Starting phenix.real_space_refine on Wed Feb 4 22:44:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq2_48511/02_2026/9mq2_48511.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 73 5.16 5 C 8384 2.51 5 N 2259 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13312 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2507 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2507 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2507 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "H" Number of atoms: 956 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Conformer: "B" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} bond proxies already assigned to first conformer: 969 Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 851 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "a" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1260 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "b" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1196 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "c" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1260 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "C" 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: "a" 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER H 82A" occ=0.39 ... (10 atoms not shown) pdb=" OG BSER H 82A" occ=0.61 Time building chain proxies: 3.22, per 1000 atoms: 0.24 Number of scatterers: 13312 At special positions: 0 Unit cell: (89.75, 117.752, 162.986, 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 73 16.00 O 2596 8.00 N 2259 7.00 C 8384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.04 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 289 " " NAG B 401 " - " ASN B 289 " " NAG B 402 " - " ASN B 21 " " NAG B 403 " - " ASN B 33 " " NAG C 401 " - " ASN C 289 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 33 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN B 169 " " NAG F 1 " - " ASN C 169 " " NAG a 301 " - " ASN a 154 " " NAG c 301 " - " ASN c 154 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 409.0 milliseconds 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 40 sheets defined 22.5% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 4.107A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 80' Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.568A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.895A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 80' Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.536A pdb=" N TRP B 127 " --> pdb=" O LYS B 125A" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'a' and resid 37 through 59 Processing helix chain 'a' and resid 74 through 127 removed outlier: 3.765A pdb=" N LEU a 101 " --> pdb=" O GLU a 97 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG a 106 " --> pdb=" O MET a 102 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU a 118 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL a 122 " --> pdb=" O LEU a 118 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN a 125 " --> pdb=" O LYS a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 155 removed outlier: 4.235A pdb=" N SER a 151 " --> pdb=" O GLU a 147 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL a 152 " --> pdb=" O CYS a 148 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG a 153 " --> pdb=" O MET a 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 59 removed outlier: 3.618A pdb=" N THR b 41 " --> pdb=" O ASP b 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET b 59 " --> pdb=" O ILE b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 120 removed outlier: 4.312A pdb=" N ASN b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU b 105 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS b 111 " --> pdb=" O THR b 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL b 115 " --> pdb=" O HIS b 111 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU b 118 " --> pdb=" O ASN b 114 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR b 119 " --> pdb=" O VAL b 115 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 125 Processing helix chain 'b' and resid 145 through 155 removed outlier: 3.917A pdb=" N MET b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 37 through 59 removed outlier: 3.687A pdb=" N MET c 59 " --> pdb=" O ILE c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 103 removed outlier: 3.608A pdb=" N LEU c 101 " --> pdb=" O GLU c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 127 removed outlier: 3.729A pdb=" N TYR c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL c 122 " --> pdb=" O LEU c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 155 removed outlier: 4.051A pdb=" N VAL c 152 " --> pdb=" O CYS c 148 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG c 153 " --> pdb=" O MET c 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 3.587A pdb=" N GLY a 33 " --> pdb=" O HIS a 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.796A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.502A pdb=" N HIS A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.062A pdb=" N LEU A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.509A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.427A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS A 117 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS A 262A" --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 115 " --> pdb=" O LYS A 262A" (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.427A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.472A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.543A pdb=" N CYS B 14 " --> pdb=" O HIS b 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.404A pdb=" N LEU B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 61 removed outlier: 6.513A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 4.248A pdb=" N ASP B 175 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS B 117 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 8.075A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.439A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AC4, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.471A pdb=" N LEU C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AC9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.398A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS C 117 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS C 262A" --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 115 " --> pdb=" O LYS C 262A" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.398A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.592A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.670A pdb=" N LEU C 209 " --> pdb=" O THR C 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.909A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.880A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.880A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.522A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 130 through 132 removed outlier: 3.574A pdb=" N GLU a 139 " --> pdb=" O LYS a 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 26 through 27 removed outlier: 3.724A pdb=" N GLY c 33 " --> pdb=" O HIS c 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 130 through 132 498 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 3262 1.46 - 1.59: 5980 1.59 - 1.71: 1 1.71 - 1.83: 106 Bond restraints: 13618 Sorted by residual: bond pdb=" N ASN C 169 " pdb=" CA ASN C 169 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" CA ILE B 13 " pdb=" CB ILE B 13 " ideal model delta sigma weight residual 1.540 1.596 -0.056 2.70e-02 1.37e+03 4.31e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" CB ILE B 13 " pdb=" CG2 ILE B 13 " ideal model delta sigma weight residual 1.521 1.573 -0.052 3.30e-02 9.18e+02 2.48e+00 ... (remaining 13613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17360 1.58 - 3.17: 910 3.17 - 4.75: 136 4.75 - 6.33: 59 6.33 - 7.92: 4 Bond angle restraints: 18469 Sorted by residual: angle pdb=" N HIS b 25 " pdb=" CA HIS b 25 " pdb=" C HIS b 25 " ideal model delta sigma weight residual 109.50 103.57 5.93 1.58e+00 4.01e-01 1.41e+01 angle pdb=" CA TYR b 141 " pdb=" CB TYR b 141 " pdb=" CG TYR b 141 " ideal model delta sigma weight residual 113.90 119.26 -5.36 1.80e+00 3.09e-01 8.85e+00 angle pdb=" N ARG c 106 " pdb=" CA ARG c 106 " pdb=" C ARG c 106 " ideal model delta sigma weight residual 112.89 109.24 3.65 1.24e+00 6.50e-01 8.69e+00 angle pdb=" N VAL b 115 " pdb=" CA VAL b 115 " pdb=" C VAL b 115 " ideal model delta sigma weight residual 113.39 109.24 4.15 1.47e+00 4.63e-01 7.98e+00 angle pdb=" CB ILE a 55 " pdb=" CG1 ILE a 55 " pdb=" CD1 ILE a 55 " ideal model delta sigma weight residual 113.80 119.61 -5.81 2.10e+00 2.27e-01 7.66e+00 ... (remaining 18464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 7711 16.58 - 33.15: 557 33.15 - 49.73: 96 49.73 - 66.31: 17 66.31 - 82.88: 6 Dihedral angle restraints: 8387 sinusoidal: 3637 harmonic: 4750 Sorted by residual: dihedral pdb=" CB CYS a 144 " pdb=" SG CYS a 144 " pdb=" SG CYS a 148 " pdb=" CB CYS a 148 " ideal model delta sinusoidal sigma weight residual 93.00 37.43 55.57 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS b 144 " pdb=" SG CYS b 144 " pdb=" SG CYS b 148 " pdb=" CB CYS b 148 " ideal model delta sinusoidal sigma weight residual -86.00 -131.17 45.17 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CA VAL H 67 " pdb=" C VAL H 67 " pdb=" N THR H 68 " pdb=" CA THR H 68 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1801 0.076 - 0.151: 241 0.151 - 0.227: 11 0.227 - 0.302: 0 0.302 - 0.378: 1 Chirality restraints: 2054 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.35e+01 chirality pdb=" C1 FUC F 3 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 3 " pdb=" O5 FUC F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.43e+00 chirality pdb=" C1 NAG a 301 " pdb=" ND2 ASN a 154 " pdb=" C2 NAG a 301 " pdb=" O5 NAG a 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 2051 not shown) Planarity restraints: 2383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.295 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG F 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.053 2.00e-02 2.50e+03 4.37e-02 2.39e+01 pdb=" C7 NAG F 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.068 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU b 108 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU b 108 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU b 108 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP b 109 " -0.022 2.00e-02 2.50e+03 ... (remaining 2380 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 229 2.66 - 3.22: 12216 3.22 - 3.78: 20087 3.78 - 4.34: 29241 4.34 - 4.90: 48229 Nonbonded interactions: 110002 Sorted by model distance: nonbonded pdb=" O GLU b 103 " pdb=" OG1 THR b 107 " model vdw 2.103 3.040 nonbonded pdb=" OG SER b 113 " pdb=" O LEU c 2 " model vdw 2.114 3.040 nonbonded pdb=" O GLU a 103 " pdb=" OG1 THR a 107 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASN C 150 " pdb=" OH TYR C 258 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 185 " pdb=" OE1 GLN A 191 " model vdw 2.217 3.040 ... (remaining 109997 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'a' and resid 11 through 157) selection = chain 'b' selection = (chain 'c' and resid 11 through 157) } 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=0.39 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: 11.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.280 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.005 0.056 13654 Z= 0.214 Angle : 0.840 11.069 18561 Z= 0.437 Chirality : 0.051 0.378 2054 Planarity : 0.008 0.250 2369 Dihedral : 11.731 82.882 5301 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.19), residues: 1627 helix: -0.60 (0.28), residues: 335 sheet: -1.00 (0.30), residues: 300 loop : -1.64 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 149 TYR 0.039 0.002 TYR b 22 PHE 0.023 0.002 PHE A 118 TRP 0.017 0.001 TRP H 47 HIS 0.012 0.001 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00508 (13618) covalent geometry : angle 0.83044 (18469) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.43842 ( 32) hydrogen bonds : bond 0.15249 ( 455) hydrogen bonds : angle 8.37152 ( 1365) link_BETA1-4 : bond 0.00299 ( 3) link_BETA1-4 : angle 0.89868 ( 9) link_BETA1-6 : bond 0.00385 ( 3) link_BETA1-6 : angle 1.33544 ( 9) link_NAG-ASN : bond 0.00607 ( 14) link_NAG-ASN : angle 2.55919 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8339 (ptpp) cc_final: 0.8094 (ttpp) REVERT: B 75 MET cc_start: 0.7617 (mmm) cc_final: 0.7131 (mpp) REVERT: B 196 LYS cc_start: 0.8221 (tptt) cc_final: 0.7994 (tptp) REVERT: B 268 MET cc_start: 0.8365 (ttm) cc_final: 0.8163 (ttm) REVERT: C 27 ASP cc_start: 0.8234 (p0) cc_final: 0.7917 (p0) REVERT: C 141 TYR cc_start: 0.7706 (t80) cc_final: 0.7336 (t80) REVERT: C 186 ASN cc_start: 0.7914 (m-40) cc_final: 0.7343 (t0) REVERT: C 192 THR cc_start: 0.8249 (m) cc_final: 0.7921 (p) REVERT: C 227 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7742 (mtm110) REVERT: L 24 ARG cc_start: 0.7121 (mtm110) cc_final: 0.6906 (ttm110) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1271 time to fit residues: 59.9212 Evaluate side-chains 226 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 94 ASN C 150 ASN C 226 GLN C 250 ASN L 38 GLN b 25 HIS b 72 ASN b 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143130 restraints weight = 39172.830| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.83 r_work: 0.3464 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13654 Z= 0.123 Angle : 0.606 9.872 18561 Z= 0.316 Chirality : 0.046 0.368 2054 Planarity : 0.005 0.072 2369 Dihedral : 5.655 53.882 2180 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.66 % Allowed : 7.69 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1627 helix: 0.19 (0.29), residues: 339 sheet: -0.76 (0.30), residues: 319 loop : -1.47 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 227 TYR 0.018 0.001 TYR b 22 PHE 0.025 0.002 PHE H 78 TRP 0.011 0.001 TRP H 103 HIS 0.006 0.001 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00271 (13618) covalent geometry : angle 0.59005 (18469) SS BOND : bond 0.00386 ( 16) SS BOND : angle 1.46672 ( 32) hydrogen bonds : bond 0.04059 ( 455) hydrogen bonds : angle 6.00975 ( 1365) link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.30885 ( 9) link_BETA1-6 : bond 0.00401 ( 3) link_BETA1-6 : angle 1.65288 ( 9) link_NAG-ASN : bond 0.00442 ( 14) link_NAG-ASN : angle 2.53406 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7842 (mmm) cc_final: 0.7090 (mmt) REVERT: B 75 MET cc_start: 0.7930 (mmm) cc_final: 0.7376 (mpp) REVERT: B 196 LYS cc_start: 0.8224 (tptt) cc_final: 0.7886 (tptp) REVERT: C 17 TYR cc_start: 0.7351 (p90) cc_final: 0.7031 (p90) REVERT: C 27 ASP cc_start: 0.8245 (p0) cc_final: 0.7898 (p0) REVERT: C 75 MET cc_start: 0.7861 (mmm) cc_final: 0.6857 (mtm) REVERT: C 186 ASN cc_start: 0.7836 (m-40) cc_final: 0.7389 (t0) REVERT: L 61 ARG cc_start: 0.7452 (ptp-170) cc_final: 0.7072 (ptt-90) REVERT: a 29 GLU cc_start: 0.6062 (mp0) cc_final: 0.5857 (mp0) REVERT: a 147 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7224 (mp0) REVERT: c 24 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.5981 (t80) outliers start: 24 outliers final: 15 residues processed: 260 average time/residue: 0.1223 time to fit residues: 43.6007 Evaluate side-chains 215 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 142 HIS Chi-restraints excluded: chain c residue 24 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN C 295 HIS b 53 ASN b 117 ASN c 25 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140531 restraints weight = 30606.192| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.29 r_work: 0.3451 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13654 Z= 0.134 Angle : 0.568 9.762 18561 Z= 0.295 Chirality : 0.045 0.371 2054 Planarity : 0.004 0.065 2369 Dihedral : 5.637 57.052 2180 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 8.94 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1627 helix: 0.49 (0.29), residues: 343 sheet: -0.53 (0.30), residues: 309 loop : -1.38 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.018 0.001 TYR b 22 PHE 0.023 0.002 PHE H 78 TRP 0.011 0.001 TRP H 103 HIS 0.008 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00306 (13618) covalent geometry : angle 0.55386 (18469) SS BOND : bond 0.00356 ( 16) SS BOND : angle 1.15167 ( 32) hydrogen bonds : bond 0.03745 ( 455) hydrogen bonds : angle 5.60358 ( 1365) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.20822 ( 9) link_BETA1-6 : bond 0.00570 ( 3) link_BETA1-6 : angle 1.49206 ( 9) link_NAG-ASN : bond 0.00498 ( 14) link_NAG-ASN : angle 2.46264 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.352 Fit side-chains REVERT: B 75 MET cc_start: 0.7853 (mmm) cc_final: 0.7323 (mpp) REVERT: B 196 LYS cc_start: 0.8228 (tptt) cc_final: 0.7969 (tptp) REVERT: C 17 TYR cc_start: 0.7540 (p90) cc_final: 0.7328 (p90) REVERT: C 27 ASP cc_start: 0.8107 (p0) cc_final: 0.7801 (p0) REVERT: C 227 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7713 (mtm110) REVERT: C 280 LYS cc_start: 0.7913 (ptpp) cc_final: 0.7335 (mtmt) REVERT: L 61 ARG cc_start: 0.7571 (ptp-170) cc_final: 0.7201 (ptt-90) REVERT: a 29 GLU cc_start: 0.6129 (mp0) cc_final: 0.5899 (mp0) REVERT: a 147 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7206 (mp0) REVERT: c 24 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.5846 (t80) outliers start: 28 outliers final: 20 residues processed: 233 average time/residue: 0.1369 time to fit residues: 43.5231 Evaluate side-chains 221 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain c residue 24 TYR Chi-restraints excluded: chain c residue 25 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN b 25 HIS ** b 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136974 restraints weight = 24151.819| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.10 r_work: 0.3437 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13654 Z= 0.174 Angle : 0.587 9.656 18561 Z= 0.306 Chirality : 0.046 0.376 2054 Planarity : 0.004 0.063 2369 Dihedral : 5.762 59.301 2180 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 10.12 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1627 helix: 0.72 (0.29), residues: 335 sheet: -0.60 (0.30), residues: 319 loop : -1.38 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 227 TYR 0.037 0.002 TYR H 50 PHE 0.023 0.002 PHE H 78 TRP 0.018 0.001 TRP c 14 HIS 0.017 0.002 HIS c 25 Details of bonding type rmsd covalent geometry : bond 0.00406 (13618) covalent geometry : angle 0.57210 (18469) SS BOND : bond 0.00447 ( 16) SS BOND : angle 1.31318 ( 32) hydrogen bonds : bond 0.03736 ( 455) hydrogen bonds : angle 5.56804 ( 1365) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.40028 ( 9) link_BETA1-6 : bond 0.00429 ( 3) link_BETA1-6 : angle 1.41585 ( 9) link_NAG-ASN : bond 0.00507 ( 14) link_NAG-ASN : angle 2.52074 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.340 Fit side-chains REVERT: B 75 MET cc_start: 0.8081 (mmm) cc_final: 0.7451 (mpp) REVERT: B 196 LYS cc_start: 0.8310 (tptt) cc_final: 0.8036 (tptp) REVERT: C 27 ASP cc_start: 0.8289 (p0) cc_final: 0.7986 (p0) REVERT: C 175 ASP cc_start: 0.8510 (m-30) cc_final: 0.8283 (m-30) REVERT: C 227 ARG cc_start: 0.8647 (mtt90) cc_final: 0.7900 (mtm110) REVERT: C 280 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7488 (mtpt) REVERT: L 61 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.7278 (ptt-90) REVERT: a 29 GLU cc_start: 0.6222 (mp0) cc_final: 0.5973 (mp0) REVERT: c 24 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6297 (t80) REVERT: c 75 ARG cc_start: 0.8703 (mmt180) cc_final: 0.8488 (mmt180) outliers start: 32 outliers final: 26 residues processed: 233 average time/residue: 0.1322 time to fit residues: 42.3660 Evaluate side-chains 225 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 142 HIS Chi-restraints excluded: chain c residue 24 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 312 ASN B 18 HIS B 186 ASN C 38 HIS C 183 HIS b 135 ASN c 25 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132127 restraints weight = 29182.474| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.36 r_work: 0.3369 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13654 Z= 0.205 Angle : 0.624 9.791 18561 Z= 0.325 Chirality : 0.048 0.378 2054 Planarity : 0.004 0.060 2369 Dihedral : 5.957 59.868 2180 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.98 % Allowed : 11.23 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1627 helix: 0.66 (0.28), residues: 335 sheet: -0.41 (0.31), residues: 288 loop : -1.42 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 149 TYR 0.023 0.002 TYR H 50 PHE 0.023 0.002 PHE H 78 TRP 0.016 0.001 TRP H 103 HIS 0.010 0.002 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00483 (13618) covalent geometry : angle 0.60949 (18469) SS BOND : bond 0.00562 ( 16) SS BOND : angle 1.29429 ( 32) hydrogen bonds : bond 0.03861 ( 455) hydrogen bonds : angle 5.69627 ( 1365) link_BETA1-4 : bond 0.00216 ( 3) link_BETA1-4 : angle 1.59928 ( 9) link_BETA1-6 : bond 0.00455 ( 3) link_BETA1-6 : angle 1.47313 ( 9) link_NAG-ASN : bond 0.00523 ( 14) link_NAG-ASN : angle 2.58672 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8163 (mmm) cc_final: 0.7479 (mpp) REVERT: B 196 LYS cc_start: 0.8342 (tptt) cc_final: 0.8035 (tptp) REVERT: C 27 ASP cc_start: 0.8311 (p0) cc_final: 0.8016 (p0) REVERT: C 175 ASP cc_start: 0.8640 (m-30) cc_final: 0.8434 (m-30) REVERT: C 227 ARG cc_start: 0.8755 (mtt90) cc_final: 0.7934 (mtm110) REVERT: C 280 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7520 (mtpt) REVERT: L 61 ARG cc_start: 0.7541 (ptp-170) cc_final: 0.7237 (ptt-90) REVERT: a 29 GLU cc_start: 0.6266 (mp0) cc_final: 0.5982 (mp0) REVERT: b 82 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7930 (tttp) REVERT: c 75 ARG cc_start: 0.8726 (mmt180) cc_final: 0.8510 (mmt180) outliers start: 43 outliers final: 33 residues processed: 233 average time/residue: 0.1376 time to fit residues: 44.5929 Evaluate side-chains 228 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 142 HIS Chi-restraints excluded: chain c residue 25 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 110 HIS A 312 ASN B 150 ASN L 27 GLN b 129 ASN c 25 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.157086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136315 restraints weight = 24309.221| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.03 r_work: 0.3428 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13654 Z= 0.125 Angle : 0.572 9.547 18561 Z= 0.294 Chirality : 0.045 0.364 2054 Planarity : 0.004 0.056 2369 Dihedral : 5.956 58.882 2180 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.70 % Allowed : 12.34 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1627 helix: 1.03 (0.29), residues: 335 sheet: -0.31 (0.32), residues: 288 loop : -1.36 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.019 0.001 TYR H 50 PHE 0.019 0.001 PHE H 78 TRP 0.011 0.001 TRP H 103 HIS 0.014 0.001 HIS c 25 Details of bonding type rmsd covalent geometry : bond 0.00289 (13618) covalent geometry : angle 0.54605 (18469) SS BOND : bond 0.00390 ( 16) SS BOND : angle 1.95919 ( 32) hydrogen bonds : bond 0.03533 ( 455) hydrogen bonds : angle 5.50441 ( 1365) link_BETA1-4 : bond 0.00322 ( 3) link_BETA1-4 : angle 1.42562 ( 9) link_BETA1-6 : bond 0.00501 ( 3) link_BETA1-6 : angle 1.42608 ( 9) link_NAG-ASN : bond 0.00492 ( 14) link_NAG-ASN : angle 3.09814 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8070 (tptp) cc_final: 0.7752 (tppt) REVERT: B 75 MET cc_start: 0.8090 (mmm) cc_final: 0.7496 (mpp) REVERT: C 27 ASP cc_start: 0.8273 (p0) cc_final: 0.7977 (p0) REVERT: C 75 MET cc_start: 0.8098 (mmm) cc_final: 0.6963 (mpp) REVERT: C 175 ASP cc_start: 0.8516 (m-30) cc_final: 0.8304 (m-30) REVERT: C 227 ARG cc_start: 0.8662 (mtt90) cc_final: 0.7898 (mtm110) REVERT: C 280 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7431 (mtmt) REVERT: L 61 ARG cc_start: 0.7646 (ptp-170) cc_final: 0.7420 (ptt-90) REVERT: a 29 GLU cc_start: 0.6259 (mp0) cc_final: 0.6023 (mp0) REVERT: b 149 MET cc_start: 0.6551 (mmt) cc_final: 0.6147 (mmt) REVERT: c 24 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.5565 (t80) outliers start: 39 outliers final: 33 residues processed: 228 average time/residue: 0.1322 time to fit residues: 42.0089 Evaluate side-chains 230 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 24 TYR Chi-restraints excluded: chain c residue 25 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 12 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 110 HIS b 72 ASN c 25 HIS c 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135912 restraints weight = 23982.180| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.08 r_work: 0.3426 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13654 Z= 0.137 Angle : 0.577 10.103 18561 Z= 0.299 Chirality : 0.045 0.359 2054 Planarity : 0.004 0.052 2369 Dihedral : 6.004 58.509 2180 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1627 helix: 1.17 (0.29), residues: 335 sheet: -0.11 (0.32), residues: 278 loop : -1.35 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 149 TYR 0.018 0.001 TYR H 50 PHE 0.019 0.001 PHE H 78 TRP 0.012 0.001 TRP H 103 HIS 0.011 0.001 HIS c 25 Details of bonding type rmsd covalent geometry : bond 0.00317 (13618) covalent geometry : angle 0.55416 (18469) SS BOND : bond 0.00382 ( 16) SS BOND : angle 2.27284 ( 32) hydrogen bonds : bond 0.03507 ( 455) hydrogen bonds : angle 5.37186 ( 1365) link_BETA1-4 : bond 0.00288 ( 3) link_BETA1-4 : angle 1.43677 ( 9) link_BETA1-6 : bond 0.00527 ( 3) link_BETA1-6 : angle 1.39990 ( 9) link_NAG-ASN : bond 0.00504 ( 14) link_NAG-ASN : angle 2.67743 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8075 (tptp) cc_final: 0.7732 (tppt) REVERT: B 75 MET cc_start: 0.8085 (mmm) cc_final: 0.7476 (mpp) REVERT: C 27 ASP cc_start: 0.8289 (p0) cc_final: 0.7981 (p0) REVERT: C 75 MET cc_start: 0.8161 (mmm) cc_final: 0.6935 (mpp) REVERT: C 280 LYS cc_start: 0.7993 (ptpp) cc_final: 0.7444 (mtpt) REVERT: a 29 GLU cc_start: 0.6252 (mp0) cc_final: 0.6012 (mp0) REVERT: c 24 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5145 (t80) REVERT: c 59 MET cc_start: 0.7876 (mtt) cc_final: 0.7634 (mtt) REVERT: c 75 ARG cc_start: 0.8694 (mmt180) cc_final: 0.8480 (mmt180) outliers start: 39 outliers final: 31 residues processed: 225 average time/residue: 0.1297 time to fit residues: 40.5309 Evaluate side-chains 220 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 24 TYR Chi-restraints excluded: chain c residue 25 HIS Chi-restraints excluded: chain c residue 127 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 112 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 312 ASN b 72 ASN c 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134447 restraints weight = 30542.283| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.35 r_work: 0.3400 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13654 Z= 0.152 Angle : 0.574 9.438 18561 Z= 0.298 Chirality : 0.045 0.360 2054 Planarity : 0.004 0.052 2369 Dihedral : 5.984 58.773 2180 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.77 % Allowed : 13.65 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1627 helix: 1.18 (0.29), residues: 335 sheet: -0.10 (0.32), residues: 278 loop : -1.34 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 149 TYR 0.018 0.001 TYR H 50 PHE 0.019 0.001 PHE H 78 TRP 0.012 0.001 TRP H 103 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00356 (13618) covalent geometry : angle 0.55427 (18469) SS BOND : bond 0.00399 ( 16) SS BOND : angle 1.97254 ( 32) hydrogen bonds : bond 0.03528 ( 455) hydrogen bonds : angle 5.36992 ( 1365) link_BETA1-4 : bond 0.00261 ( 3) link_BETA1-4 : angle 1.45001 ( 9) link_BETA1-6 : bond 0.00462 ( 3) link_BETA1-6 : angle 1.36925 ( 9) link_NAG-ASN : bond 0.00489 ( 14) link_NAG-ASN : angle 2.56196 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.8114 (mmm) cc_final: 0.7076 (mmt) REVERT: B 75 MET cc_start: 0.8150 (mmm) cc_final: 0.7529 (mpp) REVERT: C 27 ASP cc_start: 0.8303 (p0) cc_final: 0.8014 (p0) REVERT: C 280 LYS cc_start: 0.8026 (ptpp) cc_final: 0.7442 (mtpt) REVERT: a 29 GLU cc_start: 0.6270 (mp0) cc_final: 0.6026 (mp0) REVERT: b 102 MET cc_start: 0.8028 (mtm) cc_final: 0.7799 (mtt) REVERT: c 75 ARG cc_start: 0.8722 (mmt180) cc_final: 0.8514 (mmt180) outliers start: 40 outliers final: 37 residues processed: 217 average time/residue: 0.1249 time to fit residues: 37.5551 Evaluate side-chains 224 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 25 HIS Chi-restraints excluded: chain c residue 127 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 312 ASN C 250 ASN a 125 GLN b 72 ASN c 25 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132610 restraints weight = 30472.397| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.46 r_work: 0.3379 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13654 Z= 0.210 Angle : 0.621 9.561 18561 Z= 0.322 Chirality : 0.047 0.368 2054 Planarity : 0.004 0.054 2369 Dihedral : 6.091 59.869 2180 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.05 % Allowed : 14.00 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1627 helix: 0.95 (0.29), residues: 337 sheet: -0.12 (0.32), residues: 278 loop : -1.39 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 227 TYR 0.019 0.002 TYR H 50 PHE 0.020 0.002 PHE H 78 TRP 0.015 0.001 TRP H 103 HIS 0.017 0.002 HIS c 25 Details of bonding type rmsd covalent geometry : bond 0.00500 (13618) covalent geometry : angle 0.60290 (18469) SS BOND : bond 0.00508 ( 16) SS BOND : angle 2.03180 ( 32) hydrogen bonds : bond 0.03718 ( 455) hydrogen bonds : angle 5.49115 ( 1365) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.56445 ( 9) link_BETA1-6 : bond 0.00453 ( 3) link_BETA1-6 : angle 1.42550 ( 9) link_NAG-ASN : bond 0.00505 ( 14) link_NAG-ASN : angle 2.57843 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.8088 (mmm) cc_final: 0.6958 (mmt) REVERT: A 196 LYS cc_start: 0.8091 (tptp) cc_final: 0.7851 (tppt) REVERT: A 266 THR cc_start: 0.9273 (t) cc_final: 0.8998 (p) REVERT: B 75 MET cc_start: 0.8155 (mmm) cc_final: 0.7441 (mpp) REVERT: C 27 ASP cc_start: 0.8268 (p0) cc_final: 0.7976 (p0) REVERT: C 75 MET cc_start: 0.8032 (mmm) cc_final: 0.6855 (mpp) REVERT: C 280 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7592 (mtmm) REVERT: a 147 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7247 (mp0) REVERT: b 102 MET cc_start: 0.8111 (mtm) cc_final: 0.7887 (mtt) REVERT: b 132 GLU cc_start: 0.7199 (mp0) cc_final: 0.6906 (mp0) outliers start: 44 outliers final: 41 residues processed: 214 average time/residue: 0.1254 time to fit residues: 37.3600 Evaluate side-chains 224 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 24 TYR Chi-restraints excluded: chain c residue 127 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 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 92 ASN A 276 HIS A 312 ASN b 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135293 restraints weight = 30360.017| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.46 r_work: 0.3412 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13654 Z= 0.131 Angle : 0.567 9.512 18561 Z= 0.295 Chirality : 0.045 0.360 2054 Planarity : 0.004 0.055 2369 Dihedral : 5.851 58.794 2180 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.70 % Allowed : 14.35 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1627 helix: 1.16 (0.29), residues: 336 sheet: -0.19 (0.32), residues: 288 loop : -1.34 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 149 TYR 0.019 0.001 TYR C 86 PHE 0.018 0.001 PHE H 78 TRP 0.011 0.001 TRP H 103 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00305 (13618) covalent geometry : angle 0.55012 (18469) SS BOND : bond 0.00420 ( 16) SS BOND : angle 1.70734 ( 32) hydrogen bonds : bond 0.03490 ( 455) hydrogen bonds : angle 5.36095 ( 1365) link_BETA1-4 : bond 0.00392 ( 3) link_BETA1-4 : angle 1.43190 ( 9) link_BETA1-6 : bond 0.00382 ( 3) link_BETA1-6 : angle 1.33558 ( 9) link_NAG-ASN : bond 0.00475 ( 14) link_NAG-ASN : angle 2.46208 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8039 (tptp) cc_final: 0.7810 (tppt) REVERT: A 266 THR cc_start: 0.9261 (t) cc_final: 0.9003 (p) REVERT: B 75 MET cc_start: 0.8106 (mmm) cc_final: 0.7428 (mpp) REVERT: C 27 ASP cc_start: 0.8271 (p0) cc_final: 0.7969 (p0) REVERT: C 75 MET cc_start: 0.8030 (mmm) cc_final: 0.6845 (mpp) REVERT: C 280 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7560 (mtmm) REVERT: b 102 MET cc_start: 0.8045 (mtm) cc_final: 0.7832 (mtt) REVERT: b 132 GLU cc_start: 0.7102 (mp0) cc_final: 0.6830 (mp0) REVERT: c 106 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7545 (mmm-85) outliers start: 39 outliers final: 36 residues processed: 213 average time/residue: 0.1236 time to fit residues: 36.8902 Evaluate side-chains 220 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 22 TYR Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 127 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 276 HIS A 312 ASN b 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131815 restraints weight = 31011.861| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.46 r_work: 0.3369 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13654 Z= 0.209 Angle : 0.626 9.669 18561 Z= 0.325 Chirality : 0.047 0.373 2054 Planarity : 0.004 0.054 2369 Dihedral : 6.031 59.644 2180 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.84 % Allowed : 14.14 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1627 helix: 0.95 (0.29), residues: 336 sheet: -0.15 (0.32), residues: 278 loop : -1.42 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.020 0.002 TYR H 50 PHE 0.020 0.002 PHE H 78 TRP 0.015 0.002 TRP H 103 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00498 (13618) covalent geometry : angle 0.60784 (18469) SS BOND : bond 0.00557 ( 16) SS BOND : angle 2.07548 ( 32) hydrogen bonds : bond 0.03741 ( 455) hydrogen bonds : angle 5.54966 ( 1365) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.60882 ( 9) link_BETA1-6 : bond 0.00428 ( 3) link_BETA1-6 : angle 1.40087 ( 9) link_NAG-ASN : bond 0.00508 ( 14) link_NAG-ASN : angle 2.55896 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.39 seconds wall clock time: 66 minutes 20.04 seconds (3980.04 seconds total)