Starting phenix.real_space_refine on Thu Sep 18 01:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei8_48078/09_2025/9ei8_48078.map" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 57 5.16 5 C 7751 2.51 5 N 2128 2.21 5 O 2537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12473 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2531 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 20, 'TRANS': 304} Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2523 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "C" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1397 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2538 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain: "E" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1397 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1397 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "E" 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: "F" 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 Time building chain proxies: 3.67, per 1000 atoms: 0.29 Number of scatterers: 12473 At special positions: 0 Unit cell: (88.806, 102.885, 155.952, 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 57 16.00 O 2537 8.00 N 2128 7.00 C 7751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG A 401 " - " ASN A 133 " " NAG A 402 " - " ASN A 22 " " NAG A 403 " - " ASN A 158 " " NAG A 404 " - " ASN A 126 " " NAG B 401 " - " ASN B 133 " " NAG B 402 " - " ASN B 22 " " NAG B 403 " - " ASN B 63 " " NAG B 404 " - " ASN B 158 " " NAG B 405 " - " ASN B 126 " " NAG C 301 " - " ASN C 154 " " NAG D 401 " - " ASN D 133 " " NAG D 402 " - " ASN D 22 " " NAG D 403 " - " ASN D 63 " " NAG D 404 " - " ASN D 158 " " NAG D 405 " - " ASN D 126 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG G 1 " - " ASN A 246 " " NAG H 1 " - " ASN A 38 " " NAG I 1 " - " ASN A 285 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 63 " " NAG L 1 " - " ASN B 246 " " NAG M 1 " - " ASN B 38 " " NAG N 1 " - " ASN B 285 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN D 246 " " NAG Q 1 " - " ASN D 38 " " NAG R 1 " - " ASN D 285 " " NAG S 1 " - " ASN D 165 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 621.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 32 sheets defined 26.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.760A pdb=" N ASN A 8 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 9 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 10 " --> pdb=" O ASP A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 10' Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.823A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.515A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.715A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY B 78 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.542A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.845A pdb=" N GLN C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 126 removed outlier: 3.513A pdb=" N GLU C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.506A pdb=" N GLU C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 172 removed outlier: 3.594A pdb=" N ASN C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.923A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLY D 78 " --> pdb=" O GLN D 75 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 79 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.678A pdb=" N GLY D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'E' and resid 37 through 56 removed outlier: 3.641A pdb=" N THR E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA E 43 " --> pdb=" O LYS E 39 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 126 removed outlier: 3.539A pdb=" N ASP E 86 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 125 " --> pdb=" O LYS E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.763A pdb=" N GLU E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 172 Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.637A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 125 removed outlier: 3.589A pdb=" N ILE F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 4.312A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 removed outlier: 4.003A pdb=" N ALA F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 36 removed outlier: 3.985A pdb=" N ALA C 35 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 24 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 16 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 25 " --> pdb=" O CYS A 14 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 12 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.807A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.954A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.030A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.609A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.609A pdb=" N LYS A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A 257 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.533A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 201 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'E' and resid 35 through 36 removed outlier: 4.196A pdb=" N GLY E 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY B 16 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 12 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU E 131 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.949A pdb=" N ILE B 34 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.684A pdb=" N THR B 40 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 316 " --> pdb=" O THR B 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.256A pdb=" N ILE B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.916A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 136 through 140 removed outlier: 4.837A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.675A pdb=" N GLY B 181 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP B 180 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 166 through 167 removed outlier: 3.642A pdb=" N ARG B 201 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.358A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 288 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 305 removed outlier: 3.733A pdb=" N LYS E 62 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 305 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN E 60 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 14 through 17 removed outlier: 3.855A pdb=" N GLY D 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY F 23 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 35 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.594A pdb=" N ILE D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'D' and resid 58 through 59 removed outlier: 3.650A pdb=" N VAL D 88 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 100 through 101 removed outlier: 6.838A pdb=" N ASP D 101 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N TRP D 234 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE D 179 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'D' and resid 151 through 153 Processing sheet with id=AD4, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.605A pdb=" N LEU D 244 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 205 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 131 through 132 366 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4053 1.35 - 1.47: 3185 1.47 - 1.60: 5405 1.60 - 1.73: 0 1.73 - 1.86: 75 Bond restraints: 12718 Sorted by residual: bond pdb=" CB CYS E 144 " pdb=" SG CYS E 144 " ideal model delta sigma weight residual 1.808 1.855 -0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" C SER D 54 " pdb=" N PRO D 55 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.84e+00 bond pdb=" CA THR B 248 " pdb=" C THR B 248 " ideal model delta sigma weight residual 1.520 1.534 -0.015 1.12e-02 7.97e+03 1.72e+00 bond pdb=" C SER A 54 " pdb=" N PRO A 55 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.55e+00 bond pdb=" N TYR E 141 " pdb=" CA TYR E 141 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.35e-02 5.49e+03 1.25e+00 ... (remaining 12713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16870 1.99 - 3.98: 292 3.98 - 5.97: 40 5.97 - 7.95: 8 7.95 - 9.94: 2 Bond angle restraints: 17212 Sorted by residual: angle pdb=" C ALA D 11 " pdb=" N THR D 12 " pdb=" CA THR D 12 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ALA C 5 " pdb=" N ILE C 6 " pdb=" CA ILE C 6 " ideal model delta sigma weight residual 121.97 128.82 -6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sigma weight residual 107.29 117.01 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C GLU D 62 " pdb=" N ASN D 63 " pdb=" CA ASN D 63 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C ILE E 10 " pdb=" N GLU E 11 " pdb=" CA GLU E 11 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 ... (remaining 17207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 7985 17.07 - 34.14: 277 34.14 - 51.20: 38 51.20 - 68.27: 27 68.27 - 85.34: 9 Dihedral angle restraints: 8336 sinusoidal: 4037 harmonic: 4299 Sorted by residual: dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 176.13 -83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CA SER A 54 " pdb=" C SER A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA CYS E 144 " pdb=" CB CYS E 144 " pdb=" SG CYS E 144 " pdb=" SG CYS E 148 " ideal model delta sinusoidal sigma weight residual -73.00 -3.92 -69.08 1 2.00e+01 2.50e-03 1.54e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1611 0.051 - 0.103: 287 0.103 - 0.154: 102 0.154 - 0.205: 7 0.205 - 0.257: 7 Chirality restraints: 2014 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR A 248 " pdb=" CA THR A 248 " pdb=" OG1 THR A 248 " pdb=" CG2 THR A 248 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG F 301 " pdb=" ND2 ASN F 154 " pdb=" C2 NAG F 301 " pdb=" O5 NAG F 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2011 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 102 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 103 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 226 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 227 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 323 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 324 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.025 5.00e-02 4.00e+02 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2381 2.78 - 3.31: 11239 3.31 - 3.84: 19046 3.84 - 4.37: 20885 4.37 - 4.90: 37577 Nonbonded interactions: 91128 Sorted by model distance: nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 131 " pdb=" OG1 THR A 155 " model vdw 2.256 3.040 nonbonded pdb=" OG SER F 151 " pdb=" O THR F 156 " model vdw 2.268 3.040 nonbonded pdb=" OG SER D 279 " pdb=" OG SER D 287 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR B 131 " pdb=" OG1 THR B 155 " model vdw 2.269 3.040 ... (remaining 91123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 404) selection = (chain 'B' and (resid 5 through 327 or resid 402 through 405)) selection = (chain 'D' and (resid 5 through 327 or resid 402 through 405)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.003 0.047 12787 Z= 0.142 Angle : 0.676 10.779 17401 Z= 0.350 Chirality : 0.048 0.257 2014 Planarity : 0.004 0.052 2184 Dihedral : 9.504 85.338 5522 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.19), residues: 1479 helix: -1.89 (0.20), residues: 326 sheet: 0.05 (0.35), residues: 225 loop : -1.42 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.022 0.001 TYR D 98 PHE 0.015 0.001 PHE B 120 TRP 0.014 0.001 TRP B 153 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00279 (12718) covalent geometry : angle 0.65326 (17212) SS BOND : bond 0.00264 ( 18) SS BOND : angle 1.63494 ( 36) hydrogen bonds : bond 0.29714 ( 364) hydrogen bonds : angle 9.34305 ( 1023) link_BETA1-4 : bond 0.00597 ( 21) link_BETA1-4 : angle 1.98886 ( 63) link_NAG-ASN : bond 0.00496 ( 30) link_NAG-ASN : angle 1.72150 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.541 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 SER cc_start: 0.9196 (p) cc_final: 0.8992 (p) REVERT: F 113 SER cc_start: 0.8468 (p) cc_final: 0.7673 (p) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1695 time to fit residues: 59.6435 Evaluate side-chains 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 250 ASN A 295 GLN A 311 HIS B 56 HIS B 250 ASN C 65 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 322 ASN E 125 GLN ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.075182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059091 restraints weight = 56930.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061030 restraints weight = 30718.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062316 restraints weight = 20509.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.063172 restraints weight = 15541.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.063736 restraints weight = 12788.730| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12787 Z= 0.188 Angle : 0.746 15.911 17401 Z= 0.367 Chirality : 0.048 0.295 2014 Planarity : 0.005 0.045 2184 Dihedral : 6.743 57.933 2669 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.92 % Favored : 95.88 % Rotamer: Outliers : 1.08 % Allowed : 8.91 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1479 helix: 0.61 (0.27), residues: 336 sheet: -0.20 (0.32), residues: 250 loop : -1.22 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 201 TYR 0.016 0.001 TYR A 159 PHE 0.024 0.002 PHE B 120 TRP 0.030 0.002 TRP A 180 HIS 0.014 0.002 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00408 (12718) covalent geometry : angle 0.69379 (17212) SS BOND : bond 0.00721 ( 18) SS BOND : angle 1.48739 ( 36) hydrogen bonds : bond 0.06786 ( 364) hydrogen bonds : angle 6.00178 ( 1023) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.90165 ( 63) link_NAG-ASN : bond 0.00572 ( 30) link_NAG-ASN : angle 3.48431 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.521 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: symmetry clash REVERT: A 35 GLU cc_start: 0.8906 (tt0) cc_final: 0.8697 (tt0) REVERT: A 50 GLU cc_start: 0.7923 (pm20) cc_final: 0.7719 (pm20) REVERT: B 33 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8324 (mtp-110) REVERT: B 35 GLU cc_start: 0.8643 (tt0) cc_final: 0.8288 (tt0) REVERT: B 325 GLU cc_start: 0.5401 (tm-30) cc_final: 0.5110 (tm-30) REVERT: C 85 GLU cc_start: 0.8946 (tp30) cc_final: 0.8669 (tp30) REVERT: C 133 MET cc_start: 0.8316 (ttm) cc_final: 0.7934 (mtp) REVERT: D 233 TYR cc_start: 0.9020 (m-80) cc_final: 0.8616 (m-10) REVERT: E 42 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8766 (mm-40) REVERT: E 45 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.7884 (tp) REVERT: E 158 ASP cc_start: 0.8390 (t0) cc_final: 0.8164 (t0) REVERT: F 78 GLN cc_start: 0.8486 (tt0) cc_final: 0.7968 (mt0) REVERT: F 103 GLU cc_start: 0.9025 (tt0) cc_final: 0.8635 (tp30) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.1386 time to fit residues: 23.8682 Evaluate side-chains 92 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 HIS E 49 ASN F 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058953 restraints weight = 55817.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060931 restraints weight = 29685.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062221 restraints weight = 19604.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063059 restraints weight = 14780.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.063676 restraints weight = 12175.323| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12787 Z= 0.124 Angle : 0.612 13.651 17401 Z= 0.301 Chirality : 0.044 0.199 2014 Planarity : 0.004 0.038 2184 Dihedral : 6.622 58.880 2669 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.85 % Favored : 95.94 % Rotamer: Outliers : 1.23 % Allowed : 9.75 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1479 helix: 1.43 (0.28), residues: 341 sheet: -0.29 (0.32), residues: 250 loop : -1.22 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 153 TYR 0.022 0.001 TYR B 100 PHE 0.013 0.001 PHE E 138 TRP 0.015 0.001 TRP A 180 HIS 0.007 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00261 (12718) covalent geometry : angle 0.57644 (17212) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.90520 ( 36) hydrogen bonds : bond 0.05860 ( 364) hydrogen bonds : angle 5.47292 ( 1023) link_BETA1-4 : bond 0.00481 ( 21) link_BETA1-4 : angle 1.85024 ( 63) link_NAG-ASN : bond 0.00540 ( 30) link_NAG-ASN : angle 2.47112 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8890 (tt0) cc_final: 0.8479 (tt0) REVERT: A 180 TRP cc_start: 0.9316 (p-90) cc_final: 0.8907 (p-90) REVERT: B 33 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8295 (mtp-110) REVERT: B 35 GLU cc_start: 0.8635 (tt0) cc_final: 0.8274 (tt0) REVERT: C 25 ARG cc_start: 0.8292 (ptm160) cc_final: 0.8002 (ptm160) REVERT: C 81 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8845 (mm-30) REVERT: C 85 GLU cc_start: 0.8902 (tp30) cc_final: 0.8562 (tp30) REVERT: C 133 MET cc_start: 0.8162 (ttm) cc_final: 0.7791 (mtp) REVERT: D 233 TYR cc_start: 0.9025 (m-80) cc_final: 0.8639 (m-10) REVERT: E 42 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8622 (mm-40) REVERT: E 158 ASP cc_start: 0.8415 (t0) cc_final: 0.8153 (t0) REVERT: F 42 GLN cc_start: 0.8946 (tp40) cc_final: 0.8547 (tp40) REVERT: F 103 GLU cc_start: 0.9025 (tt0) cc_final: 0.8641 (tp30) outliers start: 16 outliers final: 6 residues processed: 107 average time/residue: 0.1148 time to fit residues: 18.3450 Evaluate side-chains 88 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 18 HIS ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 56 HIS D 156 HIS F 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054244 restraints weight = 55595.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056098 restraints weight = 29520.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057317 restraints weight = 19646.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058118 restraints weight = 14899.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058647 restraints weight = 12336.543| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12787 Z= 0.213 Angle : 0.695 11.264 17401 Z= 0.340 Chirality : 0.046 0.243 2014 Planarity : 0.004 0.048 2184 Dihedral : 7.129 59.290 2669 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.73 % Favored : 95.06 % Rotamer: Outliers : 2.30 % Allowed : 9.60 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.21), residues: 1479 helix: 1.58 (0.28), residues: 347 sheet: -0.33 (0.33), residues: 236 loop : -1.22 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 25 TYR 0.023 0.002 TYR B 100 PHE 0.017 0.002 PHE E 119 TRP 0.013 0.002 TRP D 84 HIS 0.007 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00469 (12718) covalent geometry : angle 0.66622 (17212) SS BOND : bond 0.00577 ( 18) SS BOND : angle 1.37202 ( 36) hydrogen bonds : bond 0.05301 ( 364) hydrogen bonds : angle 5.32109 ( 1023) link_BETA1-4 : bond 0.00429 ( 21) link_BETA1-4 : angle 1.89360 ( 63) link_NAG-ASN : bond 0.00528 ( 30) link_NAG-ASN : angle 2.30404 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.456 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 48 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 50 GLU cc_start: 0.8359 (pm20) cc_final: 0.7982 (pm20) REVERT: A 168 MET cc_start: 0.8927 (tpt) cc_final: 0.8676 (tpt) REVERT: B 33 ARG cc_start: 0.8825 (ttm110) cc_final: 0.8395 (mtp-110) REVERT: B 35 GLU cc_start: 0.8709 (tt0) cc_final: 0.8312 (tt0) REVERT: C 21 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: C 25 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7525 (mtm110) REVERT: C 85 GLU cc_start: 0.8905 (tp30) cc_final: 0.8586 (tp30) REVERT: E 42 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8823 (mm-40) REVERT: E 141 TYR cc_start: 0.6402 (m-80) cc_final: 0.6039 (m-80) REVERT: E 158 ASP cc_start: 0.8480 (t0) cc_final: 0.8140 (t0) REVERT: F 42 GLN cc_start: 0.9073 (tp40) cc_final: 0.8606 (tp40) REVERT: F 103 GLU cc_start: 0.9001 (tt0) cc_final: 0.8604 (tp30) outliers start: 30 outliers final: 17 residues processed: 112 average time/residue: 0.1226 time to fit residues: 19.9507 Evaluate side-chains 91 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain C residue 9 PHE Chi-restraints excluded: chain C residue 21 TRP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 159 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 134 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053937 restraints weight = 55187.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055813 restraints weight = 29403.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057059 restraints weight = 19508.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.057878 restraints weight = 14806.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058444 restraints weight = 12232.484| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12787 Z= 0.132 Angle : 0.600 11.096 17401 Z= 0.294 Chirality : 0.044 0.190 2014 Planarity : 0.003 0.038 2184 Dihedral : 6.905 59.507 2669 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.06 % Favored : 95.74 % Rotamer: Outliers : 2.00 % Allowed : 10.75 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1479 helix: 1.85 (0.28), residues: 347 sheet: -0.29 (0.32), residues: 242 loop : -1.17 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 25 TYR 0.016 0.001 TYR B 100 PHE 0.010 0.001 PHE F 138 TRP 0.008 0.001 TRP D 84 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00291 (12718) covalent geometry : angle 0.57218 (17212) SS BOND : bond 0.00211 ( 18) SS BOND : angle 1.00969 ( 36) hydrogen bonds : bond 0.04781 ( 364) hydrogen bonds : angle 5.08122 ( 1023) link_BETA1-4 : bond 0.00464 ( 21) link_BETA1-4 : angle 1.83365 ( 63) link_NAG-ASN : bond 0.00472 ( 30) link_NAG-ASN : angle 2.08248 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8974 (tpt) cc_final: 0.8766 (tpt) REVERT: B 33 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8383 (mtp-110) REVERT: C 21 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: C 65 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (mm-40) REVERT: C 85 GLU cc_start: 0.8825 (tp30) cc_final: 0.8535 (tp30) REVERT: C 133 MET cc_start: 0.8162 (ttm) cc_final: 0.7903 (mtp) REVERT: E 115 MET cc_start: 0.9438 (mmm) cc_final: 0.9198 (tpp) REVERT: E 141 TYR cc_start: 0.6471 (m-80) cc_final: 0.5979 (m-80) REVERT: E 158 ASP cc_start: 0.8532 (t0) cc_final: 0.8152 (t0) REVERT: F 42 GLN cc_start: 0.9058 (tp40) cc_final: 0.8590 (tp-100) REVERT: F 103 GLU cc_start: 0.9025 (tt0) cc_final: 0.8634 (tp30) REVERT: F 125 GLN cc_start: 0.8438 (mt0) cc_final: 0.8037 (mp10) outliers start: 26 outliers final: 16 residues processed: 101 average time/residue: 0.1209 time to fit residues: 18.0243 Evaluate side-chains 93 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 9 PHE Chi-restraints excluded: chain C residue 21 TRP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 159 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 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 = 0.3472 r_free = 0.3472 target = 0.068953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054745 restraints weight = 52274.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056487 restraints weight = 28525.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057623 restraints weight = 19114.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058355 restraints weight = 14552.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.058890 restraints weight = 12092.163| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12787 Z= 0.140 Angle : 0.603 10.758 17401 Z= 0.294 Chirality : 0.044 0.199 2014 Planarity : 0.004 0.052 2184 Dihedral : 6.898 60.000 2669 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 2.07 % Allowed : 11.44 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1479 helix: 1.95 (0.28), residues: 347 sheet: -0.21 (0.33), residues: 245 loop : -1.11 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 163 TYR 0.014 0.001 TYR B 100 PHE 0.009 0.001 PHE F 138 TRP 0.009 0.001 TRP C 14 HIS 0.011 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00312 (12718) covalent geometry : angle 0.57552 (17212) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.88417 ( 36) hydrogen bonds : bond 0.04600 ( 364) hydrogen bonds : angle 5.00083 ( 1023) link_BETA1-4 : bond 0.00462 ( 21) link_BETA1-4 : angle 1.84069 ( 63) link_NAG-ASN : bond 0.00435 ( 30) link_NAG-ASN : angle 2.06116 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8681 (ttm110) cc_final: 0.8321 (mtp-110) REVERT: C 21 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: C 85 GLU cc_start: 0.8686 (tp30) cc_final: 0.8397 (tp30) REVERT: E 25 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (mtt180) REVERT: E 42 GLN cc_start: 0.9361 (mm-40) cc_final: 0.8929 (mm-40) REVERT: E 115 MET cc_start: 0.9375 (mmm) cc_final: 0.9103 (tpp) REVERT: E 158 ASP cc_start: 0.8457 (t0) cc_final: 0.8081 (t0) REVERT: F 42 GLN cc_start: 0.9060 (tp40) cc_final: 0.8534 (tp-100) REVERT: F 103 GLU cc_start: 0.8829 (tt0) cc_final: 0.8554 (tp30) REVERT: F 123 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8536 (ptpp) REVERT: F 125 GLN cc_start: 0.8447 (mt0) cc_final: 0.8120 (mp10) outliers start: 27 outliers final: 21 residues processed: 97 average time/residue: 0.1230 time to fit residues: 17.4207 Evaluate side-chains 97 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 9 PHE Chi-restraints excluded: chain C residue 21 TRP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 159 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 0.0370 chunk 7 optimal weight: 0.0030 chunk 145 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.070200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055669 restraints weight = 54372.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057424 restraints weight = 29459.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.058583 restraints weight = 19866.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059363 restraints weight = 15167.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059876 restraints weight = 12588.331| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12787 Z= 0.104 Angle : 0.582 10.450 17401 Z= 0.284 Chirality : 0.044 0.195 2014 Planarity : 0.003 0.048 2184 Dihedral : 6.709 59.560 2669 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.99 % Favored : 95.81 % Rotamer: Outliers : 1.69 % Allowed : 12.29 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.21), residues: 1479 helix: 2.04 (0.28), residues: 347 sheet: -0.19 (0.33), residues: 245 loop : -1.05 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 269 TYR 0.025 0.001 TYR E 141 PHE 0.009 0.001 PHE E 24 TRP 0.007 0.001 TRP C 92 HIS 0.005 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00221 (12718) covalent geometry : angle 0.55531 (17212) SS BOND : bond 0.00183 ( 18) SS BOND : angle 0.91533 ( 36) hydrogen bonds : bond 0.04363 ( 364) hydrogen bonds : angle 4.83989 ( 1023) link_BETA1-4 : bond 0.00485 ( 21) link_BETA1-4 : angle 1.81482 ( 63) link_NAG-ASN : bond 0.00451 ( 30) link_NAG-ASN : angle 1.97155 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.518 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: B 33 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8371 (mtp-110) REVERT: C 65 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7665 (mm-40) REVERT: C 81 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8674 (mm-30) REVERT: C 85 GLU cc_start: 0.8801 (tp30) cc_final: 0.8518 (tp30) REVERT: E 25 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7765 (mtt180) REVERT: E 42 GLN cc_start: 0.9402 (mm-40) cc_final: 0.8958 (mm-40) REVERT: E 141 TYR cc_start: 0.6510 (m-80) cc_final: 0.6197 (m-80) REVERT: E 158 ASP cc_start: 0.8465 (t0) cc_final: 0.8075 (t0) REVERT: F 42 GLN cc_start: 0.9096 (tp40) cc_final: 0.8596 (tp-100) REVERT: F 103 GLU cc_start: 0.8974 (tt0) cc_final: 0.8594 (tp30) REVERT: F 125 GLN cc_start: 0.8414 (mt0) cc_final: 0.8028 (mp10) outliers start: 22 outliers final: 16 residues processed: 101 average time/residue: 0.1174 time to fit residues: 17.2823 Evaluate side-chains 95 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 159 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055755 restraints weight = 51474.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057472 restraints weight = 27780.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058599 restraints weight = 18532.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059404 restraints weight = 14090.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059899 restraints weight = 11518.491| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12787 Z= 0.114 Angle : 0.586 10.275 17401 Z= 0.286 Chirality : 0.044 0.200 2014 Planarity : 0.003 0.045 2184 Dihedral : 6.656 59.708 2669 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.99 % Favored : 95.74 % Rotamer: Outliers : 1.69 % Allowed : 12.67 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1479 helix: 2.07 (0.29), residues: 347 sheet: -0.16 (0.33), residues: 245 loop : -1.04 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 163 TYR 0.019 0.001 TYR E 141 PHE 0.009 0.001 PHE F 3 TRP 0.008 0.001 TRP D 127 HIS 0.006 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00250 (12718) covalent geometry : angle 0.56059 (17212) SS BOND : bond 0.00232 ( 18) SS BOND : angle 0.92000 ( 36) hydrogen bonds : bond 0.04209 ( 364) hydrogen bonds : angle 4.82852 ( 1023) link_BETA1-4 : bond 0.00464 ( 21) link_BETA1-4 : angle 1.79091 ( 63) link_NAG-ASN : bond 0.00417 ( 30) link_NAG-ASN : angle 1.93664 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8644 (ttm110) cc_final: 0.8295 (mtp-110) REVERT: C 65 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7755 (mm-40) REVERT: C 85 GLU cc_start: 0.8638 (tp30) cc_final: 0.8373 (tp30) REVERT: E 25 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: E 42 GLN cc_start: 0.9398 (mm-40) cc_final: 0.8937 (mm-40) REVERT: E 145 ASP cc_start: 0.8598 (p0) cc_final: 0.8338 (p0) REVERT: E 158 ASP cc_start: 0.8426 (t0) cc_final: 0.8016 (t0) REVERT: F 42 GLN cc_start: 0.9078 (tp40) cc_final: 0.8514 (tp-100) outliers start: 22 outliers final: 16 residues processed: 101 average time/residue: 0.1156 time to fit residues: 17.0553 Evaluate side-chains 92 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055034 restraints weight = 51355.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056748 restraints weight = 27968.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057911 restraints weight = 18677.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058674 restraints weight = 14093.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059167 restraints weight = 11577.595| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12787 Z= 0.122 Angle : 0.601 9.619 17401 Z= 0.294 Chirality : 0.044 0.200 2014 Planarity : 0.003 0.044 2184 Dihedral : 6.646 59.664 2669 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.19 % Favored : 95.54 % Rotamer: Outliers : 1.77 % Allowed : 12.98 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.21), residues: 1479 helix: 2.06 (0.28), residues: 344 sheet: -0.13 (0.33), residues: 245 loop : -1.02 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 163 TYR 0.017 0.001 TYR E 141 PHE 0.013 0.001 PHE E 119 TRP 0.008 0.001 TRP D 84 HIS 0.006 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00273 (12718) covalent geometry : angle 0.57674 (17212) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.92108 ( 36) hydrogen bonds : bond 0.04125 ( 364) hydrogen bonds : angle 4.82690 ( 1023) link_BETA1-4 : bond 0.00455 ( 21) link_BETA1-4 : angle 1.77767 ( 63) link_NAG-ASN : bond 0.00411 ( 30) link_NAG-ASN : angle 1.89004 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8350 (mtp-110) REVERT: C 21 TRP cc_start: 0.8638 (OUTLIER) cc_final: 0.7967 (m-10) REVERT: C 65 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7752 (mm-40) REVERT: C 85 GLU cc_start: 0.8753 (tp30) cc_final: 0.8476 (tp30) REVERT: E 25 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7937 (mtt180) REVERT: E 42 GLN cc_start: 0.9426 (mm-40) cc_final: 0.8994 (mm-40) REVERT: E 115 MET cc_start: 0.9315 (mmm) cc_final: 0.8900 (tpp) REVERT: E 145 ASP cc_start: 0.8574 (p0) cc_final: 0.8268 (p0) REVERT: E 158 ASP cc_start: 0.8452 (t0) cc_final: 0.8045 (t0) REVERT: F 42 GLN cc_start: 0.9082 (tp40) cc_final: 0.8868 (tp-100) REVERT: F 105 GLN cc_start: 0.8783 (mm110) cc_final: 0.8401 (mm110) REVERT: F 113 SER cc_start: 0.8951 (p) cc_final: 0.8721 (t) REVERT: F 117 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8819 (mtmt) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.1128 time to fit residues: 16.3706 Evaluate side-chains 96 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain C residue 21 TRP Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain F residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 145 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 47 GLN ** 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 = 0.3521 r_free = 0.3521 target = 0.070165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056391 restraints weight = 51292.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058106 restraints weight = 27556.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059241 restraints weight = 18302.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060027 restraints weight = 13803.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060555 restraints weight = 11280.547| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12787 Z= 0.104 Angle : 0.591 9.390 17401 Z= 0.289 Chirality : 0.044 0.197 2014 Planarity : 0.003 0.043 2184 Dihedral : 6.562 59.551 2669 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.92 % Favored : 95.81 % Rotamer: Outliers : 1.54 % Allowed : 13.13 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1479 helix: 2.11 (0.28), residues: 344 sheet: -0.15 (0.33), residues: 245 loop : -1.00 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 25 TYR 0.017 0.001 TYR E 141 PHE 0.008 0.001 PHE D 125 TRP 0.010 0.001 TRP C 14 HIS 0.006 0.001 HIS C 26 Details of bonding type rmsd covalent geometry : bond 0.00229 (12718) covalent geometry : angle 0.56791 (17212) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.97838 ( 36) hydrogen bonds : bond 0.03957 ( 364) hydrogen bonds : angle 4.77374 ( 1023) link_BETA1-4 : bond 0.00474 ( 21) link_BETA1-4 : angle 1.76254 ( 63) link_NAG-ASN : bond 0.00399 ( 30) link_NAG-ASN : angle 1.83517 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8342 (mtp-110) REVERT: B 35 GLU cc_start: 0.8573 (tt0) cc_final: 0.8219 (tt0) REVERT: C 65 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7716 (mm-40) REVERT: D 168 MET cc_start: 0.7639 (tpp) cc_final: 0.7385 (tpt) REVERT: E 25 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7887 (mtt180) REVERT: E 42 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8962 (mm-40) REVERT: E 115 MET cc_start: 0.9322 (mmm) cc_final: 0.8901 (tpp) REVERT: E 158 ASP cc_start: 0.8456 (t0) cc_final: 0.8042 (t0) REVERT: F 42 GLN cc_start: 0.9084 (tp40) cc_final: 0.8539 (tp-100) REVERT: F 105 GLN cc_start: 0.8802 (mm110) cc_final: 0.8392 (mm110) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.1088 time to fit residues: 16.8328 Evaluate side-chains 93 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN F 12 ASN F 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.050212 restraints weight = 53744.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051786 restraints weight = 29896.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052831 restraints weight = 20259.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053539 restraints weight = 15606.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054018 restraints weight = 13022.448| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12787 Z= 0.323 Angle : 0.807 16.393 17401 Z= 0.398 Chirality : 0.048 0.226 2014 Planarity : 0.005 0.067 2184 Dihedral : 7.540 59.759 2669 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 1.69 % Allowed : 13.52 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.21), residues: 1479 helix: 1.72 (0.28), residues: 338 sheet: -0.51 (0.35), residues: 228 loop : -1.29 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 163 TYR 0.021 0.002 TYR F 157 PHE 0.053 0.002 PHE F 138 TRP 0.023 0.002 TRP F 14 HIS 0.017 0.002 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00715 (12718) covalent geometry : angle 0.78575 (17212) SS BOND : bond 0.00553 ( 18) SS BOND : angle 1.43473 ( 36) hydrogen bonds : bond 0.04773 ( 364) hydrogen bonds : angle 5.34670 ( 1023) link_BETA1-4 : bond 0.00447 ( 21) link_BETA1-4 : angle 1.98395 ( 63) link_NAG-ASN : bond 0.00525 ( 30) link_NAG-ASN : angle 2.09248 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.47 seconds wall clock time: 35 minutes 36.05 seconds (2136.05 seconds total)