.6658 (pm20) REVERT: e 99 ASN cc_start: 0.7182 (m-40) cc_final: 0.6638 (p0) outliers start: 11 outliers final: 9 residues processed: 157 average time/residue: 0.2868 time to fit residues: 64.5850 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 : 1.407 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 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 L 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11778 Z= 0.308 Angle : 0.506 5.275 15989 Z= 0.268 Chirality : 0.043 0.220 1774 Planarity : 0.004 0.050 2045 Dihedral : 4.988 55.971 1701 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 7.80 % Favored : 90.51 % 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: 0.48 (0.22), residues: 1421 helix: 2.72 (0.26), residues: 343 sheet: 0.06 (0.25), residues: 417 loop : -0.80 (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 0.015 0.002 PHE L 30 TYR 0.018 0.002 TYR E 14 ARG 0.006 0.001 ARG H 6 *********************** 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 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8326 (tttt) cc_final: 0.7995 (tptp) REVERT: B 117 ASN cc_start: 0.8141 (t0) cc_final: 0.7472 (m-40) REVERT: B 241 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: H 264 GLU cc_start: 0.7067 (pp20) cc_final: 0.6848 (pm20) REVERT: P 3 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: e 99 ASN cc_start: 0.7202 (m-40) cc_final: 0.6616 (p0) outliers start: 21 outliers final: 18 residues processed: 159 average time/residue: 0.2620 time to fit residues: 58.6593 Evaluate side-chains 159 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 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 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 124 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 189 ASN L 24 ASN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11778 Z= 0.179 Angle : 0.443 4.951 15989 Z= 0.236 Chirality : 0.040 0.152 1774 Planarity : 0.003 0.032 2045 Dihedral : 4.685 54.741 1701 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.45 % Allowed : 9.73 % Favored : 88.82 % 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: 0.69 (0.22), residues: 1421 helix: 2.93 (0.26), residues: 343 sheet: 0.16 (0.26), residues: 423 loop : -0.67 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 167 HIS 0.003 0.001 HIS e 39 PHE 0.009 0.001 PHE L 30 TYR 0.015 0.001 TYR B 100 ARG 0.006 0.000 ARG D 51 *********************** 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 169 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8346 (mtm110) cc_final: 0.7970 (mtm110) REVERT: B 10 LYS cc_start: 0.8283 (tttt) cc_final: 0.7954 (tptp) REVERT: B 117 ASN cc_start: 0.8074 (t0) cc_final: 0.7499 (m-40) REVERT: B 241 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7912 (ttm170) REVERT: H 210 PRO cc_start: 0.8648 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: P 3 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: e 99 ASN cc_start: 0.7215 (m-40) cc_final: 0.6591 (p0) outliers start: 18 outliers final: 13 residues processed: 160 average time/residue: 0.2583 time to fit residues: 58.6757 Evaluate side-chains 155 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU 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 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 75 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 L 8 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11778 Z= 0.241 Angle : 0.470 4.941 15989 Z= 0.249 Chirality : 0.041 0.201 1774 Planarity : 0.004 0.035 2045 Dihedral : 4.798 55.321 1701 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.17 % Allowed : 10.06 % Favored : 87.77 % 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: 0.73 (0.22), residues: 1421 helix: 2.89 (0.26), residues: 343 sheet: 0.18 (0.25), residues: 427 loop : -0.60 (0.23), residues: 651 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 0.014 0.001 TYR B 100 ARG 0.007 0.000 ARG D 51 *********************** 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 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8294 (tttt) cc_final: 0.7836 (tptt) REVERT: B 117 ASN cc_start: 0.8115 (t0) cc_final: 0.7524 (m-40) REVERT: B 241 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7970 (ttm170) REVERT: C 81 MET cc_start: 0.7993 (mmm) cc_final: 0.7616 (mmm) REVERT: H 76 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (t) REVERT: P 3 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: e 99 ASN cc_start: 0.7225 (m-40) cc_final: 0.6601 (p0) outliers start: 27 outliers final: 21 residues processed: 157 average time/residue: 0.2553 time to fit residues: 57.5451 Evaluate side-chains 162 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 183 CYS 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 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 120 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11778 Z= 0.280 Angle : 0.492 6.664 15989 Z= 0.259 Chirality : 0.042 0.191 1774 Planarity : 0.004 0.032 2045 Dihedral : 4.892 55.871 1701 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.09 % Allowed : 10.62 % Favored : 87.29 % 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: 0.69 (0.22), residues: 1421 helix: 2.82 (0.26), residues: 343 sheet: 0.19 (0.25), residues: 433 loop : -0.63 (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 0.013 0.002 PHE L 30 TYR 0.016 0.002 TYR E 14 ARG 0.008 0.000 ARG D 51 *********************** 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 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7478 (mp0) cc_final: 0.7226 (mp0) REVERT: B 10 LYS cc_start: 0.8294 (tttt) cc_final: 0.7833 (tptt) REVERT: B 117 ASN cc_start: 0.8118 (t0) cc_final: 0.7480 (m-40) REVERT: B 241 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: E 98 GLU cc_start: 0.7714 (tp30) cc_final: 0.7472 (tp30) REVERT: H 76 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8290 (t) REVERT: P 3 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: e 99 ASN cc_start: 0.7197 (m-40) cc_final: 0.6527 (p0) outliers start: 26 outliers final: 22 residues processed: 158 average time/residue: 0.2623 time to fit residues: 58.5080 Evaluate side-chains 164 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 11778 Z= 0.361 Angle : 0.534 6.359 15989 Z= 0.280 Chirality : 0.043 0.201 1774 Planarity : 0.004 0.036 2045 Dihedral : 5.099 57.529 1701 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.33 % Allowed : 11.10 % 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: 0.48 (0.22), residues: 1421 helix: 2.67 (0.26), residues: 343 sheet: 0.10 (0.25), residues: 411 loop : -0.79 (0.23), residues: 667 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 0.015 0.002 PHE L 30 TYR 0.018 0.002 TYR E 14 ARG 0.007 0.001 ARG D 51 *********************** 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 175 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7495 (mp0) cc_final: 0.7251 (mp0) REVERT: B 10 LYS cc_start: 0.8305 (tttt) cc_final: 0.7907 (tptt) REVERT: B 241 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7961 (ttm170) REVERT: C 81 MET cc_start: 0.7996 (mmm) cc_final: 0.7690 (mmm) REVERT: E 98 GLU cc_start: 0.7756 (tp30) cc_final: 0.7516 (tp30) REVERT: H 76 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (t) REVERT: P 3 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: e 99 ASN cc_start: 0.7243 (m-40) cc_final: 0.6492 (p0) outliers start: 29 outliers final: 25 residues processed: 162 average time/residue: 0.2602 time to fit residues: 59.3141 Evaluate side-chains 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 29 THR 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: 0.6980 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11778 Z= 0.212 Angle : 0.468 6.809 15989 Z= 0.246 Chirality : 0.041 0.175 1774 Planarity : 0.004 0.033 2045 Dihedral : 4.867 55.729 1701 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.17 % Allowed : 11.83 % 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 (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: 0.68 (0.22), residues: 1421 helix: 2.87 (0.26), residues: 344 sheet: 0.16 (0.25), residues: 434 loop : -0.68 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 167 HIS 0.004 0.001 HIS e 39 PHE 0.011 0.001 PHE L 30 TYR 0.016 0.001 TYR B 100 ARG 0.008 0.000 ARG D 51 *********************** 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 170 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 10 LYS cc_start: 0.8312 (tttt) cc_final: 0.7902 (tptt) REVERT: B 117 ASN cc_start: 0.7890 (t0) cc_final: 0.7339 (m-40) REVERT: B 241 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7956 (ttm170) REVERT: C 81 MET cc_start: 0.8073 (mmm) cc_final: 0.7736 (mmm) REVERT: E 98 GLU cc_start: 0.7754 (tp30) cc_final: 0.7501 (tp30) REVERT: H 76 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8281 (t) REVERT: P 3 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: e 73 TYR cc_start: 0.8535 (m-80) cc_final: 0.8259 (m-80) REVERT: e 99 ASN cc_start: 0.7246 (m-40) cc_final: 0.6528 (p0) outliers start: 27 outliers final: 20 residues processed: 159 average time/residue: 0.2539 time to fit residues: 57.4548 Evaluate side-chains 161 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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 29 THR 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 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 127 optimal weight: 0.0000 chunk 116 optimal weight: 0.0770 chunk 123 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.4742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11778 Z= 0.193 Angle : 0.462 7.140 15989 Z= 0.243 Chirality : 0.041 0.167 1774 Planarity : 0.003 0.035 2045 Dihedral : 4.834 54.996 1701 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.09 % Allowed : 11.99 % Favored : 85.92 % 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: 0.76 (0.22), residues: 1421 helix: 2.93 (0.26), residues: 345 sheet: 0.21 (0.25), residues: 435 loop : -0.63 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 175 HIS 0.005 0.001 HIS e 39 PHE 0.009 0.001 PHE L 30 TYR 0.016 0.001 TYR B 100 ARG 0.009 0.000 ARG D 51 *********************** 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 167 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7441 (mm) REVERT: B 10 LYS cc_start: 0.8318 (tttt) cc_final: 0.7895 (tptt) REVERT: B 117 ASN cc_start: 0.7902 (t0) cc_final: 0.7395 (m-40) REVERT: B 241 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7921 (ttm170) REVERT: C 81 MET cc_start: 0.8152 (mmm) cc_final: 0.7799 (mmm) REVERT: E 98 GLU cc_start: 0.7728 (tp30) cc_final: 0.7488 (tp30) REVERT: H 76 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8262 (t) REVERT: P 3 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: e 99 ASN cc_start: 0.7221 (m-40) cc_final: 0.6572 (p0) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.2479 time to fit residues: 55.8592 Evaluate side-chains 162 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 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 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 52 SER 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 79 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 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 113 GLN A 189 ASN H 262 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11778 Z= 0.279 Angle : 0.502 7.650 15989 Z= 0.263 Chirality : 0.042 0.184 1774 Planarity : 0.004 0.037 2045 Dihedral : 4.952 56.063 1701 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.09 % Allowed : 12.15 % 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: 0.67 (0.22), residues: 1421 helix: 2.81 (0.26), residues: 344 sheet: 0.14 (0.25), residues: 431 loop : -0.63 (0.24), residues: 646 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 0.013 0.002 PHE L 30 TYR 0.015 0.002 TYR E 14 ARG 0.009 0.001 ARG D 51 ********************** 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 172 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7435 (mm) REVERT: B 10 LYS cc_start: 0.8324 (tttt) cc_final: 0.7995 (tptp) REVERT: B 241 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7968 (ttm170) REVERT: C 81 MET cc_start: 0.8131 (mmm) cc_final: 0.7786 (mmm) REVERT: H 76 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (t) REVERT: P 3 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: e 99 ASN cc_start: 0.7245 (m-40) cc_final: 0.6555 (p0) outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 0.2496 time to fit residues: 57.5962 Evaluate side-chains 169 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 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 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 49 VAL Chi-restraints excluded: chain L residue 52 SER 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 33 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 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 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 = 0.4046 r_free = 0.4046 target = 0.183590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151768 restraints weight = 12283.770| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.46 r_work: 0.3231 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.003 0.054 11778 Z= 0.225 Angle : 0.473 7.362 15989 Z= 0.249 Chirality : 0.041 0.170 1774 Planarity : 0.004 0.036 2045 Dihedral : 4.882 55.500 1701 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 12.31 % 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 (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: 0.73 (0.22), residues: 1421 helix: 2.87 (0.26), residues: 345 sheet: 0.20 (0.25), residues: 432 loop : -0.62 (0.24), residues: 644 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 0.015 0.001 TYR B 100 ARG 0.009 0.000 ARG D 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.53 seconds wall clock time: 48 minutes 50.45 seconds (2930.45 seconds total)