Starting phenix.real_space_refine on Thu Feb 15 07:22:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_2024/7phr_13427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_2024/7phr_13427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_2024/7phr_13427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_2024/7phr_13427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/02_2024/7phr_13427.pdb" } 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 Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.44, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.49 Conformation dependent library (CDL) restraints added in 2.1 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: 1.38 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: 3.71 Time building geometry restraints manager: 4.81 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: 99.81 - 106.77: 330 106.77 - 113.73: 6487 113.73 - 120.69: 4876 120.69 - 127.65: 4175 127.65 - 134.61: 121 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 2.440 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 2.520 ... (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 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: 2.450 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: 12.640 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.600 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.371 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: 0.2945 time to fit residues: 63.7563 Evaluate side-chains 133 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 20.0000 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 B 212 GLN E 38 GLN e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11778 Z= 0.281 Angle : 0.502 5.446 15989 Z= 0.267 Chirality : 0.042 0.150 1774 Planarity : 0.004 0.042 2045 Dihedral : 5.318 54.819 1701 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.37 % Allowed : 6.03 % Favored : 92.60 % 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: 0.31 (0.22), residues: 1421 helix: 2.63 (0.27), residues: 343 sheet: -0.07 (0.25), residues: 414 loop : -0.91 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 167 HIS 0.003 0.001 HIS D 107 PHE 0.013 0.002 PHE L 30 TYR 0.019 0.002 TYR B 251 ARG 0.005 0.001 ARG H 44 *********************** 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 171 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.374 Fit side-chains REVERT: A 126 LYS cc_start: 0.7137 (mptt) cc_final: 0.6828 (mmtt) REVERT: B 10 LYS cc_start: 0.8236 (tttt) cc_final: 0.7893 (tptp) REVERT: H 264 GLU cc_start: 0.7140 (pp20) cc_final: 0.6754 (pm20) REVERT: e 99 ASN cc_start: 0.7244 (m-40) cc_final: 0.6663 (p0) outliers start: 17 outliers final: 16 residues processed: 159 average time/residue: 0.2609 time to fit residues: 58.1955 Evaluate side-chains 158 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 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 L residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 104 optimal weight: 0.0000 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 L 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11778 Z= 0.228 Angle : 0.463 5.199 15989 Z= 0.246 Chirality : 0.041 0.209 1774 Planarity : 0.004 0.039 2045 Dihedral : 4.898 55.569 1701 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.85 % Allowed : 8.21 % Favored : 89.94 % 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: 0.50 (0.22), residues: 1421 helix: 2.77 (0.26), residues: 343 sheet: 0.12 (0.26), residues: 410 loop : -0.83 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 167 HIS 0.002 0.001 HIS D 107 PHE 0.011 0.001 PHE L 30 TYR 0.016 0.001 TYR H 99 ARG 0.006 0.000 ARG H 44 *********************** 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 171 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8309 (tttt) cc_final: 0.8004 (tptp) REVERT: C 81 MET cc_start: 0.8085 (mmm) cc_final: 0.7773 (mmm) REVERT: P 3 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: e 99 ASN cc_start: 0.7219 (m-40) cc_final: 0.6585 (p0) outliers start: 23 outliers final: 17 residues processed: 158 average time/residue: 0.2619 time to fit residues: 57.5251 Evaluate side-chains 156 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 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 68 THR 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: 3.9990 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 L 84 HIS e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11778 Z= 0.204 Angle : 0.447 4.984 15989 Z= 0.237 Chirality : 0.041 0.159 1774 Planarity : 0.003 0.048 2045 Dihedral : 4.688 55.045 1701 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.09 % Allowed : 9.41 % 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: 0.63 (0.22), residues: 1421 helix: 2.88 (0.26), residues: 343 sheet: 0.22 (0.26), residues: 412 loop : -0.77 (0.23), residues: 666 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 0.010 0.001 PHE L 30 TYR 0.016 0.001 TYR H 99 ARG 0.005 0.000 ARG H 6 *********************** 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 175 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8331 (tttt) cc_final: 0.8016 (tptp) REVERT: C 81 MET cc_start: 0.8127 (mmm) cc_final: 0.7833 (mmm) REVERT: P 3 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: e 99 ASN cc_start: 0.7196 (m-40) cc_final: 0.6558 (p0) outliers start: 26 outliers final: 23 residues processed: 159 average time/residue: 0.2487 time to fit residues: 56.2247 Evaluate side-chains 168 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 68 THR 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: 6.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 8 GLN e 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11778 Z= 0.364 Angle : 0.523 5.639 15989 Z= 0.276 Chirality : 0.043 0.220 1774 Planarity : 0.004 0.055 2045 Dihedral : 5.000 57.483 1701 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 10.46 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.22), residues: 1421 helix: 2.64 (0.26), residues: 343 sheet: 0.14 (0.26), residues: 411 loop : -0.82 (0.22), residues: 667 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 0.016 0.002 PHE L 30 TYR 0.020 0.002 TYR E 14 ARG 0.004 0.000 ARG H 44 *********************** 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 173 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8323 (tttt) cc_final: 0.7883 (tptt) REVERT: C 81 MET cc_start: 0.8077 (mmm) cc_final: 0.7842 (mmm) REVERT: P 3 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: e 99 ASN cc_start: 0.7180 (m-40) cc_final: 0.6486 (p0) outliers start: 32 outliers final: 26 residues processed: 156 average time/residue: 0.2361 time to fit residues: 53.0811 Evaluate side-chains 164 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP 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 177 GLU Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 68 THR 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: 0.7980 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11778 Z= 0.215 Angle : 0.455 5.003 15989 Z= 0.242 Chirality : 0.041 0.183 1774 Planarity : 0.003 0.035 2045 Dihedral : 4.808 56.031 1701 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 11.34 % 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: 0.60 (0.22), residues: 1421 helix: 2.83 (0.26), residues: 344 sheet: 0.20 (0.26), residues: 410 loop : -0.78 (0.23), residues: 667 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 0.003 0.000 ARG H 44 *********************** 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 175 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: B 10 LYS cc_start: 0.8297 (tttt) cc_final: 0.7875 (tptt) REVERT: E 98 GLU cc_start: 0.7737 (tp30) cc_final: 0.7456 (tp30) REVERT: H 76 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8327 (t) REVERT: P 3 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: e 99 ASN cc_start: 0.7201 (m-40) cc_final: 0.6520 (p0) outliers start: 33 outliers final: 26 residues processed: 155 average time/residue: 0.2561 time to fit residues: 57.0725 Evaluate side-chains 169 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 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 68 THR 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: 4.9990 chunk 97 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.0000 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.5702 ------------------------------------------------------------------------------- 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 B 83 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11778 Z= 0.213 Angle : 0.455 5.441 15989 Z= 0.240 Chirality : 0.041 0.170 1774 Planarity : 0.003 0.034 2045 Dihedral : 4.772 55.565 1701 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.65 % Allowed : 11.34 % 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: 0.63 (0.22), residues: 1421 helix: 2.89 (0.26), residues: 344 sheet: 0.17 (0.26), residues: 418 loop : -0.75 (0.23), residues: 659 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 0.010 0.001 PHE L 30 TYR 0.016 0.001 TYR B 100 ARG 0.004 0.000 ARG H 35 *********************** 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 178 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 10 LYS cc_start: 0.8276 (tttt) cc_final: 0.7968 (tptp) REVERT: B 138 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: E 98 GLU cc_start: 0.7717 (tp30) cc_final: 0.7456 (tp30) REVERT: P 3 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: e 99 ASN cc_start: 0.7191 (m-40) cc_final: 0.6542 (p0) outliers start: 33 outliers final: 25 residues processed: 160 average time/residue: 0.2623 time to fit residues: 59.8883 Evaluate side-chains 170 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 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 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 68 THR 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 79 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11778 Z= 0.268 Angle : 0.480 8.398 15989 Z= 0.252 Chirality : 0.041 0.180 1774 Planarity : 0.004 0.040 2045 Dihedral : 4.850 56.033 1701 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.49 % Allowed : 11.83 % 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: 0.61 (0.22), residues: 1421 helix: 2.85 (0.26), residues: 343 sheet: 0.15 (0.26), residues: 416 loop : -0.75 (0.23), residues: 662 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 0.012 0.001 PHE L 30 TYR 0.015 0.001 TYR E 14 ARG 0.004 0.000 ARG H 35 *********************** 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 175 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7426 (mm) REVERT: B 10 LYS cc_start: 0.8277 (tttt) cc_final: 0.7968 (tptp) REVERT: E 98 GLU cc_start: 0.7686 (tp30) cc_final: 0.7434 (tp30) REVERT: P 3 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: e 99 ASN cc_start: 0.7168 (m-40) cc_final: 0.6511 (p0) outliers start: 31 outliers final: 27 residues processed: 160 average time/residue: 0.2401 time to fit residues: 54.8666 Evaluate side-chains 172 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 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 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 68 THR Chi-restraints excluded: chain P residue 1 TYR 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: 0.0670 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 B 83 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11778 Z= 0.239 Angle : 0.467 7.652 15989 Z= 0.246 Chirality : 0.041 0.174 1774 Planarity : 0.003 0.035 2045 Dihedral : 4.816 55.878 1701 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.65 % Allowed : 11.83 % Favored : 85.52 % 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: 0.65 (0.22), residues: 1421 helix: 2.89 (0.26), residues: 344 sheet: 0.19 (0.26), residues: 416 loop : -0.73 (0.23), residues: 661 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 0.011 0.001 PHE L 30 TYR 0.015 0.001 TYR B 100 ARG 0.005 0.000 ARG H 35 *********************** 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 175 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7488 (mp0) cc_final: 0.7242 (mp0) REVERT: A 248 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 10 LYS cc_start: 0.8232 (tttt) cc_final: 0.7955 (tptp) REVERT: B 138 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: E 98 GLU cc_start: 0.7725 (tp30) cc_final: 0.7465 (tp30) REVERT: P 3 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: e 99 ASN cc_start: 0.7179 (m-40) cc_final: 0.6504 (p0) outliers start: 33 outliers final: 27 residues processed: 161 average time/residue: 0.2484 time to fit residues: 56.8423 Evaluate side-chains 171 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 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 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 68 THR 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 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 11778 Z= 0.422 Angle : 0.560 7.746 15989 Z= 0.292 Chirality : 0.044 0.208 1774 Planarity : 0.004 0.055 2045 Dihedral : 5.155 58.445 1701 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.65 % Allowed : 11.83 % Favored : 85.52 % 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: 0.37 (0.22), residues: 1421 helix: 2.57 (0.27), residues: 343 sheet: 0.05 (0.25), residues: 412 loop : -0.86 (0.23), residues: 666 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 0.017 0.002 PHE L 30 TYR 0.023 0.002 TYR B 103 ARG 0.005 0.000 ARG H 35 ********************** 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 fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7481 (mp0) cc_final: 0.7233 (mp0) REVERT: A 248 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7396 (mm) REVERT: B 10 LYS cc_start: 0.8265 (tttt) cc_final: 0.7976 (tptp) REVERT: B 138 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: E 98 GLU cc_start: 0.7766 (tp30) cc_final: 0.7511 (tp30) REVERT: P 3 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: e 99 ASN cc_start: 0.7345 (m-40) cc_final: 0.6570 (p0) outliers start: 33 outliers final: 26 residues processed: 160 average time/residue: 0.2656 time to fit residues: 60.5910 Evaluate side-chains 169 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 82 CYS 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 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 L residue 68 THR Chi-restraints excluded: chain P residue 1 TYR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain e residue 35 ILE 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: 0.8980 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.181227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147292 restraints weight = 12443.018| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.54 r_work: 0.3217 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11778 Z= 0.261 Angle : 0.488 9.390 15989 Z= 0.256 Chirality : 0.041 0.178 1774 Planarity : 0.004 0.035 2045 Dihedral : 4.948 56.756 1701 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.33 % Allowed : 12.47 % Favored : 85.20 % 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: 0.50 (0.22), residues: 1421 helix: 2.75 (0.26), residues: 344 sheet: 0.03 (0.25), residues: 423 loop : -0.77 (0.23), residues: 654 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 0.013 0.001 PHE L 30 TYR 0.016 0.001 TYR B 100 ARG 0.004 0.000 ARG H 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.35 seconds wall clock time: 49 minutes 37.77 seconds (2977.77 seconds total)