Starting phenix.real_space_refine on Sat Feb 7 13:41:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540.map" model { file = "/net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qoj_18540/02_2026/8qoj_18540_trim.cif" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 156 5.16 5 C 11244 2.51 5 N 2724 2.21 5 O 3006 1.98 5 F 72 1.80 5 H 16908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34110 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "D" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "E" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "F" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "H" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "I" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "J" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "L" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2803 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 6.37, per 1000 atoms: 0.19 Number of scatterers: 34110 At special positions: 0 Unit cell: (112.2, 99, 147.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 F 72 9.00 O 3006 8.00 N 2724 7.00 C 11244 6.00 H 16908 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " 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 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 804.1 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 76.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 3.559A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 101 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 222 removed outlier: 4.225A pdb=" N ILE A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'B' and resid 21 through 46 removed outlier: 5.374A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 101 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 222 removed outlier: 3.833A pdb=" N ILE B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'C' and resid 20 through 46 removed outlier: 5.364A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 101 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 222 removed outlier: 4.004A pdb=" N ILE C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'D' and resid 20 through 46 removed outlier: 3.817A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 101 Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 222 removed outlier: 3.851A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'D' and resid 276 through 282 removed outlier: 3.671A pdb=" N ILE D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 46 removed outlier: 3.695A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 101 Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 222 removed outlier: 3.845A pdb=" N ILE E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 201 " --> pdb=" O ARG E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'E' and resid 276 through 282 Processing helix chain 'F' and resid 20 through 46 removed outlier: 5.385A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 101 Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 222 removed outlier: 3.899A pdb=" N ILE F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE F 201 " --> pdb=" O ARG F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'G' and resid 20 through 46 removed outlier: 5.440A pdb=" N GLU G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 101 Proline residue: G 89 - end of helix Processing helix chain 'G' and resid 195 through 222 removed outlier: 4.083A pdb=" N ILE G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE G 201 " --> pdb=" O ARG G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'G' and resid 276 through 282 removed outlier: 3.690A pdb=" N ILE G 280 " --> pdb=" O GLY G 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 46 removed outlier: 5.418A pdb=" N GLU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 101 Proline residue: H 89 - end of helix Processing helix chain 'H' and resid 195 through 222 removed outlier: 4.327A pdb=" N ILE H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE H 201 " --> pdb=" O ARG H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'H' and resid 276 through 282 Processing helix chain 'I' and resid 20 through 46 removed outlier: 5.370A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 101 Proline residue: I 89 - end of helix Processing helix chain 'I' and resid 195 through 222 removed outlier: 4.068A pdb=" N ILE I 200 " --> pdb=" O SER I 196 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'I' and resid 276 through 282 removed outlier: 3.651A pdb=" N ILE I 280 " --> pdb=" O GLY I 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 46 removed outlier: 5.363A pdb=" N GLU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 101 Proline residue: J 89 - end of helix removed outlier: 3.526A pdb=" N SER J 101 " --> pdb=" O SER J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 removed outlier: 3.671A pdb=" N TYR J 199 " --> pdb=" O ILE J 195 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 201 " --> pdb=" O ARG J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'J' and resid 276 through 282 removed outlier: 3.601A pdb=" N ILE J 280 " --> pdb=" O GLY J 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 46 removed outlier: 5.399A pdb=" N GLU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 101 Proline residue: K 89 - end of helix Processing helix chain 'K' and resid 195 through 222 removed outlier: 3.937A pdb=" N ILE K 200 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 201 " --> pdb=" O ARG K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'K' and resid 276 through 281 removed outlier: 3.537A pdb=" N ILE K 280 " --> pdb=" O GLY K 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 46 removed outlier: 5.342A pdb=" N GLU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 101 Proline residue: L 89 - end of helix Processing helix chain 'L' and resid 195 through 222 removed outlier: 4.030A pdb=" N ILE L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L 201 " --> pdb=" O ARG L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 276 Processing helix chain 'L' and resid 276 through 282 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.505A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.500A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.509A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 1267 hydrogen bonds defined for protein. 3738 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: 6.43 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16872 1.03 - 1.23: 119 1.23 - 1.42: 7441 1.42 - 1.62: 9744 1.62 - 1.82: 204 Bond restraints: 34380 Sorted by residual: bond pdb=" CB ARG B 278 " pdb=" CG ARG B 278 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CB MET J 21 " pdb=" CG MET J 21 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 bond pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.22e-01 bond pdb=" CB MET C 21 " pdb=" CG MET C 21 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.02e-01 bond pdb=" C LYS L 238 " pdb=" O LYS L 238 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.50e-03 1.11e+04 7.38e-01 ... (remaining 34375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 61253 1.68 - 3.36: 613 3.36 - 5.05: 66 5.05 - 6.73: 7 6.73 - 8.41: 5 Bond angle restraints: 61944 Sorted by residual: angle pdb=" C LYS L 238 " pdb=" CA LYS L 238 " pdb=" CB LYS L 238 " ideal model delta sigma weight residual 117.23 111.77 5.46 1.36e+00 5.41e-01 1.61e+01 angle pdb=" CB MET J 21 " pdb=" CG MET J 21 " pdb=" SD MET J 21 " ideal model delta sigma weight residual 112.70 121.11 -8.41 3.00e+00 1.11e-01 7.86e+00 angle pdb=" CB MET C 21 " pdb=" CG MET C 21 " pdb=" SD MET C 21 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" CB MET F 21 " pdb=" CG MET F 21 " pdb=" SD MET F 21 " ideal model delta sigma weight residual 112.70 120.94 -8.24 3.00e+00 1.11e-01 7.54e+00 angle pdb=" CB ARG B 278 " pdb=" CG ARG B 278 " pdb=" CD ARG B 278 " ideal model delta sigma weight residual 111.30 117.54 -6.24 2.30e+00 1.89e-01 7.36e+00 ... (remaining 61939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14545 17.95 - 35.89: 1191 35.89 - 53.84: 450 53.84 - 71.79: 145 71.79 - 89.74: 13 Dihedral angle restraints: 16344 sinusoidal: 8748 harmonic: 7596 Sorted by residual: dihedral pdb=" CB CYS K 62 " pdb=" SG CYS K 62 " pdb=" SG CYS K 236 " pdb=" CB CYS K 236 " ideal model delta sinusoidal sigma weight residual 93.00 121.41 -28.41 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " pdb=" CD GLU C 241 " pdb=" OE1 GLU C 241 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG C 24 " pdb=" CD ARG C 24 " pdb=" NE ARG C 24 " pdb=" CZ ARG C 24 " ideal model delta sinusoidal sigma weight residual -90.00 -134.22 44.22 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 16341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1674 0.026 - 0.051: 502 0.051 - 0.077: 395 0.077 - 0.103: 121 0.103 - 0.129: 44 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL J 225 " pdb=" N VAL J 225 " pdb=" C VAL J 225 " pdb=" CB VAL J 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 2733 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 278 " 0.154 9.50e-02 1.11e+02 5.15e-02 3.08e+00 pdb=" NE ARG C 278 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 278 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 278 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 278 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 278 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 278 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG C 278 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG C 278 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C VAL J 38 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL J 38 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA J 39 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 38 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C VAL D 38 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL D 38 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA D 39 " -0.008 2.00e-02 2.50e+03 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 5959 2.29 - 2.87: 75200 2.87 - 3.44: 88103 3.44 - 4.02: 120385 4.02 - 4.60: 180940 Nonbonded interactions: 470587 Sorted by model distance: nonbonded pdb=" HE ARG K 34 " pdb=" O HOH K 502 " model vdw 1.712 2.450 nonbonded pdb="HE22 GLN C 59 " pdb=" OE1 GLN J 59 " model vdw 1.724 2.450 nonbonded pdb=" HH TYR H 199 " pdb=" OE2 GLU H 271 " model vdw 1.742 2.450 nonbonded pdb=" OD2 ASP D 68 " pdb=" HG1 THR E 248 " model vdw 1.748 2.450 nonbonded pdb=" HH TYR A 199 " pdb=" OE2 GLU A 271 " model vdw 1.749 2.450 ... (remaining 470582 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 28.580 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 0.002 0.031 17508 Z= 0.115 Angle : 0.512 8.411 23868 Z= 0.267 Chirality : 0.039 0.129 2736 Planarity : 0.003 0.069 2868 Dihedral : 17.163 89.737 6276 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.60 % Allowed : 16.29 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.18), residues: 2028 helix: 3.14 (0.12), residues: 1524 sheet: 0.20 (0.36), residues: 204 loop : -0.05 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 278 TYR 0.013 0.001 TYR C 96 PHE 0.006 0.001 PHE F 258 TRP 0.008 0.001 TRP F 277 HIS 0.011 0.001 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00247 (17472) covalent geometry : angle 0.51106 (23796) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.70116 ( 72) hydrogen bonds : bond 0.13428 ( 1267) hydrogen bonds : angle 4.44311 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.930 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5897 (t) cc_final: 0.5575 (p) REVERT: A 47 ASP cc_start: 0.6894 (t70) cc_final: 0.6658 (t70) REVERT: A 91 LEU cc_start: 0.4988 (mt) cc_final: 0.4486 (tm) REVERT: A 202 GLN cc_start: 0.5787 (tt0) cc_final: 0.5577 (tm-30) REVERT: A 207 ASN cc_start: 0.5884 (OUTLIER) cc_final: 0.5458 (m-40) REVERT: A 210 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6208 (mm-30) REVERT: A 230 GLU cc_start: 0.7207 (mp0) cc_final: 0.6727 (mt-10) REVERT: B 29 VAL cc_start: 0.5645 (t) cc_final: 0.5367 (p) REVERT: B 88 THR cc_start: 0.5243 (OUTLIER) cc_final: 0.4845 (m) REVERT: B 199 TYR cc_start: 0.4860 (t80) cc_final: 0.4465 (t80) REVERT: B 207 ASN cc_start: 0.6123 (m-40) cc_final: 0.5515 (m110) REVERT: B 210 GLU cc_start: 0.6334 (tp30) cc_final: 0.5993 (mm-30) REVERT: B 230 GLU cc_start: 0.7250 (mp0) cc_final: 0.6739 (mt-10) REVERT: B 233 ARG cc_start: 0.6255 (ttt180) cc_final: 0.5643 (ttm170) REVERT: C 88 THR cc_start: 0.5247 (OUTLIER) cc_final: 0.4891 (m) REVERT: C 91 LEU cc_start: 0.4948 (mt) cc_final: 0.4450 (tm) REVERT: C 199 TYR cc_start: 0.4983 (t80) cc_final: 0.4547 (t80) REVERT: C 202 GLN cc_start: 0.5880 (tt0) cc_final: 0.5610 (tt0) REVERT: C 206 ARG cc_start: 0.6126 (ttp-170) cc_final: 0.5815 (ttp-170) REVERT: C 207 ASN cc_start: 0.6042 (m-40) cc_final: 0.5797 (m110) REVERT: C 230 GLU cc_start: 0.7151 (mp0) cc_final: 0.6548 (mt-10) REVERT: C 239 GLU cc_start: 0.7297 (tt0) cc_final: 0.6819 (mt-10) REVERT: D 47 ASP cc_start: 0.6971 (t70) cc_final: 0.6733 (t70) REVERT: D 88 THR cc_start: 0.5343 (OUTLIER) cc_final: 0.5077 (m) REVERT: D 91 LEU cc_start: 0.5130 (mt) cc_final: 0.4739 (tt) REVERT: D 199 TYR cc_start: 0.4692 (t80) cc_final: 0.4180 (t80) REVERT: D 207 ASN cc_start: 0.6003 (m-40) cc_final: 0.5553 (m-40) REVERT: D 210 GLU cc_start: 0.6448 (mm-30) cc_final: 0.6210 (mm-30) REVERT: D 220 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6743 (mt) REVERT: D 230 GLU cc_start: 0.6865 (tt0) cc_final: 0.5640 (pm20) REVERT: D 239 GLU cc_start: 0.6881 (tt0) cc_final: 0.6181 (tt0) REVERT: E 29 VAL cc_start: 0.5545 (t) cc_final: 0.5233 (p) REVERT: E 88 THR cc_start: 0.5275 (OUTLIER) cc_final: 0.4870 (m) REVERT: E 199 TYR cc_start: 0.4762 (t80) cc_final: 0.4278 (t80) REVERT: E 206 ARG cc_start: 0.6035 (ttp-170) cc_final: 0.5754 (ttp-170) REVERT: E 207 ASN cc_start: 0.6199 (OUTLIER) cc_final: 0.5576 (m110) REVERT: E 210 GLU cc_start: 0.6348 (tp30) cc_final: 0.6039 (mm-30) REVERT: E 230 GLU cc_start: 0.7199 (mp0) cc_final: 0.6719 (mt-10) REVERT: E 233 ARG cc_start: 0.6205 (ttt180) cc_final: 0.5661 (ttm170) REVERT: F 91 LEU cc_start: 0.4844 (mt) cc_final: 0.4360 (tm) REVERT: F 199 TYR cc_start: 0.4945 (t80) cc_final: 0.4582 (t80) REVERT: F 202 GLN cc_start: 0.5755 (tt0) cc_final: 0.5501 (tt0) REVERT: F 206 ARG cc_start: 0.6095 (ttp-170) cc_final: 0.5811 (ttp-170) REVERT: F 207 ASN cc_start: 0.5929 (m-40) cc_final: 0.5699 (m110) REVERT: F 230 GLU cc_start: 0.7176 (mp0) cc_final: 0.6622 (mt-10) REVERT: F 239 GLU cc_start: 0.7268 (tt0) cc_final: 0.6834 (mt-10) REVERT: G 88 THR cc_start: 0.5221 (OUTLIER) cc_final: 0.4838 (m) REVERT: G 91 LEU cc_start: 0.4834 (mt) cc_final: 0.4359 (tm) REVERT: G 199 TYR cc_start: 0.4890 (t80) cc_final: 0.4554 (t80) REVERT: G 202 GLN cc_start: 0.5810 (tt0) cc_final: 0.5514 (tt0) REVERT: G 206 ARG cc_start: 0.6149 (ttp-170) cc_final: 0.5848 (ttp-170) REVERT: G 207 ASN cc_start: 0.5996 (m-40) cc_final: 0.5753 (m110) REVERT: G 230 GLU cc_start: 0.6906 (mp0) cc_final: 0.6625 (mt-10) REVERT: G 239 GLU cc_start: 0.7251 (tt0) cc_final: 0.6920 (mt-10) REVERT: H 29 VAL cc_start: 0.5941 (t) cc_final: 0.5622 (p) REVERT: H 47 ASP cc_start: 0.6940 (t70) cc_final: 0.6705 (t70) REVERT: H 88 THR cc_start: 0.5261 (OUTLIER) cc_final: 0.4987 (m) REVERT: H 91 LEU cc_start: 0.5038 (mt) cc_final: 0.4547 (tm) REVERT: H 202 GLN cc_start: 0.5780 (tt0) cc_final: 0.5540 (tm-30) REVERT: H 207 ASN cc_start: 0.6007 (m-40) cc_final: 0.5584 (m-40) REVERT: H 210 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6215 (mm-30) REVERT: H 230 GLU cc_start: 0.7152 (mp0) cc_final: 0.6677 (mt-10) REVERT: H 233 ARG cc_start: 0.6149 (ttt180) cc_final: 0.5645 (ttm170) REVERT: I 47 ASP cc_start: 0.6750 (t70) cc_final: 0.6445 (t70) REVERT: I 199 TYR cc_start: 0.4787 (t80) cc_final: 0.4238 (t80) REVERT: I 202 GLN cc_start: 0.5736 (tt0) cc_final: 0.5519 (tt0) REVERT: I 207 ASN cc_start: 0.6137 (m-40) cc_final: 0.5550 (m110) REVERT: I 210 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6373 (mm-30) REVERT: I 230 GLU cc_start: 0.7246 (mp0) cc_final: 0.6735 (mt-10) REVERT: J 88 THR cc_start: 0.5005 (OUTLIER) cc_final: 0.4634 (m) REVERT: J 202 GLN cc_start: 0.5805 (tm-30) cc_final: 0.5526 (tm-30) REVERT: J 205 PHE cc_start: 0.5922 (m-80) cc_final: 0.5557 (m-80) REVERT: J 207 ASN cc_start: 0.5996 (t0) cc_final: 0.5716 (t0) REVERT: J 210 GLU cc_start: 0.6578 (tp30) cc_final: 0.6217 (mm-30) REVERT: J 220 LEU cc_start: 0.6770 (tp) cc_final: 0.6558 (tp) REVERT: J 230 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: J 232 ASN cc_start: 0.6743 (t0) cc_final: 0.6252 (p0) REVERT: J 233 ARG cc_start: 0.6427 (ttt180) cc_final: 0.6127 (ttm170) REVERT: K 29 VAL cc_start: 0.5911 (t) cc_final: 0.5525 (p) REVERT: K 47 ASP cc_start: 0.6874 (t70) cc_final: 0.6640 (t70) REVERT: K 91 LEU cc_start: 0.5103 (mt) cc_final: 0.4553 (tm) REVERT: K 202 GLN cc_start: 0.5883 (tt0) cc_final: 0.5664 (tm-30) REVERT: K 207 ASN cc_start: 0.5936 (OUTLIER) cc_final: 0.5495 (m-40) REVERT: K 230 GLU cc_start: 0.7138 (mp0) cc_final: 0.6713 (mt-10) REVERT: L 29 VAL cc_start: 0.5643 (t) cc_final: 0.5336 (p) REVERT: L 88 THR cc_start: 0.5379 (OUTLIER) cc_final: 0.4947 (m) REVERT: L 199 TYR cc_start: 0.4755 (t80) cc_final: 0.4327 (t80) REVERT: L 206 ARG cc_start: 0.6073 (ttp-170) cc_final: 0.5790 (ttp-170) REVERT: L 210 GLU cc_start: 0.6347 (tp30) cc_final: 0.6044 (mm-30) REVERT: L 230 GLU cc_start: 0.7222 (mp0) cc_final: 0.6730 (mt-10) REVERT: L 233 ARG cc_start: 0.6319 (ttt180) cc_final: 0.5713 (ttm170) outliers start: 30 outliers final: 13 residues processed: 303 average time/residue: 1.1948 time to fit residues: 405.5902 Evaluate side-chains 267 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 246 ARG Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 246 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 230 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 246 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130233 restraints weight = 35419.046| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.05 r_work: 0.3188 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17508 Z= 0.141 Angle : 0.561 6.960 23868 Z= 0.300 Chirality : 0.041 0.137 2736 Planarity : 0.004 0.033 2868 Dihedral : 9.324 56.435 2546 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.35 % Allowed : 15.65 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.74 (0.17), residues: 2028 helix: 3.14 (0.12), residues: 1524 sheet: 1.14 (0.40), residues: 144 loop : -0.11 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 278 TYR 0.015 0.002 TYR D 67 PHE 0.010 0.001 PHE C 53 TRP 0.005 0.001 TRP H 277 HIS 0.016 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00270 (17472) covalent geometry : angle 0.55936 (23796) SS BOND : bond 0.00327 ( 36) SS BOND : angle 0.87161 ( 72) hydrogen bonds : bond 0.05871 ( 1267) hydrogen bonds : angle 3.98172 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 1.091 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: A 91 LEU cc_start: 0.6034 (mt) cc_final: 0.5455 (tm) REVERT: A 207 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7012 (m-40) REVERT: A 230 GLU cc_start: 0.7591 (mp0) cc_final: 0.7217 (pm20) REVERT: B 29 VAL cc_start: 0.7555 (t) cc_final: 0.7215 (p) REVERT: B 199 TYR cc_start: 0.5792 (t80) cc_final: 0.5440 (t80) REVERT: C 91 LEU cc_start: 0.6021 (mt) cc_final: 0.5435 (tm) REVERT: C 196 SER cc_start: 0.5125 (OUTLIER) cc_final: 0.4898 (m) REVERT: C 199 TYR cc_start: 0.5782 (t80) cc_final: 0.5069 (t80) REVERT: C 202 GLN cc_start: 0.6835 (tt0) cc_final: 0.6589 (tt0) REVERT: C 230 GLU cc_start: 0.7950 (mp0) cc_final: 0.7739 (mt-10) REVERT: C 239 GLU cc_start: 0.8176 (tt0) cc_final: 0.7767 (mt-10) REVERT: D 199 TYR cc_start: 0.5550 (t80) cc_final: 0.5259 (t80) REVERT: D 230 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: D 239 GLU cc_start: 0.7828 (tt0) cc_final: 0.7617 (mt-10) REVERT: E 29 VAL cc_start: 0.7503 (t) cc_final: 0.7147 (p) REVERT: E 199 TYR cc_start: 0.5721 (t80) cc_final: 0.5409 (t80) REVERT: E 281 LYS cc_start: 0.2072 (OUTLIER) cc_final: 0.1794 (ttmm) REVERT: F 91 LEU cc_start: 0.5996 (mt) cc_final: 0.5416 (tm) REVERT: F 196 SER cc_start: 0.4854 (OUTLIER) cc_final: 0.4576 (m) REVERT: F 199 TYR cc_start: 0.5808 (t80) cc_final: 0.5407 (t80) REVERT: F 202 GLN cc_start: 0.6811 (tt0) cc_final: 0.6565 (tt0) REVERT: F 206 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.7081 (ttp-170) REVERT: F 239 GLU cc_start: 0.8222 (tt0) cc_final: 0.7849 (mt-10) REVERT: G 91 LEU cc_start: 0.6001 (mt) cc_final: 0.5430 (tm) REVERT: G 196 SER cc_start: 0.5096 (OUTLIER) cc_final: 0.4852 (m) REVERT: G 199 TYR cc_start: 0.5725 (t80) cc_final: 0.5197 (t80) REVERT: G 202 GLN cc_start: 0.6852 (tt0) cc_final: 0.6532 (tt0) REVERT: G 239 GLU cc_start: 0.8235 (tt0) cc_final: 0.7905 (mt-10) REVERT: H 196 SER cc_start: 0.5138 (OUTLIER) cc_final: 0.4852 (m) REVERT: H 202 GLN cc_start: 0.6710 (tt0) cc_final: 0.6414 (tt0) REVERT: H 230 GLU cc_start: 0.7840 (mp0) cc_final: 0.7636 (mt-10) REVERT: I 196 SER cc_start: 0.4948 (OUTLIER) cc_final: 0.4726 (m) REVERT: I 199 TYR cc_start: 0.5692 (t80) cc_final: 0.5370 (t80) REVERT: I 207 ASN cc_start: 0.7626 (m-40) cc_final: 0.7257 (m110) REVERT: I 210 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7519 (mm-30) REVERT: I 230 GLU cc_start: 0.7960 (mp0) cc_final: 0.7760 (mt-10) REVERT: J 88 THR cc_start: 0.6401 (OUTLIER) cc_final: 0.5963 (m) REVERT: J 196 SER cc_start: 0.4478 (OUTLIER) cc_final: 0.4230 (t) REVERT: J 199 TYR cc_start: 0.5559 (t80) cc_final: 0.5248 (t80) REVERT: J 202 GLN cc_start: 0.6807 (tm-30) cc_final: 0.6578 (tm-30) REVERT: J 205 PHE cc_start: 0.7053 (m-80) cc_final: 0.6743 (m-80) REVERT: J 207 ASN cc_start: 0.7211 (t0) cc_final: 0.6945 (t0) REVERT: J 210 GLU cc_start: 0.7713 (tp30) cc_final: 0.7434 (mm-30) REVERT: J 220 LEU cc_start: 0.7869 (tp) cc_final: 0.7614 (mt) REVERT: K 29 VAL cc_start: 0.7657 (t) cc_final: 0.7258 (p) REVERT: K 196 SER cc_start: 0.4854 (OUTLIER) cc_final: 0.4627 (m) REVERT: K 207 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7030 (m-40) REVERT: L 29 VAL cc_start: 0.7520 (t) cc_final: 0.7172 (p) REVERT: L 199 TYR cc_start: 0.5793 (t80) cc_final: 0.5444 (t80) outliers start: 44 outliers final: 13 residues processed: 285 average time/residue: 1.2288 time to fit residues: 396.1769 Evaluate side-chains 261 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 196 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 196 SER Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 92 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 202 GLN B 50 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN E 100 GLN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN G 207 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 50 GLN K 99 HIS K 202 GLN L 50 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130865 restraints weight = 34748.942| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.17 r_work: 0.3115 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17508 Z= 0.201 Angle : 0.661 7.080 23868 Z= 0.360 Chirality : 0.044 0.168 2736 Planarity : 0.005 0.065 2868 Dihedral : 8.826 51.957 2511 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.17), residues: 2028 helix: 2.69 (0.12), residues: 1512 sheet: -0.03 (0.31), residues: 204 loop : -0.15 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 77 TYR 0.018 0.003 TYR C 243 PHE 0.016 0.002 PHE G 33 TRP 0.005 0.002 TRP D 79 HIS 0.017 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00414 (17472) covalent geometry : angle 0.65749 (23796) SS BOND : bond 0.00701 ( 36) SS BOND : angle 1.44680 ( 72) hydrogen bonds : bond 0.07162 ( 1267) hydrogen bonds : angle 4.36193 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.3660 (OUTLIER) cc_final: 0.3183 (tp40) REVERT: A 230 GLU cc_start: 0.7835 (mp0) cc_final: 0.7511 (pm20) REVERT: B 99 HIS cc_start: 0.3472 (OUTLIER) cc_final: 0.3030 (t-90) REVERT: C 21 MET cc_start: 0.3517 (tpp) cc_final: 0.3128 (tpp) REVERT: C 91 LEU cc_start: 0.6186 (mt) cc_final: 0.5568 (tm) REVERT: C 196 SER cc_start: 0.5222 (OUTLIER) cc_final: 0.4986 (m) REVERT: C 199 TYR cc_start: 0.5780 (t80) cc_final: 0.5041 (t80) REVERT: C 202 GLN cc_start: 0.6852 (tt0) cc_final: 0.6485 (tt0) REVERT: C 239 GLU cc_start: 0.8168 (tt0) cc_final: 0.7859 (mt-10) REVERT: C 271 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5666 (tt0) REVERT: D 21 MET cc_start: 0.3447 (pmm) cc_final: 0.3226 (ttp) REVERT: D 199 TYR cc_start: 0.5680 (t80) cc_final: 0.5379 (t80) REVERT: D 239 GLU cc_start: 0.8157 (tt0) cc_final: 0.7956 (mt-10) REVERT: D 272 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5771 (mt) REVERT: E 100 GLN cc_start: 0.3670 (OUTLIER) cc_final: 0.3222 (tp40) REVERT: E 199 TYR cc_start: 0.5717 (t80) cc_final: 0.5474 (t80) REVERT: E 207 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7161 (m110) REVERT: E 271 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5424 (tp30) REVERT: E 281 LYS cc_start: 0.2129 (OUTLIER) cc_final: 0.1868 (ttmm) REVERT: F 91 LEU cc_start: 0.6092 (mt) cc_final: 0.5474 (tm) REVERT: F 99 HIS cc_start: 0.3439 (OUTLIER) cc_final: 0.3071 (t-90) REVERT: F 196 SER cc_start: 0.4919 (OUTLIER) cc_final: 0.4644 (m) REVERT: F 199 TYR cc_start: 0.5824 (t80) cc_final: 0.5464 (t80) REVERT: F 202 GLN cc_start: 0.6833 (tt0) cc_final: 0.6503 (tt0) REVERT: F 239 GLU cc_start: 0.8196 (tt0) cc_final: 0.7941 (mt-10) REVERT: F 271 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5654 (tt0) REVERT: F 281 LYS cc_start: 0.2426 (OUTLIER) cc_final: 0.1969 (mmmt) REVERT: G 91 LEU cc_start: 0.6119 (mt) cc_final: 0.5512 (tm) REVERT: G 196 SER cc_start: 0.5196 (OUTLIER) cc_final: 0.4964 (m) REVERT: G 199 TYR cc_start: 0.5733 (t80) cc_final: 0.5204 (t80) REVERT: G 202 GLN cc_start: 0.6915 (tt0) cc_final: 0.6568 (tt0) REVERT: G 239 GLU cc_start: 0.8245 (tt0) cc_final: 0.7978 (mt-10) REVERT: G 271 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5720 (tt0) REVERT: H 99 HIS cc_start: 0.3386 (OUTLIER) cc_final: 0.2944 (t70) REVERT: H 196 SER cc_start: 0.5146 (OUTLIER) cc_final: 0.4890 (m) REVERT: H 202 GLN cc_start: 0.6725 (tt0) cc_final: 0.6449 (tt0) REVERT: I 21 MET cc_start: 0.3128 (tpp) cc_final: 0.2834 (mmp) REVERT: I 100 GLN cc_start: 0.3646 (OUTLIER) cc_final: 0.3173 (tp40) REVERT: I 271 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5381 (tp30) REVERT: I 272 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5824 (mt) REVERT: I 281 LYS cc_start: 0.2119 (OUTLIER) cc_final: 0.1878 (ttmm) REVERT: J 91 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5252 (tm) REVERT: J 196 SER cc_start: 0.4605 (OUTLIER) cc_final: 0.4294 (t) REVERT: J 205 PHE cc_start: 0.7172 (m-80) cc_final: 0.6875 (m-80) REVERT: J 207 ASN cc_start: 0.7303 (t0) cc_final: 0.7099 (t0) REVERT: J 210 GLU cc_start: 0.7696 (tp30) cc_final: 0.7433 (mm-30) REVERT: J 239 GLU cc_start: 0.8221 (tt0) cc_final: 0.7907 (mt-10) REVERT: L 29 VAL cc_start: 0.7658 (t) cc_final: 0.7294 (p) REVERT: L 199 TYR cc_start: 0.5793 (t80) cc_final: 0.5481 (t80) outliers start: 45 outliers final: 12 residues processed: 259 average time/residue: 1.2489 time to fit residues: 365.3180 Evaluate side-chains 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 196 SER Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 140 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.0040 chunk 115 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 9 optimal weight: 7.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 207 ASN F 207 ASN G 207 ASN J 202 GLN K 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132892 restraints weight = 34967.622| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.13 r_work: 0.3143 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17508 Z= 0.140 Angle : 0.562 5.564 23868 Z= 0.307 Chirality : 0.041 0.140 2736 Planarity : 0.005 0.069 2868 Dihedral : 8.268 51.417 2504 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.82 % Allowed : 14.32 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.17), residues: 2028 helix: 2.88 (0.12), residues: 1512 sheet: 0.05 (0.32), residues: 204 loop : -0.14 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 206 TYR 0.014 0.002 TYR G 243 PHE 0.010 0.001 PHE C 53 TRP 0.003 0.001 TRP H 277 HIS 0.020 0.002 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00268 (17472) covalent geometry : angle 0.55998 (23796) SS BOND : bond 0.00360 ( 36) SS BOND : angle 0.96005 ( 72) hydrogen bonds : bond 0.06063 ( 1267) hydrogen bonds : angle 4.15988 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.3367 (OUTLIER) cc_final: 0.2560 (tm-30) REVERT: A 230 GLU cc_start: 0.7765 (mp0) cc_final: 0.7522 (pm20) REVERT: C 21 MET cc_start: 0.3478 (tpp) cc_final: 0.3259 (tpp) REVERT: C 91 LEU cc_start: 0.6125 (mt) cc_final: 0.5515 (tm) REVERT: C 196 SER cc_start: 0.5221 (OUTLIER) cc_final: 0.5008 (m) REVERT: C 199 TYR cc_start: 0.5777 (t80) cc_final: 0.5107 (t80) REVERT: C 202 GLN cc_start: 0.6830 (tt0) cc_final: 0.6612 (tt0) REVERT: C 239 GLU cc_start: 0.8170 (tt0) cc_final: 0.7872 (mt-10) REVERT: D 199 TYR cc_start: 0.5597 (t80) cc_final: 0.5296 (t80) REVERT: D 239 GLU cc_start: 0.8167 (tt0) cc_final: 0.7957 (mt-10) REVERT: D 272 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5715 (mt) REVERT: E 100 GLN cc_start: 0.3574 (OUTLIER) cc_final: 0.3061 (tp40) REVERT: E 199 TYR cc_start: 0.5691 (t80) cc_final: 0.5462 (t80) REVERT: E 207 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7156 (m110) REVERT: E 281 LYS cc_start: 0.2077 (OUTLIER) cc_final: 0.1463 (tttp) REVERT: F 91 LEU cc_start: 0.6024 (mt) cc_final: 0.5432 (tm) REVERT: F 99 HIS cc_start: 0.3431 (OUTLIER) cc_final: 0.3102 (t-90) REVERT: F 196 SER cc_start: 0.4824 (OUTLIER) cc_final: 0.4551 (m) REVERT: F 199 TYR cc_start: 0.5789 (t80) cc_final: 0.5444 (t80) REVERT: F 202 GLN cc_start: 0.6812 (tt0) cc_final: 0.6594 (tt0) REVERT: F 239 GLU cc_start: 0.8182 (tt0) cc_final: 0.7917 (mt-10) REVERT: F 281 LYS cc_start: 0.2448 (OUTLIER) cc_final: 0.1970 (mmmt) REVERT: G 91 LEU cc_start: 0.6080 (mt) cc_final: 0.5490 (tm) REVERT: G 196 SER cc_start: 0.5202 (OUTLIER) cc_final: 0.4982 (m) REVERT: G 199 TYR cc_start: 0.5722 (t80) cc_final: 0.5219 (t80) REVERT: G 202 GLN cc_start: 0.6891 (tt0) cc_final: 0.6548 (tt0) REVERT: G 239 GLU cc_start: 0.8234 (tt0) cc_final: 0.7981 (mt-10) REVERT: H 196 SER cc_start: 0.5254 (OUTLIER) cc_final: 0.4982 (m) REVERT: H 202 GLN cc_start: 0.6707 (tt0) cc_final: 0.6435 (tt0) REVERT: I 100 GLN cc_start: 0.3520 (OUTLIER) cc_final: 0.3085 (tp40) REVERT: I 272 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5837 (mt) REVERT: J 21 MET cc_start: 0.3697 (pmm) cc_final: 0.3379 (ptt) REVERT: J 91 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5261 (tm) REVERT: J 196 SER cc_start: 0.4662 (OUTLIER) cc_final: 0.4359 (t) REVERT: J 210 GLU cc_start: 0.7680 (tp30) cc_final: 0.7458 (mm-30) REVERT: J 239 GLU cc_start: 0.8220 (tt0) cc_final: 0.7927 (mt-10) REVERT: L 199 TYR cc_start: 0.5719 (t80) cc_final: 0.5410 (t80) outliers start: 34 outliers final: 13 residues processed: 248 average time/residue: 1.1311 time to fit residues: 319.7658 Evaluate side-chains 244 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 196 SER Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 207 ASN F 207 ASN G 207 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN K 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122614 restraints weight = 34489.044| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.05 r_work: 0.3132 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17508 Z= 0.214 Angle : 0.696 6.942 23868 Z= 0.381 Chirality : 0.046 0.155 2736 Planarity : 0.006 0.063 2868 Dihedral : 9.098 55.969 2504 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.72 % Allowed : 12.71 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.17), residues: 2028 helix: 2.41 (0.12), residues: 1512 sheet: -0.18 (0.31), residues: 204 loop : -0.02 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 206 TYR 0.019 0.004 TYR B 67 PHE 0.017 0.003 PHE G 33 TRP 0.006 0.002 TRP J 277 HIS 0.018 0.003 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00447 (17472) covalent geometry : angle 0.69233 (23796) SS BOND : bond 0.00780 ( 36) SS BOND : angle 1.54448 ( 72) hydrogen bonds : bond 0.07396 ( 1267) hydrogen bonds : angle 4.50078 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5673 (mt) REVERT: B 99 HIS cc_start: 0.3435 (OUTLIER) cc_final: 0.3087 (t-90) REVERT: B 281 LYS cc_start: 0.1942 (OUTLIER) cc_final: 0.1347 (tttp) REVERT: C 91 LEU cc_start: 0.6191 (mt) cc_final: 0.5894 (tt) REVERT: C 100 GLN cc_start: 0.3685 (OUTLIER) cc_final: 0.3052 (tp40) REVERT: C 196 SER cc_start: 0.5276 (OUTLIER) cc_final: 0.5061 (m) REVERT: C 199 TYR cc_start: 0.5781 (t80) cc_final: 0.5110 (t80) REVERT: C 202 GLN cc_start: 0.6778 (tt0) cc_final: 0.6500 (tt0) REVERT: C 239 GLU cc_start: 0.8079 (tt0) cc_final: 0.7823 (mt-10) REVERT: C 271 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5664 (tt0) REVERT: C 272 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5805 (mt) REVERT: D 199 TYR cc_start: 0.5654 (t80) cc_final: 0.5385 (t80) REVERT: D 239 GLU cc_start: 0.8170 (tt0) cc_final: 0.7967 (mt-10) REVERT: D 272 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5748 (mt) REVERT: E 207 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7123 (m110) REVERT: E 239 GLU cc_start: 0.8097 (tt0) cc_final: 0.7766 (mt-10) REVERT: E 271 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5474 (tp30) REVERT: E 272 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5951 (tp) REVERT: E 281 LYS cc_start: 0.2250 (OUTLIER) cc_final: 0.1636 (tttp) REVERT: F 91 LEU cc_start: 0.6085 (mt) cc_final: 0.5468 (tm) REVERT: F 196 SER cc_start: 0.4974 (OUTLIER) cc_final: 0.4713 (m) REVERT: F 202 GLN cc_start: 0.6735 (tt0) cc_final: 0.6486 (tt0) REVERT: F 239 GLU cc_start: 0.8133 (tt0) cc_final: 0.7882 (mt-10) REVERT: F 271 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: F 281 LYS cc_start: 0.2657 (OUTLIER) cc_final: 0.2160 (mmmt) REVERT: G 91 LEU cc_start: 0.6136 (mt) cc_final: 0.5531 (tm) REVERT: G 199 TYR cc_start: 0.5721 (t80) cc_final: 0.5213 (t80) REVERT: G 202 GLN cc_start: 0.6863 (tt0) cc_final: 0.6581 (tt0) REVERT: G 239 GLU cc_start: 0.8188 (tt0) cc_final: 0.7931 (mt-10) REVERT: G 271 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5733 (tt0) REVERT: H 99 HIS cc_start: 0.3342 (OUTLIER) cc_final: 0.2949 (t-90) REVERT: H 196 SER cc_start: 0.5313 (OUTLIER) cc_final: 0.5036 (m) REVERT: H 202 GLN cc_start: 0.6626 (tt0) cc_final: 0.6426 (tt0) REVERT: I 272 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5796 (mt) REVERT: I 281 LYS cc_start: 0.2025 (OUTLIER) cc_final: 0.1800 (ttmm) REVERT: J 21 MET cc_start: 0.3692 (pmm) cc_final: 0.3392 (ptt) REVERT: J 24 ARG cc_start: 0.5099 (OUTLIER) cc_final: 0.4543 (mmm160) REVERT: J 91 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5256 (tm) REVERT: J 210 GLU cc_start: 0.7559 (tp30) cc_final: 0.7340 (mm-30) REVERT: J 239 GLU cc_start: 0.8139 (tt0) cc_final: 0.7873 (mt-10) REVERT: K 207 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.6984 (m-40) REVERT: K 271 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5503 (tp30) REVERT: L 199 TYR cc_start: 0.5683 (t80) cc_final: 0.5435 (t80) REVERT: L 271 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5520 (tp30) outliers start: 51 outliers final: 15 residues processed: 259 average time/residue: 1.1489 time to fit residues: 337.4208 Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 271 GLU Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN F 207 ASN G 207 ASN J 202 GLN K 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126606 restraints weight = 34525.535| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.07 r_work: 0.3136 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17508 Z= 0.152 Angle : 0.592 5.753 23868 Z= 0.325 Chirality : 0.042 0.142 2736 Planarity : 0.005 0.068 2868 Dihedral : 8.623 55.019 2504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.03 % Allowed : 13.30 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.17), residues: 2028 helix: 2.65 (0.12), residues: 1512 sheet: -0.10 (0.31), residues: 204 loop : 0.00 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 24 TYR 0.016 0.002 TYR H 243 PHE 0.011 0.001 PHE G 53 TRP 0.004 0.001 TRP D 79 HIS 0.015 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00298 (17472) covalent geometry : angle 0.58990 (23796) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.13216 ( 72) hydrogen bonds : bond 0.06401 ( 1267) hydrogen bonds : angle 4.27137 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.6199 (mt) cc_final: 0.5475 (tp) REVERT: A 272 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5698 (mt) REVERT: C 91 LEU cc_start: 0.6166 (mt) cc_final: 0.5552 (tm) REVERT: C 196 SER cc_start: 0.5342 (OUTLIER) cc_final: 0.5130 (m) REVERT: C 199 TYR cc_start: 0.5767 (t80) cc_final: 0.5096 (t80) REVERT: C 202 GLN cc_start: 0.6795 (tt0) cc_final: 0.6522 (tt0) REVERT: C 239 GLU cc_start: 0.8102 (tt0) cc_final: 0.7855 (mt-10) REVERT: C 272 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5824 (mt) REVERT: D 199 TYR cc_start: 0.5675 (t80) cc_final: 0.5465 (t80) REVERT: D 239 GLU cc_start: 0.8171 (tt0) cc_final: 0.7956 (mt-10) REVERT: D 272 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5768 (mt) REVERT: E 207 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7114 (m110) REVERT: E 239 GLU cc_start: 0.8150 (tt0) cc_final: 0.7836 (mt-10) REVERT: E 272 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5871 (tp) REVERT: E 281 LYS cc_start: 0.2289 (OUTLIER) cc_final: 0.1640 (tttp) REVERT: F 91 LEU cc_start: 0.6060 (mt) cc_final: 0.5473 (tm) REVERT: F 196 SER cc_start: 0.4807 (OUTLIER) cc_final: 0.4533 (m) REVERT: F 202 GLN cc_start: 0.6749 (tt0) cc_final: 0.6481 (tt0) REVERT: F 239 GLU cc_start: 0.8141 (tt0) cc_final: 0.7885 (mt-10) REVERT: F 281 LYS cc_start: 0.2569 (OUTLIER) cc_final: 0.2084 (mmmt) REVERT: G 91 LEU cc_start: 0.6138 (mt) cc_final: 0.5544 (tm) REVERT: G 199 TYR cc_start: 0.5685 (t80) cc_final: 0.5175 (t80) REVERT: G 202 GLN cc_start: 0.6864 (tt0) cc_final: 0.6592 (tt0) REVERT: G 239 GLU cc_start: 0.8201 (tt0) cc_final: 0.7969 (mt-10) REVERT: G 272 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5797 (mt) REVERT: H 99 HIS cc_start: 0.3312 (OUTLIER) cc_final: 0.2898 (t-90) REVERT: H 196 SER cc_start: 0.5344 (OUTLIER) cc_final: 0.5055 (m) REVERT: H 202 GLN cc_start: 0.6685 (tt0) cc_final: 0.6477 (tt0) REVERT: I 272 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5817 (mt) REVERT: J 21 MET cc_start: 0.3538 (pmm) cc_final: 0.3292 (ptt) REVERT: J 91 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5202 (tm) REVERT: J 210 GLU cc_start: 0.7575 (tp30) cc_final: 0.7333 (mm-30) REVERT: J 239 GLU cc_start: 0.8140 (tt0) cc_final: 0.7867 (mt-10) REVERT: L 199 TYR cc_start: 0.5675 (t80) cc_final: 0.5433 (t80) outliers start: 38 outliers final: 15 residues processed: 246 average time/residue: 1.0478 time to fit residues: 293.3489 Evaluate side-chains 238 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN E 100 GLN F 207 ASN G 207 ASN ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 GLN K 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.124317 restraints weight = 34375.247| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.09 r_work: 0.3113 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17508 Z= 0.210 Angle : 0.687 6.817 23868 Z= 0.377 Chirality : 0.045 0.169 2736 Planarity : 0.006 0.068 2868 Dihedral : 8.991 56.503 2504 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.67 % Allowed : 12.13 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.17), residues: 2028 helix: 2.36 (0.12), residues: 1512 sheet: -0.13 (0.31), residues: 204 loop : -0.02 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 206 TYR 0.018 0.004 TYR B 67 PHE 0.016 0.002 PHE J 205 TRP 0.007 0.002 TRP J 277 HIS 0.017 0.003 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00441 (17472) covalent geometry : angle 0.68242 (23796) SS BOND : bond 0.00754 ( 36) SS BOND : angle 1.55540 ( 72) hydrogen bonds : bond 0.07306 ( 1267) hydrogen bonds : angle 4.50607 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.943 Fit side-chains REVERT: A 91 LEU cc_start: 0.6230 (mt) cc_final: 0.5494 (tp) REVERT: A 272 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5712 (mt) REVERT: C 91 LEU cc_start: 0.6153 (mt) cc_final: 0.5860 (tt) REVERT: C 196 SER cc_start: 0.5471 (OUTLIER) cc_final: 0.5265 (m) REVERT: C 199 TYR cc_start: 0.5797 (t80) cc_final: 0.5086 (t80) REVERT: C 202 GLN cc_start: 0.6764 (tt0) cc_final: 0.6509 (tt0) REVERT: C 239 GLU cc_start: 0.8112 (tt0) cc_final: 0.7855 (mt-10) REVERT: C 271 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5759 (tt0) REVERT: C 272 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5798 (mt) REVERT: D 239 GLU cc_start: 0.8217 (tt0) cc_final: 0.8001 (mt-10) REVERT: D 272 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5702 (mt) REVERT: E 100 GLN cc_start: 0.3606 (OUTLIER) cc_final: 0.3059 (tp40) REVERT: E 207 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7143 (m110) REVERT: E 239 GLU cc_start: 0.8119 (tt0) cc_final: 0.7832 (mt-10) REVERT: E 272 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5872 (tp) REVERT: E 281 LYS cc_start: 0.2237 (OUTLIER) cc_final: 0.1625 (tttp) REVERT: F 91 LEU cc_start: 0.6123 (mt) cc_final: 0.5451 (tm) REVERT: F 99 HIS cc_start: 0.3443 (OUTLIER) cc_final: 0.3081 (t-90) REVERT: F 196 SER cc_start: 0.4866 (OUTLIER) cc_final: 0.4619 (m) REVERT: F 202 GLN cc_start: 0.6731 (tt0) cc_final: 0.6511 (tt0) REVERT: F 239 GLU cc_start: 0.8146 (tt0) cc_final: 0.7914 (mt-10) REVERT: F 271 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5686 (tt0) REVERT: F 281 LYS cc_start: 0.2548 (OUTLIER) cc_final: 0.2067 (mmmt) REVERT: G 91 LEU cc_start: 0.6156 (mt) cc_final: 0.5493 (tm) REVERT: G 99 HIS cc_start: 0.3335 (OUTLIER) cc_final: 0.2993 (t-90) REVERT: G 199 TYR cc_start: 0.5692 (t80) cc_final: 0.5194 (t80) REVERT: G 202 GLN cc_start: 0.6806 (tt0) cc_final: 0.6459 (tt0) REVERT: G 239 GLU cc_start: 0.8205 (tt0) cc_final: 0.7978 (mt-10) REVERT: G 271 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: G 272 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5860 (mt) REVERT: H 99 HIS cc_start: 0.3362 (OUTLIER) cc_final: 0.2951 (t-90) REVERT: H 196 SER cc_start: 0.5367 (OUTLIER) cc_final: 0.5074 (m) REVERT: H 271 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5634 (tp30) REVERT: I 271 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5455 (tp30) REVERT: I 272 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5749 (mt) REVERT: J 21 MET cc_start: 0.3517 (pmm) cc_final: 0.3280 (ptt) REVERT: J 24 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.4546 (mmm160) REVERT: J 91 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5274 (tm) REVERT: J 202 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6731 (tt0) REVERT: J 239 GLU cc_start: 0.8123 (tt0) cc_final: 0.7875 (mt-10) REVERT: L 199 TYR cc_start: 0.5630 (t80) cc_final: 0.5349 (t80) REVERT: L 239 GLU cc_start: 0.8163 (tt0) cc_final: 0.7810 (mt-10) REVERT: L 271 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5561 (tp30) outliers start: 50 outliers final: 16 residues processed: 254 average time/residue: 1.1217 time to fit residues: 324.1409 Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 271 GLU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 202 GLN Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 180 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 207 ASN F 207 ASN G 207 ASN H 202 GLN K 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.177280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126814 restraints weight = 34638.061| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.08 r_work: 0.3137 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17508 Z= 0.146 Angle : 0.589 7.792 23868 Z= 0.323 Chirality : 0.042 0.138 2736 Planarity : 0.005 0.058 2868 Dihedral : 8.636 56.237 2504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.92 % Allowed : 12.93 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.17), residues: 2028 helix: 2.61 (0.12), residues: 1512 sheet: -0.09 (0.31), residues: 204 loop : -0.00 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 24 TYR 0.016 0.002 TYR A 243 PHE 0.011 0.001 PHE G 53 TRP 0.003 0.001 TRP D 79 HIS 0.016 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00281 (17472) covalent geometry : angle 0.58686 (23796) SS BOND : bond 0.00400 ( 36) SS BOND : angle 1.06989 ( 72) hydrogen bonds : bond 0.06318 ( 1267) hydrogen bonds : angle 4.25775 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.869 Fit side-chains REVERT: A 91 LEU cc_start: 0.6189 (mt) cc_final: 0.5462 (tp) REVERT: A 272 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5708 (mt) REVERT: C 91 LEU cc_start: 0.6110 (mt) cc_final: 0.5839 (tt) REVERT: C 196 SER cc_start: 0.5466 (OUTLIER) cc_final: 0.5256 (m) REVERT: C 199 TYR cc_start: 0.5752 (t80) cc_final: 0.5079 (t80) REVERT: C 202 GLN cc_start: 0.6769 (tt0) cc_final: 0.6512 (tt0) REVERT: C 239 GLU cc_start: 0.8117 (tt0) cc_final: 0.7864 (mt-10) REVERT: C 272 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5772 (mt) REVERT: D 239 GLU cc_start: 0.8196 (tt0) cc_final: 0.7964 (mt-10) REVERT: D 272 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5761 (mt) REVERT: E 239 GLU cc_start: 0.8123 (tt0) cc_final: 0.7863 (mt-10) REVERT: E 281 LYS cc_start: 0.2272 (OUTLIER) cc_final: 0.1630 (tttp) REVERT: F 91 LEU cc_start: 0.6063 (mt) cc_final: 0.5413 (tm) REVERT: F 99 HIS cc_start: 0.3436 (OUTLIER) cc_final: 0.3082 (t-90) REVERT: F 196 SER cc_start: 0.4633 (OUTLIER) cc_final: 0.4420 (m) REVERT: F 239 GLU cc_start: 0.8149 (tt0) cc_final: 0.7919 (mt-10) REVERT: F 281 LYS cc_start: 0.2468 (OUTLIER) cc_final: 0.2031 (mmmt) REVERT: G 91 LEU cc_start: 0.6127 (mt) cc_final: 0.5815 (tt) REVERT: G 99 HIS cc_start: 0.3455 (OUTLIER) cc_final: 0.3076 (t-90) REVERT: G 199 TYR cc_start: 0.5662 (t80) cc_final: 0.5161 (t80) REVERT: G 202 GLN cc_start: 0.6816 (tt0) cc_final: 0.6566 (tt0) REVERT: G 239 GLU cc_start: 0.8200 (tt0) cc_final: 0.7979 (mt-10) REVERT: G 272 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5828 (mt) REVERT: H 99 HIS cc_start: 0.3339 (OUTLIER) cc_final: 0.2897 (t-90) REVERT: H 196 SER cc_start: 0.5322 (OUTLIER) cc_final: 0.5024 (m) REVERT: I 272 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5813 (mt) REVERT: J 21 MET cc_start: 0.3551 (pmm) cc_final: 0.3289 (ptt) REVERT: J 91 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5206 (tm) REVERT: J 200 ILE cc_start: 0.5920 (pp) cc_final: 0.5621 (mt) REVERT: J 239 GLU cc_start: 0.8123 (tt0) cc_final: 0.7880 (mt-10) REVERT: L 199 TYR cc_start: 0.5623 (t80) cc_final: 0.5414 (t80) REVERT: L 239 GLU cc_start: 0.8162 (tt0) cc_final: 0.7818 (mt-10) outliers start: 36 outliers final: 16 residues processed: 243 average time/residue: 1.1494 time to fit residues: 317.8174 Evaluate side-chains 239 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 170 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 207 ASN F 202 GLN F 207 ASN G 207 ASN H 202 GLN J 202 GLN K 202 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.177661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.126169 restraints weight = 34389.337| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.08 r_work: 0.3148 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17508 Z= 0.140 Angle : 0.561 6.209 23868 Z= 0.308 Chirality : 0.041 0.139 2736 Planarity : 0.005 0.055 2868 Dihedral : 8.324 57.464 2502 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.82 % Allowed : 12.87 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.17), residues: 2028 helix: 2.78 (0.12), residues: 1512 sheet: 0.01 (0.32), residues: 204 loop : -0.05 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 233 TYR 0.015 0.002 TYR A 243 PHE 0.010 0.001 PHE D 53 TRP 0.004 0.001 TRP D 79 HIS 0.014 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00270 (17472) covalent geometry : angle 0.55885 (23796) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.02465 ( 72) hydrogen bonds : bond 0.05996 ( 1267) hydrogen bonds : angle 4.15439 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.004 Fit side-chains REVERT: A 91 LEU cc_start: 0.6174 (mt) cc_final: 0.5480 (tp) REVERT: A 272 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5694 (mt) REVERT: C 91 LEU cc_start: 0.6094 (mt) cc_final: 0.5454 (tm) REVERT: C 199 TYR cc_start: 0.5724 (t80) cc_final: 0.5064 (t80) REVERT: C 202 GLN cc_start: 0.6765 (tt0) cc_final: 0.6511 (tt0) REVERT: C 239 GLU cc_start: 0.8134 (tt0) cc_final: 0.7878 (mt-10) REVERT: C 272 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5776 (mt) REVERT: D 239 GLU cc_start: 0.8212 (tt0) cc_final: 0.7986 (mt-10) REVERT: D 272 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5787 (mt) REVERT: E 239 GLU cc_start: 0.8134 (tt0) cc_final: 0.7852 (mt-10) REVERT: F 91 LEU cc_start: 0.6074 (mt) cc_final: 0.5437 (tm) REVERT: F 239 GLU cc_start: 0.8160 (tt0) cc_final: 0.7926 (mt-10) REVERT: F 281 LYS cc_start: 0.2396 (OUTLIER) cc_final: 0.1968 (mmmt) REVERT: G 91 LEU cc_start: 0.6136 (mt) cc_final: 0.5503 (tm) REVERT: G 99 HIS cc_start: 0.3442 (OUTLIER) cc_final: 0.3060 (t-90) REVERT: G 199 TYR cc_start: 0.5662 (t80) cc_final: 0.5196 (t80) REVERT: G 202 GLN cc_start: 0.6797 (tt0) cc_final: 0.6476 (tt0) REVERT: G 239 GLU cc_start: 0.8196 (tt0) cc_final: 0.7965 (mt-10) REVERT: G 272 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5790 (mt) REVERT: H 99 HIS cc_start: 0.3356 (OUTLIER) cc_final: 0.2909 (t-90) REVERT: H 196 SER cc_start: 0.5334 (OUTLIER) cc_final: 0.5047 (m) REVERT: I 272 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5793 (mt) REVERT: J 91 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5214 (tm) REVERT: J 200 ILE cc_start: 0.6065 (pp) cc_final: 0.5753 (mt) REVERT: J 202 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6792 (pt0) REVERT: J 239 GLU cc_start: 0.8109 (tt0) cc_final: 0.7864 (mt-10) REVERT: L 199 TYR cc_start: 0.5640 (t80) cc_final: 0.5422 (t80) REVERT: L 239 GLU cc_start: 0.8158 (tt0) cc_final: 0.7823 (mt-10) outliers start: 34 outliers final: 15 residues processed: 240 average time/residue: 1.1618 time to fit residues: 318.6992 Evaluate side-chains 235 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 202 GLN Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 207 ASN E 207 ASN F 207 ASN G 207 ASN H 202 GLN K 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127660 restraints weight = 34709.085| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.01 r_work: 0.3155 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 17508 Z= 0.169 Angle : 0.741 59.199 23868 Z= 0.437 Chirality : 0.041 0.140 2736 Planarity : 0.005 0.054 2868 Dihedral : 8.320 57.464 2502 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.76 % Allowed : 12.98 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.17), residues: 2028 helix: 2.78 (0.12), residues: 1512 sheet: 0.02 (0.32), residues: 204 loop : -0.06 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.015 0.002 TYR G 243 PHE 0.010 0.001 PHE D 53 TRP 0.004 0.001 TRP E 277 HIS 0.014 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00336 (17472) covalent geometry : angle 0.74020 (23796) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.02153 ( 72) hydrogen bonds : bond 0.05995 ( 1267) hydrogen bonds : angle 4.15339 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.965 Fit side-chains REVERT: A 91 LEU cc_start: 0.6172 (mt) cc_final: 0.5476 (tp) REVERT: A 272 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5695 (mt) REVERT: C 91 LEU cc_start: 0.6095 (mt) cc_final: 0.5454 (tm) REVERT: C 199 TYR cc_start: 0.5719 (t80) cc_final: 0.5066 (t80) REVERT: C 239 GLU cc_start: 0.8100 (tt0) cc_final: 0.7844 (mt-10) REVERT: C 272 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5774 (mt) REVERT: D 239 GLU cc_start: 0.8175 (tt0) cc_final: 0.7947 (mt-10) REVERT: D 272 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5785 (mt) REVERT: E 207 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7108 (m110) REVERT: E 239 GLU cc_start: 0.8099 (tt0) cc_final: 0.7818 (mt-10) REVERT: F 91 LEU cc_start: 0.6077 (mt) cc_final: 0.5438 (tm) REVERT: F 99 HIS cc_start: 0.3435 (OUTLIER) cc_final: 0.3065 (t-90) REVERT: F 239 GLU cc_start: 0.8125 (tt0) cc_final: 0.7889 (mt-10) REVERT: F 281 LYS cc_start: 0.2400 (OUTLIER) cc_final: 0.1972 (mmmt) REVERT: G 91 LEU cc_start: 0.6152 (mt) cc_final: 0.5517 (tm) REVERT: G 99 HIS cc_start: 0.3438 (OUTLIER) cc_final: 0.3057 (t-90) REVERT: G 199 TYR cc_start: 0.5660 (t80) cc_final: 0.5194 (t80) REVERT: G 202 GLN cc_start: 0.6784 (tt0) cc_final: 0.6463 (tt0) REVERT: G 239 GLU cc_start: 0.8162 (tt0) cc_final: 0.7931 (mt-10) REVERT: G 272 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5787 (mt) REVERT: H 99 HIS cc_start: 0.3352 (OUTLIER) cc_final: 0.2904 (t-90) REVERT: H 196 SER cc_start: 0.5336 (OUTLIER) cc_final: 0.5050 (m) REVERT: I 272 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5793 (mt) REVERT: J 91 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5210 (tm) REVERT: J 200 ILE cc_start: 0.6033 (pp) cc_final: 0.5726 (mt) REVERT: J 202 GLN cc_start: 0.6938 (tm-30) cc_final: 0.6688 (tm-30) REVERT: J 239 GLU cc_start: 0.8082 (tt0) cc_final: 0.7836 (mt-10) REVERT: L 199 TYR cc_start: 0.5642 (t80) cc_final: 0.5425 (t80) REVERT: L 239 GLU cc_start: 0.8127 (tt0) cc_final: 0.7793 (mt-10) outliers start: 33 outliers final: 17 residues processed: 239 average time/residue: 1.0518 time to fit residues: 287.4637 Evaluate side-chains 238 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 92 CYS Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 207 ASN F 207 ASN G 207 ASN H 202 GLN J 207 ASN K 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125690 restraints weight = 34364.798| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.08 r_work: 0.3155 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 17508 Z= 0.169 Angle : 0.741 59.199 23868 Z= 0.437 Chirality : 0.041 0.140 2736 Planarity : 0.005 0.054 2868 Dihedral : 8.320 57.464 2502 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.71 % Allowed : 13.09 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.17), residues: 2028 helix: 2.78 (0.12), residues: 1512 sheet: 0.02 (0.32), residues: 204 loop : -0.06 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 206 TYR 0.015 0.002 TYR G 243 PHE 0.010 0.001 PHE D 53 TRP 0.004 0.001 TRP E 277 HIS 0.014 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00336 (17472) covalent geometry : angle 0.74020 (23796) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.02153 ( 72) hydrogen bonds : bond 0.05995 ( 1267) hydrogen bonds : angle 4.15339 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14023.97 seconds wall clock time: 237 minutes 16.56 seconds (14236.56 seconds total)