Starting phenix.real_space_refine on Sat Aug 23 07:56:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3e_45166/08_2025/9c3e_45166.cif" } resolution = 3.5 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= 0.030 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 60 5.16 5 C 6799 2.51 5 N 1768 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10619 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1931 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 239} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2187 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 853 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 859 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 830 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 218 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 199 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2531 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 308} Chain breaks: 7 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 112 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.25 Number of scatterers: 10619 At special positions: 0 Unit cell: (89.64, 128.52, 168.48, 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 60 16.00 O 1992 8.00 N 1768 7.00 C 6799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS Y 32 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS H 425 " - pdb=" SG CYS H 488 " distance=2.06 Simple disulfide: pdb=" SG CYS H 527 " - pdb=" SG CYS H 583 " distance=2.05 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 N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 301 " - " ASN A 41 " " NAG A 302 " - " ASN A 82 " " NAG A 303 " - " ASN A 166 " " NAG A 304 " - " ASN A 200 " " NAG A 305 " - " ASN A 211 " " NAG B 601 " - " ASN B 84 " " NAG D 201 " - " ASN D 74 " " NAG G 201 " - " ASN G 52 " " NAG N 1 " - " ASN D 38 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 393.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 23 sheets defined 24.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.504A pdb=" N SER A 104 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.881A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 271 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.577A pdb=" N THR B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.554A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 266 through 294 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 100 through 125 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 126 through 150 removed outlier: 3.645A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 153 removed outlier: 3.763A pdb=" N LEU F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 137 Processing helix chain 'X' and resid 24 through 28 removed outlier: 3.704A pdb=" N ASP X 28 " --> pdb=" O GLY X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 46 removed outlier: 3.741A pdb=" N TYR X 33 " --> pdb=" O PRO X 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP X 36 " --> pdb=" O CYS X 32 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE X 38 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU X 39 " --> pdb=" O LEU X 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU X 46 " --> pdb=" O TYR X 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 53 Processing helix chain 'H' and resid 380 through 409 removed outlier: 3.554A pdb=" N TRP H 384 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY H 403 " --> pdb=" O ARG H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 475 Processing helix chain 'H' and resid 475 through 486 removed outlier: 4.400A pdb=" N GLN H 479 " --> pdb=" O HIS H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 499 Processing helix chain 'H' and resid 499 through 504 removed outlier: 3.996A pdb=" N GLN H 504 " --> pdb=" O LYS H 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.522A pdb=" N ASN A 41 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.492A pdb=" N LEU A 30 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS A 132 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 32 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP A 54 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.492A pdb=" N LEU A 30 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS A 132 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 32 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 111 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 145 removed outlier: 4.678A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 145 removed outlier: 4.678A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 33 removed outlier: 3.848A pdb=" N VAL B 107 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET B 51 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 67 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP B 53 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 33 Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 146 removed outlier: 5.981A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 146 removed outlier: 5.981A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 26 through 27 removed outlier: 5.775A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 41 through 46 removed outlier: 4.492A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 66 removed outlier: 3.950A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL F 97 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG F 115 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY G 63 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS G 57 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N MET G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 32 through 34 removed outlier: 5.421A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.781A pdb=" N TYR H 187 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU H 170 " --> pdb=" O TYR H 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AC3, first strand: chain 'H' and resid 355 through 361 removed outlier: 6.903A pdb=" N GLY H 350 " --> pdb=" O PHE H 357 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG H 359 " --> pdb=" O ALA H 348 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA H 348 " --> pdb=" O ARG H 359 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP H 361 " --> pdb=" O PHE H 346 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE H 346 " --> pdb=" O ASP H 361 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR H 442 " --> pdb=" O ASP H 446 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP H 446 " --> pdb=" O TYR H 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 510 through 514 removed outlier: 5.622A pdb=" N PHE H 565 " --> pdb=" O SER H 531 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 538 through 542 529 hydrogen bonds defined for protein. 1392 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: 1.88 Time building geometry restraints manager: 1.22 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: 3353 1.34 - 1.46: 2678 1.46 - 1.58: 4751 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 10864 Sorted by residual: bond pdb=" N GLN H 504 " pdb=" CA GLN H 504 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.37e-02 5.33e+03 6.21e+00 bond pdb=" N LYS H 470 " pdb=" CA LYS H 470 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.17e+00 bond pdb=" N LEU H 503 " pdb=" CA LEU H 503 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.07e+00 bond pdb=" N GLU H 472 " pdb=" CA GLU H 472 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.16e-02 7.43e+03 5.77e+00 bond pdb=" N ARG H 505 " pdb=" CA ARG H 505 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.50e+00 ... (remaining 10859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 14736 4.97 - 9.93: 58 9.93 - 14.90: 3 14.90 - 19.87: 0 19.87 - 24.83: 1 Bond angle restraints: 14798 Sorted by residual: angle pdb=" CA CYS H 488 " pdb=" CB CYS H 488 " pdb=" SG CYS H 488 " ideal model delta sigma weight residual 114.40 139.23 -24.83 2.30e+00 1.89e-01 1.17e+02 angle pdb=" C ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 110.79 102.06 8.73 1.66e+00 3.63e-01 2.76e+01 angle pdb=" C SER E 55 " pdb=" CA SER E 55 " pdb=" CB SER E 55 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" C CYS H 488 " pdb=" CA CYS H 488 " pdb=" CB CYS H 488 " ideal model delta sigma weight residual 110.88 103.25 7.63 1.57e+00 4.06e-01 2.36e+01 angle pdb=" N CYS H 488 " pdb=" CA CYS H 488 " pdb=" CB CYS H 488 " ideal model delta sigma weight residual 110.01 117.00 -6.99 1.45e+00 4.76e-01 2.33e+01 ... (remaining 14793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5835 17.83 - 35.66: 626 35.66 - 53.49: 147 53.49 - 71.32: 35 71.32 - 89.14: 14 Dihedral angle restraints: 6657 sinusoidal: 2720 harmonic: 3937 Sorted by residual: dihedral pdb=" CA ASN A 200 " pdb=" C ASN A 200 " pdb=" N LYS A 201 " pdb=" CA LYS A 201 " ideal model delta harmonic sigma weight residual -180.00 -133.09 -46.91 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA LYS H 161 " pdb=" C LYS H 161 " pdb=" N ASN H 162 " pdb=" CA ASN H 162 " ideal model delta harmonic sigma weight residual 180.00 136.14 43.86 0 5.00e+00 4.00e-02 7.69e+01 dihedral pdb=" CB CYS G 104 " pdb=" SG CYS G 104 " pdb=" SG CYS G 107 " pdb=" CB CYS G 107 " ideal model delta sinusoidal sigma weight residual -86.00 -18.13 -67.87 1 1.00e+01 1.00e-02 5.98e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1567 0.086 - 0.173: 145 0.173 - 0.259: 2 0.259 - 0.345: 2 0.345 - 0.431: 1 Chirality restraints: 1717 Sorted by residual: chirality pdb=" C1 NAG A 303 " pdb=" ND2 ASN A 166 " pdb=" C2 NAG A 303 " pdb=" O5 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 200 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL F 134 " pdb=" CA VAL F 134 " pdb=" CG1 VAL F 134 " pdb=" CG2 VAL F 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1714 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 200 " 0.006 2.00e-02 2.50e+03 5.33e-02 3.56e+01 pdb=" CG ASN A 200 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 200 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN A 200 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG A 304 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 84 " -0.040 2.00e-02 2.50e+03 4.00e-02 2.00e+01 pdb=" CG ASN B 84 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 84 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 84 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG B 601 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 211 " -0.003 2.00e-02 2.50e+03 3.88e-02 1.88e+01 pdb=" CG ASN A 211 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 211 " 0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN A 211 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A 305 " 0.042 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 355 2.69 - 3.24: 10471 3.24 - 3.80: 16215 3.80 - 4.35: 19848 4.35 - 4.90: 33595 Nonbonded interactions: 80484 Sorted by model distance: nonbonded pdb=" N ASP A 58 " pdb=" OD1 ASP A 58 " model vdw 2.140 3.120 nonbonded pdb=" NH2 ARG A 80 " pdb=" OE1 GLN A 100 " model vdw 2.151 3.120 nonbonded pdb=" O CYS D 37 " pdb=" OG1 THR D 56 " model vdw 2.163 3.040 nonbonded pdb=" O SER D 95 " pdb=" OG SER D 95 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 37 " pdb=" O LEU B 98 " model vdw 2.182 3.040 ... (remaining 80479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 67 or resid 74 through 79 or (resid 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 84 or (resid 85 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 100 or resid 104 through 108 or (resid 109 and (name N or name CA or name C o \ r name O or name CB )) or resid 110 through 125 or (resid 126 and (name N or nam \ e CA or name C or name O or name CB )) or resid 127 through 151)) selection = (chain 'F' and (resid 33 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 85 or (resid 86 and ( \ name N or name CA or name C or name O or name CB )) or resid 87 through 105 or ( \ resid 106 through 109 and (name N or name CA or name C or name O or name CB )) o \ r resid 110 through 119 or (resid 120 and (name N or name CA or name C or name O \ or name CB )) or resid 121 through 149 or (resid 150 through 151 and (name N or \ name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 0.064 10892 Z= 0.232 Angle : 0.957 24.832 14865 Z= 0.475 Chirality : 0.050 0.431 1717 Planarity : 0.005 0.053 1852 Dihedral : 15.757 89.145 4072 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 1.92 % Allowed : 26.60 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -0.18 (0.23), residues: 1316 helix: 1.17 (0.31), residues: 276 sheet: 0.86 (0.25), residues: 398 loop : -1.39 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 345 TYR 0.035 0.002 TYR H 495 PHE 0.038 0.002 PHE G 135 TRP 0.022 0.002 TRP A 272 HIS 0.008 0.002 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00506 (10864) covalent geometry : angle 0.89221 (14798) SS BOND : bond 0.00978 ( 17) SS BOND : angle 2.74519 ( 34) hydrogen bonds : bond 0.13063 ( 493) hydrogen bonds : angle 6.26286 ( 1392) link_BETA1-4 : bond 0.00374 ( 2) link_BETA1-4 : angle 1.97558 ( 6) link_NAG-ASN : bond 0.00540 ( 9) link_NAG-ASN : angle 7.59714 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7325 (p0) REVERT: A 91 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8265 (ttm-80) REVERT: B 287 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7666 (tppp) REVERT: B 301 MET cc_start: 0.8949 (ppp) cc_final: 0.8562 (ppp) REVERT: D 92 MET cc_start: 0.9174 (mmm) cc_final: 0.8761 (mmt) REVERT: D 120 LEU cc_start: 0.9277 (tt) cc_final: 0.8875 (mt) REVERT: E 128 MET cc_start: 0.7850 (tpp) cc_final: 0.7573 (ttm) REVERT: F 125 MET cc_start: 0.8690 (ppp) cc_final: 0.8227 (ppp) REVERT: F 139 CYS cc_start: 0.9256 (t) cc_final: 0.8742 (m) REVERT: H 433 PHE cc_start: 0.8026 (t80) cc_final: 0.7753 (t80) outliers start: 21 outliers final: 12 residues processed: 184 average time/residue: 0.0972 time to fit residues: 25.4569 Evaluate side-chains 151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 353 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065024 restraints weight = 41822.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067099 restraints weight = 20570.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067789 restraints weight = 12665.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068065 restraints weight = 10776.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068148 restraints weight = 9823.238| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10892 Z= 0.261 Angle : 0.773 12.332 14865 Z= 0.389 Chirality : 0.047 0.361 1717 Planarity : 0.005 0.048 1852 Dihedral : 7.865 58.863 1842 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 5.76 % Allowed : 20.20 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -0.11 (0.22), residues: 1316 helix: 1.41 (0.30), residues: 282 sheet: 0.80 (0.25), residues: 396 loop : -1.39 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 254 TYR 0.028 0.002 TYR H 495 PHE 0.018 0.002 PHE H 150 TRP 0.015 0.002 TRP H 471 HIS 0.007 0.002 HIS H 469 Details of bonding type rmsd covalent geometry : bond 0.00597 (10864) covalent geometry : angle 0.74158 (14798) SS BOND : bond 0.00406 ( 17) SS BOND : angle 1.49497 ( 34) hydrogen bonds : bond 0.05016 ( 493) hydrogen bonds : angle 5.30916 ( 1392) link_BETA1-4 : bond 0.00472 ( 2) link_BETA1-4 : angle 2.35411 ( 6) link_NAG-ASN : bond 0.00455 ( 9) link_NAG-ASN : angle 4.81571 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7183 (p0) REVERT: A 91 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8259 (ttm-80) REVERT: B 301 MET cc_start: 0.8745 (ppp) cc_final: 0.8249 (ppp) REVERT: D 92 MET cc_start: 0.9089 (mmm) cc_final: 0.8561 (mmm) REVERT: D 120 LEU cc_start: 0.9183 (tt) cc_final: 0.8764 (mt) REVERT: E 128 MET cc_start: 0.7545 (tpp) cc_final: 0.7279 (ttm) REVERT: F 123 MET cc_start: 0.8368 (ppp) cc_final: 0.7456 (ppp) REVERT: F 139 CYS cc_start: 0.9171 (t) cc_final: 0.8765 (m) REVERT: G 86 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: H 129 VAL cc_start: 0.7200 (p) cc_final: 0.6941 (t) REVERT: H 353 ASP cc_start: 0.5836 (m-30) cc_final: 0.4914 (t0) REVERT: H 372 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8693 (mtt90) REVERT: H 433 PHE cc_start: 0.7934 (t80) cc_final: 0.7443 (t80) outliers start: 63 outliers final: 39 residues processed: 188 average time/residue: 0.0889 time to fit residues: 25.0702 Evaluate side-chains 171 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 41 ILE Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 187 TYR Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 555 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.3980 chunk 126 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066927 restraints weight = 42311.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068698 restraints weight = 20185.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070170 restraints weight = 12865.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070178 restraints weight = 10328.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070429 restraints weight = 9436.937| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10892 Z= 0.124 Angle : 0.673 11.731 14865 Z= 0.334 Chirality : 0.045 0.341 1717 Planarity : 0.004 0.044 1852 Dihedral : 7.145 59.182 1834 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 4.48 % Allowed : 20.57 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.17 (0.23), residues: 1316 helix: 1.82 (0.30), residues: 282 sheet: 0.93 (0.26), residues: 382 loop : -1.22 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 117 TYR 0.026 0.001 TYR B 291 PHE 0.012 0.001 PHE A 253 TRP 0.012 0.001 TRP B 219 HIS 0.005 0.001 HIS H 151 Details of bonding type rmsd covalent geometry : bond 0.00275 (10864) covalent geometry : angle 0.64587 (14798) SS BOND : bond 0.00486 ( 17) SS BOND : angle 1.32801 ( 34) hydrogen bonds : bond 0.04076 ( 493) hydrogen bonds : angle 4.84367 ( 1392) link_BETA1-4 : bond 0.00461 ( 2) link_BETA1-4 : angle 1.98392 ( 6) link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 4.16755 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8302 (tt0) cc_final: 0.8076 (tt0) REVERT: A 53 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8828 (mm-40) REVERT: A 91 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8214 (ttm-80) REVERT: A 185 MET cc_start: 0.9233 (mtp) cc_final: 0.8775 (mtp) REVERT: B 301 MET cc_start: 0.8671 (ppp) cc_final: 0.8188 (ppp) REVERT: D 92 MET cc_start: 0.8934 (mmm) cc_final: 0.8675 (mmm) REVERT: D 115 THR cc_start: 0.9143 (m) cc_final: 0.8893 (p) REVERT: D 120 LEU cc_start: 0.9154 (tt) cc_final: 0.8754 (mp) REVERT: E 128 MET cc_start: 0.7345 (tpp) cc_final: 0.7092 (ttm) REVERT: F 123 MET cc_start: 0.8387 (ppp) cc_final: 0.7765 (ppp) REVERT: F 128 MET cc_start: 0.8502 (ppp) cc_final: 0.8283 (ppp) REVERT: G 86 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: H 4 MET cc_start: 0.7180 (ttm) cc_final: 0.6745 (ttp) REVERT: H 201 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6755 (ttp80) REVERT: H 372 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8614 (mtt90) REVERT: H 433 PHE cc_start: 0.7895 (t80) cc_final: 0.7458 (t80) outliers start: 49 outliers final: 31 residues processed: 183 average time/residue: 0.0964 time to fit residues: 25.8536 Evaluate side-chains 178 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.086690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065991 restraints weight = 42131.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.067882 restraints weight = 21833.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069147 restraints weight = 14634.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069941 restraints weight = 11308.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070386 restraints weight = 9567.419| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10892 Z= 0.125 Angle : 0.635 12.323 14865 Z= 0.318 Chirality : 0.044 0.318 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.800 59.433 1831 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.82 % Rotamer: Outliers : 4.66 % Allowed : 21.02 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.28 (0.23), residues: 1316 helix: 1.84 (0.30), residues: 289 sheet: 1.01 (0.26), residues: 387 loop : -1.17 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 117 TYR 0.026 0.001 TYR F 99 PHE 0.011 0.001 PHE G 135 TRP 0.010 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00281 (10864) covalent geometry : angle 0.60760 (14798) SS BOND : bond 0.00252 ( 17) SS BOND : angle 1.05532 ( 34) hydrogen bonds : bond 0.03752 ( 493) hydrogen bonds : angle 4.62567 ( 1392) link_BETA1-4 : bond 0.00728 ( 2) link_BETA1-4 : angle 1.92851 ( 6) link_NAG-ASN : bond 0.00669 ( 9) link_NAG-ASN : angle 4.20060 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8335 (tt0) cc_final: 0.8113 (tt0) REVERT: A 91 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8188 (ttm-80) REVERT: A 185 MET cc_start: 0.9329 (mtp) cc_final: 0.9039 (mtp) REVERT: A 264 ASN cc_start: 0.7560 (t0) cc_final: 0.7251 (t0) REVERT: B 262 ASP cc_start: 0.8834 (t0) cc_final: 0.8626 (t0) REVERT: B 301 MET cc_start: 0.8557 (ppp) cc_final: 0.8107 (ppp) REVERT: D 92 MET cc_start: 0.8879 (mmm) cc_final: 0.8678 (mmm) REVERT: D 111 ASP cc_start: 0.8706 (m-30) cc_final: 0.8503 (m-30) REVERT: D 115 THR cc_start: 0.9074 (m) cc_final: 0.8783 (p) REVERT: D 120 LEU cc_start: 0.9128 (tt) cc_final: 0.8726 (mp) REVERT: E 128 MET cc_start: 0.7206 (tpp) cc_final: 0.6978 (ttm) REVERT: F 64 LYS cc_start: 0.9064 (pptt) cc_final: 0.8810 (pptt) REVERT: F 123 MET cc_start: 0.8528 (ppp) cc_final: 0.8044 (ppp) REVERT: H 4 MET cc_start: 0.7235 (ttm) cc_final: 0.6852 (ttp) REVERT: H 201 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.7039 (ttp80) REVERT: H 433 PHE cc_start: 0.7994 (t80) cc_final: 0.7535 (t80) outliers start: 51 outliers final: 33 residues processed: 186 average time/residue: 0.0941 time to fit residues: 25.9605 Evaluate side-chains 174 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.0070 chunk 110 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.0470 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065751 restraints weight = 41798.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067628 restraints weight = 21713.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068853 restraints weight = 14573.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069679 restraints weight = 11304.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070177 restraints weight = 9541.905| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10892 Z= 0.129 Angle : 0.644 12.421 14865 Z= 0.318 Chirality : 0.044 0.306 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.583 59.815 1831 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.80 % Favored : 96.05 % Rotamer: Outliers : 5.30 % Allowed : 20.38 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.34 (0.23), residues: 1316 helix: 1.85 (0.30), residues: 288 sheet: 0.97 (0.26), residues: 397 loop : -1.08 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.031 0.001 TYR B 291 PHE 0.008 0.001 PHE G 127 TRP 0.010 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00291 (10864) covalent geometry : angle 0.61549 (14798) SS BOND : bond 0.00210 ( 17) SS BOND : angle 1.41556 ( 34) hydrogen bonds : bond 0.03723 ( 493) hydrogen bonds : angle 4.59854 ( 1392) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 1.78524 ( 6) link_NAG-ASN : bond 0.00652 ( 9) link_NAG-ASN : angle 4.16624 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8296 (tt0) cc_final: 0.8040 (tt0) REVERT: A 53 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8860 (mm-40) REVERT: A 91 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8251 (ttm-80) REVERT: A 185 MET cc_start: 0.9344 (mtp) cc_final: 0.9131 (mtp) REVERT: A 264 ASN cc_start: 0.7374 (t0) cc_final: 0.6773 (t0) REVERT: B 291 TYR cc_start: 0.8822 (t80) cc_final: 0.8512 (t80) REVERT: B 301 MET cc_start: 0.8527 (ppp) cc_final: 0.8065 (ppp) REVERT: D 28 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 111 ASP cc_start: 0.8760 (m-30) cc_final: 0.8553 (m-30) REVERT: D 115 THR cc_start: 0.9066 (m) cc_final: 0.8827 (p) REVERT: D 120 LEU cc_start: 0.9125 (tt) cc_final: 0.8678 (mp) REVERT: E 128 MET cc_start: 0.7232 (tpp) cc_final: 0.6993 (ttm) REVERT: F 64 LYS cc_start: 0.9056 (pptt) cc_final: 0.8835 (pptt) REVERT: F 123 MET cc_start: 0.8650 (ppp) cc_final: 0.8235 (ppp) REVERT: G 57 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7585 (ttpp) REVERT: H 201 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.7044 (ttp80) REVERT: H 372 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8577 (mtt90) REVERT: H 433 PHE cc_start: 0.7928 (t80) cc_final: 0.7476 (t80) outliers start: 58 outliers final: 37 residues processed: 185 average time/residue: 0.0922 time to fit residues: 25.5399 Evaluate side-chains 179 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 0.0030 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN G 37 GLN ** H 144 ASN ** 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 = 0.3687 r_free = 0.3687 target = 0.086080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065749 restraints weight = 41423.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067630 restraints weight = 21308.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068860 restraints weight = 14166.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069649 restraints weight = 10906.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070174 restraints weight = 9206.730| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10892 Z= 0.142 Angle : 0.648 14.488 14865 Z= 0.320 Chirality : 0.044 0.316 1717 Planarity : 0.004 0.047 1852 Dihedral : 6.422 59.282 1829 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 4.66 % Allowed : 21.21 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.39 (0.23), residues: 1316 helix: 1.85 (0.30), residues: 289 sheet: 1.00 (0.26), residues: 397 loop : -1.03 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.020 0.001 TYR F 99 PHE 0.010 0.001 PHE G 127 TRP 0.009 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00327 (10864) covalent geometry : angle 0.62063 (14798) SS BOND : bond 0.00213 ( 17) SS BOND : angle 1.24372 ( 34) hydrogen bonds : bond 0.03727 ( 493) hydrogen bonds : angle 4.60044 ( 1392) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 1.78912 ( 6) link_NAG-ASN : bond 0.00629 ( 9) link_NAG-ASN : angle 4.18715 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8361 (tt0) cc_final: 0.8123 (tt0) REVERT: A 53 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8835 (mm-40) REVERT: A 91 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8290 (ttm-80) REVERT: A 231 LYS cc_start: 0.9459 (tppp) cc_final: 0.9077 (tppt) REVERT: A 264 ASN cc_start: 0.7284 (t0) cc_final: 0.6139 (t0) REVERT: B 291 TYR cc_start: 0.8878 (t80) cc_final: 0.8459 (t80) REVERT: B 301 MET cc_start: 0.8515 (ppp) cc_final: 0.8051 (ppp) REVERT: D 111 ASP cc_start: 0.8767 (m-30) cc_final: 0.8567 (m-30) REVERT: D 115 THR cc_start: 0.9076 (m) cc_final: 0.8848 (p) REVERT: D 120 LEU cc_start: 0.9077 (tt) cc_final: 0.8663 (mp) REVERT: E 128 MET cc_start: 0.7252 (tpp) cc_final: 0.7017 (ttm) REVERT: F 48 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7693 (p) REVERT: F 64 LYS cc_start: 0.9034 (pptt) cc_final: 0.8790 (pptt) REVERT: F 123 MET cc_start: 0.8724 (ppp) cc_final: 0.8320 (ppp) REVERT: G 129 LEU cc_start: 0.8207 (mm) cc_final: 0.7990 (mm) REVERT: H 201 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: H 372 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8676 (mtm110) REVERT: H 433 PHE cc_start: 0.7988 (t80) cc_final: 0.7539 (t80) outliers start: 51 outliers final: 41 residues processed: 180 average time/residue: 0.0932 time to fit residues: 25.0897 Evaluate side-chains 182 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN E 81 HIS ** H 144 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.085906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065117 restraints weight = 41912.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067002 restraints weight = 21993.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068246 restraints weight = 14789.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069039 restraints weight = 11472.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069492 restraints weight = 9703.342| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10892 Z= 0.143 Angle : 0.647 15.410 14865 Z= 0.320 Chirality : 0.044 0.337 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.315 58.177 1829 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 4.57 % Allowed : 21.76 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1316 helix: 1.84 (0.30), residues: 291 sheet: 1.02 (0.26), residues: 397 loop : -0.97 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 117 TYR 0.022 0.001 TYR F 99 PHE 0.009 0.001 PHE H 150 TRP 0.010 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00327 (10864) covalent geometry : angle 0.61987 (14798) SS BOND : bond 0.00204 ( 17) SS BOND : angle 1.05137 ( 34) hydrogen bonds : bond 0.03690 ( 493) hydrogen bonds : angle 4.60181 ( 1392) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 1.75028 ( 6) link_NAG-ASN : bond 0.00632 ( 9) link_NAG-ASN : angle 4.19323 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8355 (tt0) cc_final: 0.8116 (tt0) REVERT: A 53 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8819 (mm-40) REVERT: A 91 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8296 (ttm-80) REVERT: A 231 LYS cc_start: 0.9461 (tppp) cc_final: 0.9074 (tppt) REVERT: A 264 ASN cc_start: 0.7317 (t0) cc_final: 0.6128 (t0) REVERT: B 73 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8887 (tp) REVERT: B 291 TYR cc_start: 0.8924 (t80) cc_final: 0.8459 (t80) REVERT: B 301 MET cc_start: 0.8462 (ppp) cc_final: 0.8014 (ppp) REVERT: D 111 ASP cc_start: 0.8763 (m-30) cc_final: 0.8560 (m-30) REVERT: D 115 THR cc_start: 0.9115 (m) cc_final: 0.8890 (p) REVERT: E 128 MET cc_start: 0.7264 (tpp) cc_final: 0.7015 (ttm) REVERT: F 48 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7727 (p) REVERT: F 64 LYS cc_start: 0.9025 (pptt) cc_final: 0.8773 (pptt) REVERT: F 123 MET cc_start: 0.8923 (ppp) cc_final: 0.8575 (ppp) REVERT: G 129 LEU cc_start: 0.8336 (mm) cc_final: 0.8074 (mm) REVERT: H 129 VAL cc_start: 0.7190 (p) cc_final: 0.6912 (t) REVERT: H 201 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7078 (ttp80) REVERT: H 372 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8671 (mtm110) REVERT: H 433 PHE cc_start: 0.7950 (t80) cc_final: 0.7503 (t80) outliers start: 50 outliers final: 40 residues processed: 177 average time/residue: 0.0897 time to fit residues: 23.8137 Evaluate side-chains 178 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 131 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065309 restraints weight = 41814.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067201 restraints weight = 21863.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068468 restraints weight = 14643.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069258 restraints weight = 11287.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069661 restraints weight = 9528.023| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10892 Z= 0.132 Angle : 0.651 15.732 14865 Z= 0.320 Chirality : 0.045 0.351 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.215 57.789 1829 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.75 % Allowed : 22.21 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.48 (0.23), residues: 1316 helix: 1.86 (0.29), residues: 291 sheet: 1.12 (0.26), residues: 386 loop : -0.97 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.025 0.001 TYR F 99 PHE 0.008 0.001 PHE H 150 TRP 0.010 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd covalent geometry : bond 0.00302 (10864) covalent geometry : angle 0.62545 (14798) SS BOND : bond 0.00189 ( 17) SS BOND : angle 0.94529 ( 34) hydrogen bonds : bond 0.03595 ( 493) hydrogen bonds : angle 4.54476 ( 1392) link_BETA1-4 : bond 0.00540 ( 2) link_BETA1-4 : angle 1.74823 ( 6) link_NAG-ASN : bond 0.00660 ( 9) link_NAG-ASN : angle 4.15605 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8340 (tt0) cc_final: 0.8064 (tt0) REVERT: A 53 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8815 (mm-40) REVERT: A 91 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8301 (ttm-80) REVERT: A 231 LYS cc_start: 0.9446 (tppp) cc_final: 0.9050 (tppt) REVERT: A 264 ASN cc_start: 0.7296 (t0) cc_final: 0.6216 (t0) REVERT: B 73 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 114 TYR cc_start: 0.8443 (m-80) cc_final: 0.8230 (m-80) REVERT: B 291 TYR cc_start: 0.8913 (t80) cc_final: 0.8494 (t80) REVERT: B 301 MET cc_start: 0.8449 (ppp) cc_final: 0.8048 (ppp) REVERT: D 111 ASP cc_start: 0.8759 (m-30) cc_final: 0.8557 (m-30) REVERT: D 115 THR cc_start: 0.9084 (m) cc_final: 0.8843 (p) REVERT: E 128 MET cc_start: 0.7250 (tpp) cc_final: 0.7004 (ttm) REVERT: F 48 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7693 (p) REVERT: F 64 LYS cc_start: 0.9023 (pptt) cc_final: 0.8771 (pptt) REVERT: F 123 MET cc_start: 0.8888 (ppp) cc_final: 0.8479 (ppp) REVERT: G 57 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7547 (ttpp) REVERT: G 129 LEU cc_start: 0.8353 (mm) cc_final: 0.8061 (mm) REVERT: H 129 VAL cc_start: 0.7080 (p) cc_final: 0.6826 (t) REVERT: H 201 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7068 (ttp80) REVERT: H 372 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8666 (mtm110) REVERT: H 433 PHE cc_start: 0.7938 (t80) cc_final: 0.7485 (t80) outliers start: 52 outliers final: 40 residues processed: 182 average time/residue: 0.0944 time to fit residues: 25.7278 Evaluate side-chains 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.085774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065319 restraints weight = 41362.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067187 restraints weight = 21411.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068440 restraints weight = 14294.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069246 restraints weight = 10985.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069713 restraints weight = 9242.882| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10892 Z= 0.142 Angle : 0.666 16.060 14865 Z= 0.328 Chirality : 0.045 0.362 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.181 56.583 1829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 4.84 % Allowed : 22.58 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.52 (0.23), residues: 1316 helix: 1.84 (0.29), residues: 291 sheet: 1.11 (0.26), residues: 398 loop : -0.93 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 117 TYR 0.013 0.001 TYR H 423 PHE 0.009 0.001 PHE H 150 TRP 0.010 0.001 TRP D 43 HIS 0.008 0.001 HIS H 475 Details of bonding type rmsd covalent geometry : bond 0.00325 (10864) covalent geometry : angle 0.64049 (14798) SS BOND : bond 0.00194 ( 17) SS BOND : angle 0.94928 ( 34) hydrogen bonds : bond 0.03694 ( 493) hydrogen bonds : angle 4.56823 ( 1392) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 1.74743 ( 6) link_NAG-ASN : bond 0.00645 ( 9) link_NAG-ASN : angle 4.17296 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8345 (tt0) cc_final: 0.8094 (tt0) REVERT: A 53 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8804 (mm-40) REVERT: A 91 ARG cc_start: 0.8646 (tpp80) cc_final: 0.8309 (ttm-80) REVERT: A 231 LYS cc_start: 0.9444 (tppp) cc_final: 0.9056 (tppt) REVERT: A 264 ASN cc_start: 0.7355 (t0) cc_final: 0.5891 (t0) REVERT: B 73 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8872 (tp) REVERT: B 78 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: B 114 TYR cc_start: 0.8395 (m-80) cc_final: 0.8173 (m-80) REVERT: B 291 TYR cc_start: 0.8982 (t80) cc_final: 0.8520 (t80) REVERT: B 301 MET cc_start: 0.8444 (ppp) cc_final: 0.8109 (ppp) REVERT: D 115 THR cc_start: 0.9074 (m) cc_final: 0.8850 (p) REVERT: E 128 MET cc_start: 0.7264 (tpp) cc_final: 0.7020 (ttm) REVERT: F 48 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7721 (p) REVERT: F 64 LYS cc_start: 0.9025 (pptt) cc_final: 0.8773 (pptt) REVERT: F 123 MET cc_start: 0.8906 (ppp) cc_final: 0.8517 (ppp) REVERT: G 37 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: G 129 LEU cc_start: 0.8374 (mm) cc_final: 0.8066 (mm) REVERT: H 129 VAL cc_start: 0.7076 (p) cc_final: 0.6859 (t) REVERT: H 201 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7003 (ttp80) REVERT: H 372 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8669 (mtm110) REVERT: H 433 PHE cc_start: 0.7960 (t80) cc_final: 0.7539 (t80) outliers start: 53 outliers final: 42 residues processed: 174 average time/residue: 0.0941 time to fit residues: 24.4276 Evaluate side-chains 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065336 restraints weight = 40931.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067183 restraints weight = 21102.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068409 restraints weight = 14102.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069172 restraints weight = 10850.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069722 restraints weight = 9169.144| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10892 Z= 0.141 Angle : 0.671 16.726 14865 Z= 0.328 Chirality : 0.046 0.376 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.092 56.557 1828 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 4.75 % Allowed : 22.39 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.53 (0.23), residues: 1316 helix: 1.81 (0.29), residues: 293 sheet: 1.13 (0.26), residues: 398 loop : -0.91 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 32 TYR 0.014 0.001 TYR H 423 PHE 0.009 0.001 PHE H 150 TRP 0.013 0.001 TRP G 72 HIS 0.007 0.001 HIS H 475 Details of bonding type rmsd covalent geometry : bond 0.00324 (10864) covalent geometry : angle 0.64582 (14798) SS BOND : bond 0.00194 ( 17) SS BOND : angle 0.92834 ( 34) hydrogen bonds : bond 0.03645 ( 493) hydrogen bonds : angle 4.55930 ( 1392) link_BETA1-4 : bond 0.00380 ( 2) link_BETA1-4 : angle 1.69297 ( 6) link_NAG-ASN : bond 0.00650 ( 9) link_NAG-ASN : angle 4.15551 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8408 (tt0) cc_final: 0.8161 (tt0) REVERT: A 53 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8880 (mm-40) REVERT: A 91 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8313 (ttm-80) REVERT: A 231 LYS cc_start: 0.9449 (tppp) cc_final: 0.9068 (tppt) REVERT: A 264 ASN cc_start: 0.7387 (t0) cc_final: 0.6078 (t0) REVERT: B 73 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8876 (tp) REVERT: B 78 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: B 291 TYR cc_start: 0.9003 (t80) cc_final: 0.8556 (t80) REVERT: B 301 MET cc_start: 0.8443 (ppp) cc_final: 0.8102 (ppp) REVERT: D 111 ASP cc_start: 0.8752 (m-30) cc_final: 0.8490 (m-30) REVERT: D 115 THR cc_start: 0.9079 (m) cc_final: 0.8864 (p) REVERT: E 128 MET cc_start: 0.7273 (tpp) cc_final: 0.7023 (ttm) REVERT: F 48 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7826 (p) REVERT: F 64 LYS cc_start: 0.9046 (pptt) cc_final: 0.8788 (pptt) REVERT: F 123 MET cc_start: 0.8929 (ppp) cc_final: 0.8597 (ppp) REVERT: G 37 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7872 (tp40) REVERT: G 129 LEU cc_start: 0.8441 (mm) cc_final: 0.8137 (mm) REVERT: H 201 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6960 (ttp80) REVERT: H 372 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8685 (mtm110) REVERT: H 433 PHE cc_start: 0.7982 (t80) cc_final: 0.7636 (t80) outliers start: 52 outliers final: 45 residues processed: 175 average time/residue: 0.0937 time to fit residues: 24.4298 Evaluate side-chains 186 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 369 MET Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 540 THR Chi-restraints excluded: chain H residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066134 restraints weight = 41724.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068027 restraints weight = 21632.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069294 restraints weight = 14436.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070079 restraints weight = 11106.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070618 restraints weight = 9389.999| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10892 Z= 0.115 Angle : 0.662 16.981 14865 Z= 0.322 Chirality : 0.046 0.381 1717 Planarity : 0.004 0.041 1852 Dihedral : 5.897 54.635 1828 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 4.20 % Allowed : 23.22 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 0.61 (0.23), residues: 1316 helix: 1.93 (0.29), residues: 291 sheet: 1.33 (0.27), residues: 370 loop : -0.89 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 74 TYR 0.013 0.001 TYR H 423 PHE 0.008 0.001 PHE H 532 TRP 0.016 0.001 TRP G 72 HIS 0.007 0.001 HIS H 475 Details of bonding type rmsd covalent geometry : bond 0.00257 (10864) covalent geometry : angle 0.63826 (14798) SS BOND : bond 0.00146 ( 17) SS BOND : angle 0.78547 ( 34) hydrogen bonds : bond 0.03418 ( 493) hydrogen bonds : angle 4.44556 ( 1392) link_BETA1-4 : bond 0.00551 ( 2) link_BETA1-4 : angle 1.67745 ( 6) link_NAG-ASN : bond 0.00740 ( 9) link_NAG-ASN : angle 4.05620 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.49 seconds wall clock time: 38 minutes 59.70 seconds (2339.70 seconds total)