Starting phenix.real_space_refine on Mon Jun 9 14:51:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3e_45166/06_2025/9c3e_45166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3e_45166/06_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_45166/06_2025/9c3e_45166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3e_45166/06_2025/9c3e_45166.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3e_45166/06_2025/9c3e_45166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3e_45166/06_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-5710/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: 8.91, per 1000 atoms: 0.84 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: 3.15 Conformation dependent library (CDL) restraints added in 1.6 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: 1.60 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: 4.62 Time building geometry restraints manager: 3.72 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: 104.380 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.240 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.890 ------------------------------------------------------------------------------- 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 : 1.282 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: 0.2774 time to fit residues: 73.0366 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 : 1.497 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066824 restraints weight = 40919.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068702 restraints weight = 21084.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069918 restraints weight = 13992.034| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 4.72038 ( 27) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 2.08711 ( 6) hydrogen bonds : bond 0.04635 ( 493) hydrogen bonds : angle 5.16758 ( 1392) SS BOND : bond 0.00249 ( 17) SS BOND : angle 1.30651 ( 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 : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8462 (tt0) cc_final: 0.8214 (tt0) REVERT: A 58 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7092 (p0) REVERT: A 91 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8193 (ttm-80) REVERT: A 241 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7756 (t) REVERT: B 78 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: B 301 MET cc_start: 0.8737 (ppp) cc_final: 0.8323 (ppp) REVERT: D 111 ASP cc_start: 0.8652 (m-30) cc_final: 0.8384 (m-30) REVERT: D 115 THR cc_start: 0.9118 (m) cc_final: 0.8899 (p) REVERT: D 120 LEU cc_start: 0.9163 (tt) cc_final: 0.8780 (mp) REVERT: E 57 ILE cc_start: 0.8278 (mt) cc_final: 0.7901 (pt) REVERT: E 128 MET cc_start: 0.7677 (tpp) cc_final: 0.7382 (ttm) REVERT: F 125 MET cc_start: 0.8794 (ppp) cc_final: 0.8499 (ppp) REVERT: F 139 CYS cc_start: 0.9126 (t) cc_final: 0.8689 (m) REVERT: H 129 VAL cc_start: 0.7156 (p) cc_final: 0.6884 (t) REVERT: H 433 PHE cc_start: 0.7840 (t80) cc_final: 0.7326 (t80) outliers start: 49 outliers final: 26 residues processed: 186 average time/residue: 0.2035 time to fit residues: 56.4301 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 : 1.408 ------------------------------------------------------------------------------- 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: 8.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066600 restraints weight = 41449.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.068492 restraints weight = 21103.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069714 restraints weight = 13939.463| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10892 Z= 0.144 Angle : 0.658 11.037 14865 Z= 0.331 Chirality : 0.044 0.334 1717 Planarity : 0.004 0.045 1852 Dihedral : 7.219 57.669 1831 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 4.30 % Allowed : 20.29 % Favored : 75.41 % 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: 0.17 (0.23), residues: 1316 helix: 1.67 (0.30), residues: 289 sheet: 0.97 (0.25), residues: 400 loop : -1.27 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 471 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 0.00584 ( 9) link_NAG-ASN : angle 4.01645 ( 27) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 1.93810 ( 6) hydrogen bonds : bond 0.04128 ( 493) hydrogen bonds : angle 4.89083 ( 1392) SS BOND : bond 0.00593 ( 17) SS BOND : angle 1.25974 ( 34) covalent geometry : bond 0.00326 (10864) covalent geometry : angle 0.63282 (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 190 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 1.695 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: 0.8406 (tt0) cc_final: 0.8170 (tt0) REVERT: A 91 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8140 (ttm-80) REVERT: A 241 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (m) REVERT: B 301 MET cc_start: 0.8719 (ppp) cc_final: 0.8275 (ppp) REVERT: D 115 THR cc_start: 0.9135 (m) cc_final: 0.8882 (p) REVERT: D 120 LEU cc_start: 0.9148 (tt) cc_final: 0.8758 (mp) REVERT: E 57 ILE cc_start: 0.8234 (mt) cc_final: 0.7854 (pt) REVERT: E 128 MET cc_start: 0.7515 (tpp) cc_final: 0.7246 (ttm) REVERT: F 123 MET cc_start: 0.8167 (ppp) cc_final: 0.7616 (ppp) REVERT: F 137 ASP cc_start: 0.9215 (t0) cc_final: 0.8912 (t0) REVERT: H 4 MET cc_start: 0.6947 (ttp) cc_final: 0.6680 (ttp) REVERT: H 369 MET cc_start: 0.7839 (mmm) cc_final: 0.7605 (mmm) REVERT: H 433 PHE cc_start: 0.7966 (t80) cc_final: 0.7552 (t80) outliers start: 47 outliers final: 29 residues processed: 176 average time/residue: 0.2991 time to fit residues: 79.7360 Evaluate side-chains 163 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 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 E residue 141 THR 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 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: 0.0030 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4068 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.087562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066938 restraints weight = 41841.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068855 restraints weight = 21799.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070087 restraints weight = 14596.076| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1957 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= 0.115 Angle : 0.623 10.611 14865 Z= 0.313 Chirality : 0.044 0.322 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.671 57.136 1829 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 4.30 % Allowed : 19.74 % 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: 0.32 (0.23), residues: 1316 helix: 1.88 (0.30), residues: 289 sheet: 1.05 (0.26), residues: 388 loop : -1.16 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.00644 ( 9) link_NAG-ASN : angle 3.83117 ( 27) link_BETA1-4 : bond 0.00617 ( 2) link_BETA1-4 : angle 1.80656 ( 6) hydrogen bonds : bond 0.03645 ( 493) hydrogen bonds : angle 4.58293 ( 1392) SS BOND : bond 0.00214 ( 17) SS BOND : angle 1.01744 ( 34) covalent geometry : bond 0.00256 (10864) covalent geometry : angle 0.59988 (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 195 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.326 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: 0.8167 (tt0) REVERT: A 53 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8826 (mm-40) REVERT: A 91 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8199 (ttm-80) REVERT: A 185 MET cc_start: 0.9133 (mtp) cc_final: 0.8608 (mtp) REVERT: A 241 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7815 (m) REVERT: B 114 TYR cc_start: 0.8441 (m-80) cc_final: 0.8117 (m-80) REVERT: B 262 ASP cc_start: 0.8827 (t0) cc_final: 0.8605 (t0) REVERT: B 301 MET cc_start: 0.8679 (ppp) cc_final: 0.8204 (ppp) REVERT: D 28 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 111 ASP cc_start: 0.8717 (m-30) cc_final: 0.8507 (m-30) REVERT: D 115 THR cc_start: 0.9078 (m) cc_final: 0.8789 (p) REVERT: D 120 LEU cc_start: 0.9154 (tt) cc_final: 0.8715 (mp) REVERT: E 57 ILE cc_start: 0.8193 (mt) cc_final: 0.7794 (pt) REVERT: E 128 MET cc_start: 0.7284 (tpp) cc_final: 0.7040 (ttm) REVERT: F 123 MET cc_start: 0.8241 (ppp) cc_final: 0.7769 (ppp) REVERT: H 4 MET cc_start: 0.7002 (ttp) cc_final: 0.6624 (ttp) REVERT: H 201 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6887 (ttp80) REVERT: H 369 MET cc_start: 0.7844 (mmm) cc_final: 0.7639 (mmm) REVERT: H 394 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7727 (m90) outliers start: 47 outliers final: 28 residues processed: 181 average time/residue: 0.2503 time to fit residues: 67.6616 Evaluate side-chains 171 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 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: 0.8980 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.084350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064034 restraints weight = 41404.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.065850 restraints weight = 21656.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067052 restraints weight = 14527.265| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 10892 Z= 0.250 Angle : 0.718 11.888 14865 Z= 0.361 Chirality : 0.045 0.297 1717 Planarity : 0.004 0.046 1852 Dihedral : 6.869 58.615 1829 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 6.03 % Allowed : 19.20 % Favored : 74.77 % 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: 0.12 (0.23), residues: 1316 helix: 1.63 (0.29), residues: 288 sheet: 0.90 (0.26), residues: 402 loop : -1.27 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 215 HIS 0.006 0.001 HIS H 398 PHE 0.016 0.002 PHE H 150 TYR 0.027 0.002 TYR B 291 ARG 0.009 0.001 ARG H 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 9) link_NAG-ASN : angle 4.20993 ( 27) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 1.95526 ( 6) hydrogen bonds : bond 0.04485 ( 493) hydrogen bonds : angle 4.97402 ( 1392) SS BOND : bond 0.00525 ( 17) SS BOND : angle 1.68063 ( 34) covalent geometry : bond 0.00571 (10864) covalent geometry : angle 0.69091 (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 205 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8327 (ttm-80) REVERT: A 185 MET cc_start: 0.9398 (mtp) cc_final: 0.9073 (mtp) REVERT: A 241 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8017 (m) REVERT: B 301 MET cc_start: 0.8642 (ppp) cc_final: 0.8222 (ppp) REVERT: D 115 THR cc_start: 0.9083 (m) cc_final: 0.8871 (p) REVERT: D 120 LEU cc_start: 0.9203 (tt) cc_final: 0.8730 (mt) REVERT: E 128 MET cc_start: 0.7341 (tpp) cc_final: 0.7126 (ttm) REVERT: F 64 LYS cc_start: 0.9114 (pptt) cc_final: 0.8890 (pptt) REVERT: F 123 MET cc_start: 0.8710 (ppp) cc_final: 0.8297 (ppp) REVERT: H 4 MET cc_start: 0.7654 (ttp) cc_final: 0.7358 (ttp) REVERT: H 150 PHE cc_start: 0.6524 (p90) cc_final: 0.6199 (p90) REVERT: H 201 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7179 (ttp80) REVERT: H 433 PHE cc_start: 0.7961 (t80) cc_final: 0.7582 (t80) outliers start: 66 outliers final: 46 residues processed: 185 average time/residue: 0.1944 time to fit residues: 53.8046 Evaluate side-chains 179 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 118 SER Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 239 THR 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 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 99 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 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 47 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 201 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 422 MET Chi-restraints excluded: chain H residue 437 TYR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 527 CYS Chi-restraints excluded: chain H residue 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: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 243 GLN E 81 HIS G 37 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.085594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064947 restraints weight = 42077.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066811 restraints weight = 21805.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067992 restraints weight = 14656.588| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10892 Z= 0.143 Angle : 0.660 14.721 14865 Z= 0.328 Chirality : 0.045 0.320 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.601 59.614 1829 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.57 % Allowed : 20.66 % Favored : 74.77 % 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: 1.91 (0.30), residues: 288 sheet: 0.97 (0.26), residues: 395 loop : -1.13 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 PHE 0.010 0.001 PHE H 150 TYR 0.016 0.001 TYR B 291 ARG 0.003 0.000 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 9) link_NAG-ASN : angle 3.92705 ( 27) link_BETA1-4 : bond 0.00627 ( 2) link_BETA1-4 : angle 1.96620 ( 6) hydrogen bonds : bond 0.03890 ( 493) hydrogen bonds : angle 4.71292 ( 1392) SS BOND : bond 0.00210 ( 17) SS BOND : angle 1.30293 ( 34) covalent geometry : bond 0.00329 (10864) covalent geometry : angle 0.63589 (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 195 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 1.561 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: 0.8327 (tt0) cc_final: 0.8080 (tt0) REVERT: A 91 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8324 (ttm-80) REVERT: A 185 MET cc_start: 0.9350 (mtp) cc_final: 0.9063 (mtp) REVERT: A 231 LYS cc_start: 0.9484 (tppp) cc_final: 0.9087 (tppt) REVERT: A 241 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7759 (m) REVERT: B 291 TYR cc_start: 0.8936 (t80) cc_final: 0.8544 (t80) REVERT: B 301 MET cc_start: 0.8569 (ppp) cc_final: 0.8126 (ppp) REVERT: D 115 THR cc_start: 0.9120 (m) cc_final: 0.8881 (p) REVERT: D 120 LEU cc_start: 0.9114 (tt) cc_final: 0.8684 (mt) REVERT: E 128 MET cc_start: 0.7240 (tpp) cc_final: 0.7003 (ttm) REVERT: F 48 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7760 (p) REVERT: F 64 LYS cc_start: 0.9108 (pptt) cc_final: 0.8861 (pptt) REVERT: F 123 MET cc_start: 0.8794 (ppp) cc_final: 0.8400 (ppp) REVERT: G 129 LEU cc_start: 0.8298 (mm) cc_final: 0.7817 (mm) REVERT: H 4 MET cc_start: 0.7667 (ttp) cc_final: 0.7400 (ttp) REVERT: H 129 VAL cc_start: 0.7007 (p) cc_final: 0.6774 (t) REVERT: H 433 PHE cc_start: 0.7878 (t80) cc_final: 0.7509 (t80) outliers start: 50 outliers final: 39 residues processed: 179 average time/residue: 0.2616 time to fit residues: 71.8399 Evaluate side-chains 179 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 PHE 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 283 ILE 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 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 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 47 THR 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: 6.9990 chunk 123 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- 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 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 = 0.3661 r_free = 0.3661 target = 0.084748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064007 restraints weight = 42866.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065865 restraints weight = 22317.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067076 restraints weight = 14971.106| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10892 Z= 0.183 Angle : 0.674 15.373 14865 Z= 0.336 Chirality : 0.045 0.322 1717 Planarity : 0.004 0.044 1852 Dihedral : 6.615 59.276 1829 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 5.03 % Allowed : 20.29 % Favored : 74.68 % 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: 0.27 (0.23), residues: 1316 helix: 1.76 (0.29), residues: 290 sheet: 0.93 (0.26), residues: 391 loop : -1.10 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 471 HIS 0.005 0.001 HIS F 81 PHE 0.012 0.001 PHE H 150 TYR 0.015 0.001 TYR H 423 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 9) link_NAG-ASN : angle 3.96139 ( 27) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 1.88810 ( 6) hydrogen bonds : bond 0.04007 ( 493) hydrogen bonds : angle 4.79341 ( 1392) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.19945 ( 34) covalent geometry : bond 0.00421 (10864) covalent geometry : angle 0.65046 (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 192 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8351 (tt0) cc_final: 0.8125 (tt0) REVERT: A 91 ARG cc_start: 0.8677 (tpp80) cc_final: 0.8346 (ttm-80) REVERT: A 185 MET cc_start: 0.9401 (mtp) cc_final: 0.9155 (mtp) REVERT: A 231 LYS cc_start: 0.9499 (tppp) cc_final: 0.9110 (tppt) REVERT: A 241 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 73 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8930 (tp) REVERT: B 291 TYR cc_start: 0.9009 (t80) cc_final: 0.8601 (t80) REVERT: B 301 MET cc_start: 0.8514 (ppp) cc_final: 0.8104 (ppp) REVERT: E 128 MET cc_start: 0.7324 (tpp) cc_final: 0.7041 (ttm) REVERT: F 48 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7783 (p) REVERT: F 64 LYS cc_start: 0.9099 (pptt) cc_final: 0.8838 (pptt) REVERT: F 123 MET cc_start: 0.8983 (ppp) cc_final: 0.8582 (ppp) REVERT: G 129 LEU cc_start: 0.8326 (mm) cc_final: 0.7993 (mm) REVERT: H 129 VAL cc_start: 0.6956 (p) cc_final: 0.6745 (t) REVERT: H 433 PHE cc_start: 0.7905 (t80) cc_final: 0.7536 (t80) outliers start: 55 outliers final: 47 residues processed: 175 average time/residue: 0.1888 time to fit residues: 50.3062 Evaluate side-chains 181 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 118 SER 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 253 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE 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 83 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 149 TYR Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 47 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.085078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064707 restraints weight = 41404.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066573 restraints weight = 21491.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067753 restraints weight = 14353.086| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10892 Z= 0.161 Angle : 0.669 14.764 14865 Z= 0.332 Chirality : 0.045 0.344 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.521 57.257 1829 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.94 % Allowed : 21.02 % 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: 0.33 (0.23), residues: 1316 helix: 1.81 (0.29), residues: 291 sheet: 0.94 (0.26), residues: 396 loop : -1.06 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 PHE 0.012 0.001 PHE H 150 TYR 0.016 0.001 TYR H 581 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 9) link_NAG-ASN : angle 3.86357 ( 27) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.86939 ( 6) hydrogen bonds : bond 0.03913 ( 493) hydrogen bonds : angle 4.71406 ( 1392) SS BOND : bond 0.00229 ( 17) SS BOND : angle 1.10397 ( 34) covalent geometry : bond 0.00369 (10864) covalent geometry : angle 0.64664 (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 189 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8394 (tt0) cc_final: 0.8154 (tt0) REVERT: A 91 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8353 (ttm-80) REVERT: A 185 MET cc_start: 0.9429 (mtp) cc_final: 0.9215 (mtp) REVERT: A 231 LYS cc_start: 0.9488 (tppp) cc_final: 0.9099 (tppt) REVERT: A 241 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (m) REVERT: B 73 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 291 TYR cc_start: 0.8991 (t80) cc_final: 0.8645 (t80) REVERT: B 301 MET cc_start: 0.8489 (ppp) cc_final: 0.8129 (ppp) REVERT: F 48 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7775 (p) REVERT: F 123 MET cc_start: 0.8976 (ppp) cc_final: 0.8604 (ppp) REVERT: G 129 LEU cc_start: 0.8369 (mm) cc_final: 0.7956 (mm) REVERT: H 433 PHE cc_start: 0.7921 (t80) cc_final: 0.7554 (t80) outliers start: 54 outliers final: 43 residues processed: 170 average time/residue: 0.1801 time to fit residues: 46.2872 Evaluate side-chains 177 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 253 PHE 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 253 VAL 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 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 76 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 47 THR 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 369 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 = 0.3677 r_free = 0.3677 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065213 restraints weight = 41275.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067097 restraints weight = 21221.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068334 restraints weight = 14123.148| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10892 Z= 0.131 Angle : 0.664 16.146 14865 Z= 0.327 Chirality : 0.045 0.362 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.324 55.984 1826 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 4.02 % Allowed : 22.30 % 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: 0.42 (0.23), residues: 1316 helix: 1.82 (0.29), 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 0.012 0.001 TRP D 43 HIS 0.005 0.001 HIS F 81 PHE 0.009 0.001 PHE H 150 TYR 0.014 0.001 TYR H 423 ARG 0.002 0.000 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 9) link_NAG-ASN : angle 3.72106 ( 27) link_BETA1-4 : bond 0.00544 ( 2) link_BETA1-4 : angle 1.85128 ( 6) hydrogen bonds : bond 0.03676 ( 493) hydrogen bonds : angle 4.61876 ( 1392) SS BOND : bond 0.00180 ( 17) SS BOND : angle 0.97886 ( 34) covalent geometry : bond 0.00299 (10864) covalent geometry : angle 0.64323 (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 183 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8362 (tt0) cc_final: 0.8092 (tt0) REVERT: A 91 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8346 (ttm-80) REVERT: A 231 LYS cc_start: 0.9481 (tppp) cc_final: 0.9091 (tppt) REVERT: A 241 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (m) REVERT: B 73 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8835 (tp) REVERT: B 114 TYR cc_start: 0.8435 (m-80) cc_final: 0.8219 (m-80) REVERT: B 301 MET cc_start: 0.8459 (ppp) cc_final: 0.8130 (ppp) REVERT: F 123 MET cc_start: 0.8952 (ppp) cc_final: 0.8587 (ppp) REVERT: G 57 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7557 (ttpp) REVERT: G 129 LEU cc_start: 0.8342 (mm) cc_final: 0.7864 (mm) REVERT: H 4 MET cc_start: 0.6923 (ttm) cc_final: 0.6694 (ttp) REVERT: H 433 PHE cc_start: 0.7838 (t80) cc_final: 0.7499 (t80) outliers start: 44 outliers final: 40 residues processed: 168 average time/residue: 0.1809 time to fit residues: 46.2147 Evaluate side-chains 175 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 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 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 E residue 146 LEU 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 G residue 76 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 47 THR 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 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.085927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065585 restraints weight = 41417.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067478 restraints weight = 21382.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068690 restraints weight = 14201.251| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10892 Z= 0.130 Angle : 0.666 16.935 14865 Z= 0.328 Chirality : 0.045 0.388 1717 Planarity : 0.004 0.042 1852 Dihedral : 6.289 58.170 1826 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 4.20 % Allowed : 22.67 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.29), residues: 291 sheet: 1.08 (0.26), residues: 386 loop : -0.99 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 72 HIS 0.010 0.001 HIS H 475 PHE 0.009 0.001 PHE H 150 TYR 0.013 0.001 TYR H 423 ARG 0.002 0.000 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 3.63563 ( 27) link_BETA1-4 : bond 0.00482 ( 2) link_BETA1-4 : angle 1.75850 ( 6) hydrogen bonds : bond 0.03647 ( 493) hydrogen bonds : angle 4.58515 ( 1392) SS BOND : bond 0.00173 ( 17) SS BOND : angle 0.92705 ( 34) covalent geometry : bond 0.00295 (10864) covalent geometry : angle 0.64700 (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 : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8361 (tt0) cc_final: 0.8098 (tt0) REVERT: A 91 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8335 (ttm-80) REVERT: A 231 LYS cc_start: 0.9469 (tppp) cc_final: 0.9075 (tppt) REVERT: A 241 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7737 (m) REVERT: B 73 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 301 MET cc_start: 0.8442 (ppp) cc_final: 0.8151 (ppp) REVERT: F 123 MET cc_start: 0.8939 (ppp) cc_final: 0.8584 (ppp) REVERT: G 57 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7549 (ttpp) REVERT: G 129 LEU cc_start: 0.8306 (mm) cc_final: 0.7985 (mm) REVERT: H 4 MET cc_start: 0.6838 (ttm) cc_final: 0.6612 (ttp) REVERT: H 433 PHE cc_start: 0.7822 (t80) cc_final: 0.7487 (t80) outliers start: 46 outliers final: 39 residues processed: 165 average time/residue: 0.1736 time to fit residues: 44.0916 Evaluate side-chains 175 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 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 B residue 293 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 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 E residue 146 LEU 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 G residue 126 ILE Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 47 THR 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 369 MET 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: 7.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.084624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064598 restraints weight = 41932.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066700 restraints weight = 20690.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067382 restraints weight = 12808.370| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10892 Z= 0.183 Angle : 0.689 16.838 14865 Z= 0.342 Chirality : 0.045 0.363 1717 Planarity : 0.004 0.043 1852 Dihedral : 6.435 56.760 1826 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 4.30 % Allowed : 22.49 % Favored : 73.22 % 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: 0.37 (0.23), residues: 1316 helix: 1.78 (0.29), residues: 289 sheet: 1.06 (0.26), residues: 387 loop : -1.04 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 72 HIS 0.007 0.001 HIS H 475 PHE 0.015 0.001 PHE H 150 TYR 0.013 0.001 TYR H 423 ARG 0.003 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 9) link_NAG-ASN : angle 3.75095 ( 27) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 1.83017 ( 6) hydrogen bonds : bond 0.03966 ( 493) hydrogen bonds : angle 4.75108 ( 1392) SS BOND : bond 0.00284 ( 17) SS BOND : angle 1.07086 ( 34) covalent geometry : bond 0.00422 (10864) covalent geometry : angle 0.66875 (14798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4326.51 seconds wall clock time: 78 minutes 15.73 seconds (4695.73 seconds total)