Starting phenix.real_space_refine on Tue May 13 15:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3e_45166/05_2025/9c3e_45166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3e_45166/05_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_45166/05_2025/9c3e_45166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3e_45166/05_2025/9c3e_45166.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3e_45166/05_2025/9c3e_45166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3e_45166/05_2025/9c3e_45166.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3} 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: {'GLU:plan': 2, 'ASP:plan': 1} 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, 'GLU:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} 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, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} 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: 7.47, per 1000 atoms: 0.70 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: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.34 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: 3.72 Time building geometry restraints manager: 2.93 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: 4.870 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.022 0.002 TRP A 272 HIS 0.008 0.002 HIS D 89 PHE 0.038 0.002 PHE G 135 TYR 0.035 0.002 TYR H 495 ARG 0.009 0.001 ARG H 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 9) link_NAG-ASN : angle 7.59714 ( 27) link_BETA1-4 : bond 0.00374 ( 2) link_BETA1-4 : angle 1.97558 ( 6) hydrogen bonds : bond 0.13063 ( 493) hydrogen bonds : angle 6.26286 ( 1392) SS BOND : bond 0.00978 ( 17) SS BOND : angle 2.74519 ( 34) covalent geometry : bond 0.00506 (10864) covalent geometry : angle 0.89221 (14798) *********************** 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 : 1.206 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: 0.8264 (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: 0.7572 (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: 0.2133 time to fit residues: 55.7651 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 : 1.112 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.087136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066809 restraints weight = 40919.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068699 restraints weight = 21066.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069942 restraints weight = 14033.286| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10892 Z= 0.150 Angle : 0.720 10.840 14865 Z= 0.358 Chirality : 0.045 0.371 1717 Planarity : 0.004 0.045 1852 Dihedral : 7.764 59.796 1842 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 4.48 % Allowed : 20.66 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1316 helix: 1.55 (0.30), residues: 282 sheet: 0.89 (0.25), residues: 398 loop : -1.27 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 5 HIS 0.005 0.001 HIS F 81 PHE 0.013 0.001 PHE G 64 TYR 0.028 0.002 TYR H 495 ARG 0.005 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 9) link_NAG-ASN : angle 4.72036 ( 27) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 2.08710 ( 6) hydrogen bonds : bond 0.04635 ( 493) hydrogen bonds : angle 5.16757 ( 1392) SS BOND : bond 0.00249 ( 17) SS BOND : angle 1.30650 ( 34) covalent geometry : bond 0.00335 (10864) covalent geometry : angle 0.68929 (14798) *********************** 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 201 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8457 (tt0) cc_final: 0.8211 (tt0) REVERT: A 58 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7096 (p0) REVERT: A 91 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8192 (ttm-80) REVERT: A 241 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7761 (t) REVERT: B 78 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: B 301 MET cc_start: 0.8734 (ppp) cc_final: 0.8320 (ppp) REVERT: D 111 ASP cc_start: 0.8652 (m-30) cc_final: 0.8384 (m-30) REVERT: D 115 THR cc_start: 0.9120 (m) cc_final: 0.8900 (p) REVERT: D 120 LEU cc_start: 0.9156 (tt) cc_final: 0.8773 (mp) REVERT: E 57 ILE cc_start: 0.8277 (mt) cc_final: 0.7901 (pt) REVERT: E 128 MET cc_start: 0.7677 (tpp) cc_final: 0.7384 (ttm) REVERT: F 125 MET cc_start: 0.8791 (ppp) cc_final: 0.8498 (ppp) REVERT: F 139 CYS cc_start: 0.9120 (t) cc_final: 0.8689 (m) REVERT: H 129 VAL cc_start: 0.7167 (p) cc_final: 0.6897 (t) REVERT: H 433 PHE cc_start: 0.7854 (t80) cc_final: 0.7344 (t80) outliers start: 49 outliers final: 26 residues processed: 186 average time/residue: 0.1946 time to fit residues: 53.8448 Evaluate side-chains 164 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 78 GLU 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 D residue 44 VAL 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 52 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 141 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 91 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.087133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067018 restraints weight = 41447.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068875 restraints weight = 21038.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070113 restraints weight = 13904.701| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10892 Z= 0.131 Angle : 0.649 10.883 14865 Z= 0.326 Chirality : 0.044 0.335 1717 Planarity : 0.004 0.045 1852 Dihedral : 7.161 59.627 1831 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.90 % Rotamer: Outliers : 4.48 % Allowed : 20.02 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1316 helix: 1.72 (0.30), residues: 289 sheet: 1.00 (0.25), residues: 400 loop : -1.25 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 219 HIS 0.005 0.001 HIS F 81 PHE 0.012 0.001 PHE G 64 TYR 0.027 0.001 TYR B 291 ARG 0.005 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 9) link_NAG-ASN : angle 3.91781 ( 27) link_BETA1-4 : bond 0.00524 ( 2) link_BETA1-4 : angle 1.92551 ( 6) hydrogen bonds : bond 0.03988 ( 493) hydrogen bonds : angle 4.81444 ( 1392) SS BOND : bond 0.00308 ( 17) SS BOND : angle 1.05721 ( 34) covalent geometry : bond 0.00293 (10864) covalent geometry : angle 0.62531 (14798) *********************** 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 196 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8452 (tt0) cc_final: 0.8177 (tt0) REVERT: A 91 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8128 (ttm-80) REVERT: A 241 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 78 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 301 MET cc_start: 0.8690 (ppp) cc_final: 0.8243 (ppp) REVERT: D 115 THR cc_start: 0.9123 (m) cc_final: 0.8870 (p) REVERT: D 120 LEU cc_start: 0.9134 (tt) cc_final: 0.8753 (mp) REVERT: E 57 ILE cc_start: 0.8189 (mt) cc_final: 0.7810 (pt) REVERT: E 128 MET cc_start: 0.7494 (tpp) cc_final: 0.7230 (ttm) REVERT: F 123 MET cc_start: 0.8073 (ppp) cc_final: 0.7529 (ppp) REVERT: F 137 ASP cc_start: 0.9240 (t0) cc_final: 0.8916 (t0) REVERT: H 4 MET cc_start: 0.6841 (ttp) cc_final: 0.6543 (ttp) REVERT: H 433 PHE cc_start: 0.7962 (t80) cc_final: 0.7553 (t80) outliers start: 49 outliers final: 31 residues processed: 182 average time/residue: 0.1785 time to fit residues: 48.7149 Evaluate side-chains 167 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 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 275 LEU Chi-restraints excluded: chain B residue 279 ILE 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 44 VAL 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 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 437 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.087570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066951 restraints weight = 41877.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068844 restraints weight = 21763.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070100 restraints weight = 14611.724| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10892 Z= 0.117 Angle : 0.617 10.573 14865 Z= 0.309 Chirality : 0.043 0.318 1717 Planarity : 0.004 0.041 1852 Dihedral : 6.656 56.922 1829 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 4.20 % Allowed : 19.74 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1316 helix: 1.89 (0.30), residues: 289 sheet: 1.05 (0.26), residues: 393 loop : -1.18 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 PHE 0.009 0.001 PHE A 253 TYR 0.024 0.001 TYR B 291 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 9) link_NAG-ASN : angle 3.81161 ( 27) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 1.85364 ( 6) hydrogen bonds : bond 0.03643 ( 493) hydrogen bonds : angle 4.57533 ( 1392) SS BOND : bond 0.00225 ( 17) SS BOND : angle 1.03872 ( 34) covalent geometry : bond 0.00262 (10864) covalent geometry : angle 0.59335 (14798) *********************** 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 193 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 1.126 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: 0.8441 (tt0) cc_final: 0.8164 (tt0) REVERT: A 53 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8841 (mm-40) REVERT: A 91 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8198 (ttm-80) REVERT: A 241 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7793 (m) REVERT: B 114 TYR cc_start: 0.8424 (m-80) cc_final: 0.8103 (m-80) REVERT: B 262 ASP cc_start: 0.8822 (t0) cc_final: 0.8599 (t0) REVERT: B 301 MET cc_start: 0.8692 (ppp) cc_final: 0.8221 (ppp) REVERT: D 28 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 111 ASP cc_start: 0.8701 (m-30) cc_final: 0.8493 (m-30) REVERT: D 115 THR cc_start: 0.9056 (m) cc_final: 0.8766 (p) REVERT: D 120 LEU cc_start: 0.9143 (tt) cc_final: 0.8718 (mp) REVERT: E 57 ILE cc_start: 0.8195 (mt) cc_final: 0.7796 (pt) REVERT: E 128 MET cc_start: 0.7290 (tpp) cc_final: 0.7046 (ttm) REVERT: F 123 MET cc_start: 0.8226 (ppp) cc_final: 0.7791 (ppp) REVERT: Y 30 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7840 (ptpp) REVERT: H 4 MET cc_start: 0.7035 (ttp) cc_final: 0.6546 (ttp) REVERT: H 394 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7722 (m90) REVERT: H 433 PHE cc_start: 0.7909 (t80) cc_final: 0.7493 (t80) outliers start: 46 outliers final: 26 residues processed: 180 average time/residue: 0.1859 time to fit residues: 49.7510 Evaluate side-chains 166 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 241 THR 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 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 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 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 394 HIS Chi-restraints excluded: chain H residue 437 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.0020 overall best weight: 1.0590 ------------------------------------------------------------------------------- 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** F 81 HIS ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 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 = 0.3687 r_free = 0.3687 target = 0.086155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065489 restraints weight = 41793.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067358 restraints weight = 21925.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068518 restraints weight = 14770.857| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10892 Z= 0.159 Angle : 0.652 11.042 14865 Z= 0.326 Chirality : 0.044 0.304 1717 Planarity : 0.004 0.044 1852 Dihedral : 6.534 58.650 1829 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 4.94 % Allowed : 19.10 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1316 helix: 1.83 (0.30), residues: 288 sheet: 1.02 (0.26), residues: 395 loop : -1.16 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 215 HIS 0.005 0.001 HIS F 81 PHE 0.011 0.001 PHE H 150 TYR 0.024 0.001 TYR F 99 ARG 0.005 0.000 ARG H 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 9) link_NAG-ASN : angle 3.87372 ( 27) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 1.77459 ( 6) hydrogen bonds : bond 0.03862 ( 493) hydrogen bonds : angle 4.67622 ( 1392) SS BOND : bond 0.00320 ( 17) SS BOND : angle 1.50578 ( 34) covalent geometry : bond 0.00366 (10864) covalent geometry : angle 0.62712 (14798) *********************** 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 195 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8742 (mm110) REVERT: A 91 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8180 (ttm-80) REVERT: A 241 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 262 ASP cc_start: 0.8837 (t0) cc_final: 0.8588 (t0) REVERT: B 291 TYR cc_start: 0.8857 (t80) cc_final: 0.8594 (t80) REVERT: B 301 MET cc_start: 0.8613 (ppp) cc_final: 0.8166 (ppp) REVERT: D 111 ASP cc_start: 0.8764 (m-30) cc_final: 0.8560 (m-30) REVERT: D 115 THR cc_start: 0.9104 (m) cc_final: 0.8849 (p) REVERT: D 120 LEU cc_start: 0.9130 (tt) cc_final: 0.8677 (mp) REVERT: E 57 ILE cc_start: 0.8229 (mt) cc_final: 0.7847 (pt) REVERT: E 128 MET cc_start: 0.7249 (tpp) cc_final: 0.7048 (ttm) REVERT: F 123 MET cc_start: 0.8593 (ppp) cc_final: 0.8185 (ppp) REVERT: G 129 LEU cc_start: 0.8329 (mm) cc_final: 0.8078 (mm) REVERT: H 4 MET cc_start: 0.7584 (ttp) cc_final: 0.7065 (ttp) REVERT: H 369 MET cc_start: 0.8113 (tpt) cc_final: 0.7861 (tpt) REVERT: H 433 PHE cc_start: 0.7824 (t80) cc_final: 0.7433 (t80) outliers start: 54 outliers final: 37 residues processed: 177 average time/residue: 0.1991 time to fit residues: 52.7771 Evaluate side-chains 176 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain A residue 241 THR 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 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 = 0.3690 r_free = 0.3690 target = 0.086332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065551 restraints weight = 42154.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067432 restraints weight = 21999.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068684 restraints weight = 14801.016| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2400 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= 0.137 Angle : 0.634 15.148 14865 Z= 0.315 Chirality : 0.044 0.302 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.381 58.915 1829 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 4.57 % Allowed : 20.29 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1316 helix: 1.96 (0.30), residues: 289 sheet: 1.07 (0.26), residues: 395 loop : -1.09 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 43 HIS 0.004 0.001 HIS F 81 PHE 0.008 0.001 PHE G 127 TYR 0.021 0.001 TYR F 99 ARG 0.003 0.000 ARG H 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 3.76817 ( 27) link_BETA1-4 : bond 0.00484 ( 2) link_BETA1-4 : angle 1.80498 ( 6) hydrogen bonds : bond 0.03687 ( 493) hydrogen bonds : angle 4.57832 ( 1392) SS BOND : bond 0.00201 ( 17) SS BOND : angle 1.17753 ( 34) covalent geometry : bond 0.00313 (10864) covalent geometry : angle 0.61075 (14798) *********************** 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 199 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 1.222 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: 0.8387 (tt0) cc_final: 0.8113 (tt0) REVERT: A 53 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8780 (mm-40) REVERT: A 91 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8260 (ttm-80) REVERT: A 231 LYS cc_start: 0.9468 (tppp) cc_final: 0.9059 (tppt) REVERT: A 241 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7779 (m) REVERT: B 114 TYR cc_start: 0.8437 (m-80) cc_final: 0.8170 (m-80) REVERT: B 291 TYR cc_start: 0.8888 (t80) cc_final: 0.8678 (t80) REVERT: B 301 MET cc_start: 0.8503 (ppp) cc_final: 0.8087 (ppp) REVERT: D 111 ASP cc_start: 0.8755 (m-30) cc_final: 0.8554 (m-30) REVERT: D 115 THR cc_start: 0.9072 (m) cc_final: 0.8837 (p) REVERT: D 120 LEU cc_start: 0.9125 (tt) cc_final: 0.8696 (mp) REVERT: E 128 MET cc_start: 0.7205 (tpp) cc_final: 0.6994 (ttm) REVERT: F 64 LYS cc_start: 0.9053 (pptt) cc_final: 0.8813 (pptt) REVERT: F 123 MET cc_start: 0.8645 (ppp) cc_final: 0.8236 (ppp) REVERT: G 129 LEU cc_start: 0.8351 (mm) cc_final: 0.8139 (mm) REVERT: H 4 MET cc_start: 0.7605 (ttp) cc_final: 0.7162 (ttp) REVERT: H 369 MET cc_start: 0.8016 (tpt) cc_final: 0.7614 (tpt) REVERT: H 433 PHE cc_start: 0.7872 (t80) cc_final: 0.7494 (t80) outliers start: 50 outliers final: 36 residues processed: 182 average time/residue: 0.1839 time to fit residues: 50.6907 Evaluate side-chains 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 241 THR 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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** E 81 HIS ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 394 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.086016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065046 restraints weight = 42569.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066942 restraints weight = 22298.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068209 restraints weight = 14956.809| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10892 Z= 0.143 Angle : 0.644 15.318 14865 Z= 0.319 Chirality : 0.044 0.339 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.300 58.059 1829 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.48 % Allowed : 21.02 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1316 helix: 1.81 (0.30), residues: 291 sheet: 1.09 (0.26), residues: 395 loop : -1.01 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 43 HIS 0.004 0.001 HIS H 151 PHE 0.009 0.001 PHE H 150 TYR 0.019 0.001 TYR F 99 ARG 0.003 0.000 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 9) link_NAG-ASN : angle 3.70569 ( 27) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 1.81096 ( 6) hydrogen bonds : bond 0.03653 ( 493) hydrogen bonds : angle 4.62902 ( 1392) SS BOND : bond 0.00205 ( 17) SS BOND : angle 1.04834 ( 34) covalent geometry : bond 0.00327 (10864) covalent geometry : angle 0.62242 (14798) *********************** 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 198 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 1.136 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: 0.8397 (tt0) cc_final: 0.8147 (tt0) REVERT: A 53 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: A 91 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8301 (ttm-80) REVERT: A 185 MET cc_start: 0.9151 (mtp) cc_final: 0.8715 (mtt) REVERT: A 231 LYS cc_start: 0.9481 (tppp) cc_final: 0.9075 (tppt) REVERT: A 241 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7840 (m) REVERT: B 114 TYR cc_start: 0.8390 (m-80) cc_final: 0.8170 (m-80) REVERT: B 291 TYR cc_start: 0.9001 (t80) cc_final: 0.8777 (t80) REVERT: B 301 MET cc_start: 0.8530 (ppp) cc_final: 0.8114 (ppp) REVERT: D 111 ASP cc_start: 0.8758 (m-30) cc_final: 0.8555 (m-30) REVERT: D 115 THR cc_start: 0.9103 (m) cc_final: 0.8870 (p) REVERT: E 57 ILE cc_start: 0.8293 (mt) cc_final: 0.7924 (pt) REVERT: E 128 MET cc_start: 0.7266 (tpp) cc_final: 0.7016 (ttm) REVERT: F 48 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7714 (p) REVERT: F 64 LYS cc_start: 0.9026 (pptt) cc_final: 0.8776 (pptt) REVERT: F 123 MET cc_start: 0.8878 (ppp) cc_final: 0.8468 (ppp) REVERT: G 129 LEU cc_start: 0.8466 (mm) cc_final: 0.8200 (mm) REVERT: H 4 MET cc_start: 0.7807 (ttp) cc_final: 0.7542 (ttp) REVERT: H 369 MET cc_start: 0.8030 (tpt) cc_final: 0.7683 (tpt) REVERT: H 433 PHE cc_start: 0.7861 (t80) cc_final: 0.7484 (t80) outliers start: 49 outliers final: 39 residues processed: 183 average time/residue: 0.1767 time to fit residues: 49.0259 Evaluate side-chains 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 241 THR 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 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 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 432 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- 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 G 37 GLN ** H 203 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 = 0.3666 r_free = 0.3666 target = 0.085026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.064265 restraints weight = 42226.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066123 restraints weight = 22229.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067351 restraints weight = 14998.949| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10892 Z= 0.186 Angle : 0.677 15.569 14865 Z= 0.338 Chirality : 0.045 0.328 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.381 56.386 1827 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 4.39 % Allowed : 21.57 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1316 helix: 1.84 (0.30), residues: 291 sheet: 1.00 (0.26), residues: 397 loop : -0.98 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 471 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.002 PHE H 150 TYR 0.014 0.001 TYR H 423 ARG 0.004 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 9) link_NAG-ASN : angle 3.78768 ( 27) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.80169 ( 6) hydrogen bonds : bond 0.03951 ( 493) hydrogen bonds : angle 4.73865 ( 1392) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.11665 ( 34) covalent geometry : bond 0.00428 (10864) covalent geometry : angle 0.65617 (14798) *********************** 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 188 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8396 (tt0) cc_final: 0.8134 (tt0) REVERT: A 91 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8328 (ttm-80) REVERT: A 185 MET cc_start: 0.9222 (mtp) cc_final: 0.8680 (mtp) REVERT: A 231 LYS cc_start: 0.9492 (tppp) cc_final: 0.9094 (tppt) REVERT: A 241 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (m) REVERT: B 73 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8870 (tp) REVERT: B 114 TYR cc_start: 0.8429 (m-80) cc_final: 0.8214 (m-80) REVERT: B 291 TYR cc_start: 0.8997 (t80) cc_final: 0.8688 (t80) REVERT: B 301 MET cc_start: 0.8525 (ppp) cc_final: 0.8111 (ppp) REVERT: D 115 THR cc_start: 0.9116 (m) cc_final: 0.8908 (p) REVERT: E 128 MET cc_start: 0.7328 (tpp) cc_final: 0.7070 (ttm) REVERT: F 48 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7778 (p) REVERT: F 64 LYS cc_start: 0.9038 (pptt) cc_final: 0.8777 (pptt) REVERT: F 123 MET cc_start: 0.8984 (ppp) cc_final: 0.8582 (ppp) REVERT: G 129 LEU cc_start: 0.8543 (mm) cc_final: 0.8298 (mm) REVERT: H 433 PHE cc_start: 0.7903 (t80) cc_final: 0.7527 (t80) outliers start: 48 outliers final: 41 residues processed: 173 average time/residue: 0.1778 time to fit residues: 46.6651 Evaluate side-chains 180 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 THR 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 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 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 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 27 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 117 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** H 203 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 = 0.3681 r_free = 0.3681 target = 0.085758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064925 restraints weight = 42036.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066830 restraints weight = 21937.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068070 restraints weight = 14716.964| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10892 Z= 0.135 Angle : 0.669 15.934 14865 Z= 0.329 Chirality : 0.045 0.367 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.187 55.180 1826 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.20 % Allowed : 21.94 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1316 helix: 1.82 (0.29), residues: 291 sheet: 1.04 (0.26), residues: 397 loop : -0.93 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 72 HIS 0.007 0.001 HIS H 475 PHE 0.009 0.001 PHE H 150 TYR 0.014 0.001 TYR H 423 ARG 0.003 0.000 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 9) link_NAG-ASN : angle 3.65470 ( 27) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 1.77585 ( 6) hydrogen bonds : bond 0.03696 ( 493) hydrogen bonds : angle 4.63884 ( 1392) SS BOND : bond 0.00178 ( 17) SS BOND : angle 0.94936 ( 34) covalent geometry : bond 0.00306 (10864) covalent geometry : angle 0.64994 (14798) *********************** 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 187 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8363 (tt0) cc_final: 0.8097 (tt0) REVERT: A 91 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8330 (ttm-80) REVERT: A 185 MET cc_start: 0.9200 (mtp) cc_final: 0.8684 (mtp) REVERT: A 231 LYS cc_start: 0.9479 (tppp) cc_final: 0.9076 (tppt) REVERT: A 241 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 73 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 114 TYR cc_start: 0.8352 (m-80) cc_final: 0.8126 (m-80) REVERT: B 301 MET cc_start: 0.8468 (ppp) cc_final: 0.8070 (ppp) REVERT: D 115 THR cc_start: 0.9104 (m) cc_final: 0.8870 (p) REVERT: E 128 MET cc_start: 0.7293 (tpp) cc_final: 0.7038 (ttm) REVERT: F 48 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7852 (p) REVERT: F 64 LYS cc_start: 0.9038 (pptt) cc_final: 0.8782 (pptt) REVERT: F 123 MET cc_start: 0.8943 (ppp) cc_final: 0.8556 (ppp) REVERT: G 57 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7555 (ttpp) REVERT: G 129 LEU cc_start: 0.8568 (mm) cc_final: 0.8287 (mm) REVERT: H 369 MET cc_start: 0.8222 (tpt) cc_final: 0.7822 (tpt) REVERT: H 433 PHE cc_start: 0.7833 (t80) cc_final: 0.7475 (t80) outliers start: 46 outliers final: 39 residues processed: 172 average time/residue: 0.1885 time to fit residues: 48.7701 Evaluate side-chains 180 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 THR 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 432 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 203 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 = 0.3674 r_free = 0.3674 target = 0.085370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064406 restraints weight = 41943.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066294 restraints weight = 22021.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067550 restraints weight = 14808.471| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10892 Z= 0.156 Angle : 0.673 16.286 14865 Z= 0.333 Chirality : 0.046 0.367 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.195 53.938 1826 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 4.20 % Allowed : 22.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1316 helix: 1.74 (0.29), residues: 297 sheet: 1.05 (0.26), residues: 397 loop : -1.05 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 72 HIS 0.008 0.001 HIS H 475 PHE 0.012 0.001 PHE H 150 TYR 0.034 0.001 TYR B 291 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 9) link_NAG-ASN : angle 3.65434 ( 27) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 1.78021 ( 6) hydrogen bonds : bond 0.03814 ( 493) hydrogen bonds : angle 4.67057 ( 1392) SS BOND : bond 0.00222 ( 17) SS BOND : angle 0.99867 ( 34) covalent geometry : bond 0.00357 (10864) covalent geometry : angle 0.65356 (14798) ********************** 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 182 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8367 (tt0) cc_final: 0.8100 (tt0) REVERT: A 91 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8327 (ttm-80) REVERT: A 185 MET cc_start: 0.9226 (mtp) cc_final: 0.8726 (mtp) REVERT: A 231 LYS cc_start: 0.9478 (tppp) cc_final: 0.9075 (tppt) REVERT: A 241 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 73 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 301 MET cc_start: 0.8490 (ppp) cc_final: 0.8136 (ppp) REVERT: D 111 ASP cc_start: 0.8780 (m-30) cc_final: 0.8513 (m-30) REVERT: D 115 THR cc_start: 0.9095 (m) cc_final: 0.8874 (p) REVERT: E 128 MET cc_start: 0.7332 (tpp) cc_final: 0.7059 (ttm) REVERT: F 48 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7893 (p) REVERT: F 64 LYS cc_start: 0.9044 (pptt) cc_final: 0.8785 (pptt) REVERT: F 123 MET cc_start: 0.8937 (ppp) cc_final: 0.8579 (ppp) REVERT: G 129 LEU cc_start: 0.8558 (mm) cc_final: 0.8208 (mm) REVERT: H 4 MET cc_start: 0.6877 (ttm) cc_final: 0.6389 (ttp) REVERT: H 129 VAL cc_start: 0.7094 (p) cc_final: 0.6775 (t) REVERT: H 433 PHE cc_start: 0.7843 (t80) cc_final: 0.7492 (t80) outliers start: 46 outliers final: 41 residues processed: 167 average time/residue: 0.1808 time to fit residues: 45.8222 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 : 1.184 ------------------------------------------------------------------------------- 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 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 THR 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 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 98 GLU 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 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 G residue 126 ILE 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 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 432 ARG Chi-restraints excluded: chain H residue 437 TYR 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 84 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 203 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 = 0.3643 r_free = 0.3643 target = 0.083990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063425 restraints weight = 40786.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065271 restraints weight = 21264.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066475 restraints weight = 14265.334| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10892 Z= 0.210 Angle : 0.710 16.047 14865 Z= 0.353 Chirality : 0.046 0.356 1717 Planarity : 0.004 0.044 1852 Dihedral : 6.444 55.125 1826 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 4.48 % Allowed : 22.12 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1316 helix: 1.57 (0.29), residues: 293 sheet: 0.97 (0.26), residues: 395 loop : -1.04 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 72 HIS 0.008 0.001 HIS H 475 PHE 0.015 0.002 PHE H 150 TYR 0.014 0.001 TYR H 423 ARG 0.004 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 9) link_NAG-ASN : angle 3.84541 ( 27) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 1.90892 ( 6) hydrogen bonds : bond 0.04132 ( 493) hydrogen bonds : angle 4.84722 ( 1392) SS BOND : bond 0.00361 ( 17) SS BOND : angle 1.16003 ( 34) covalent geometry : bond 0.00483 (10864) covalent geometry : angle 0.68924 (14798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.34 seconds wall clock time: 66 minutes 31.27 seconds (3991.27 seconds total)