Starting phenix.real_space_refine on Sat Mar 7 13:03:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jmc_22391/03_2026/7jmc_22391.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 P 12 5.49 5 S 120 5.16 5 C 14532 2.51 5 N 3084 2.21 5 O 3504 1.98 5 H 18576 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39828 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 10, 'MC3:plan-2': 10} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 10, 'MC3:plan-2': 10} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Restraints were copied for chains: G, C, D, E, F, H, I, J, K, L Time building chain proxies: 5.39, per 1000 atoms: 0.14 Number of scatterers: 39828 At special positions: 0 Unit cell: (95.403, 96.701, 161.601, 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 120 16.00 P 12 15.00 O 3504 8.00 N 3084 7.00 C 14532 6.00 H 18576 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.04 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " 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: 3.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 80.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.824A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 106 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 106 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 236 Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 106 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 236 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.824A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 106 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 236 Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 106 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 236 Processing helix chain 'F' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 106 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 236 Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 106 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 236 Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 106 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU H 155 " --> pdb=" O GLU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 236 Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 33 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 106 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 236 Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 106 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 236 Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 106 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU K 155 " --> pdb=" O GLU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 236 Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.825A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 106 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 151 through 181 removed outlier: 3.506A pdb=" N LEU L 155 " --> pdb=" O GLU L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1428 hydrogen bonds defined for protein. 4212 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: 8.84 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18564 1.03 - 1.22: 72 1.22 - 1.42: 8535 1.42 - 1.61: 12705 1.61 - 1.80: 180 Bond restraints: 40056 Sorted by residual: bond pdb=" C11 MC3 A 506 " pdb=" O3 MC3 A 506 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 MC3 E 508 " pdb=" O2 MC3 E 508 " ideal model delta sigma weight residual 1.328 1.400 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 H 501 " pdb=" O3 MC3 H 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 K 501 " pdb=" O3 MC3 K 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 B 501 " pdb=" O3 MC3 B 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 40051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 68793 3.34 - 6.67: 1587 6.67 - 10.01: 72 10.01 - 13.35: 12 13.35 - 16.69: 12 Bond angle restraints: 70476 Sorted by residual: angle pdb=" O3P MC3 L 508 " pdb=" P MC3 L 508 " pdb=" O4P MC3 L 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 C 508 " pdb=" P MC3 C 508 " pdb=" O4P MC3 C 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 J 508 " pdb=" P MC3 J 508 " pdb=" O4P MC3 J 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 D 508 " pdb=" P MC3 D 508 " pdb=" O4P MC3 D 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 G 501 " pdb=" P MC3 G 501 " pdb=" O4P MC3 G 501 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 ... (remaining 70471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 19152 35.38 - 70.75: 492 70.75 - 106.13: 36 106.13 - 141.50: 0 141.50 - 176.88: 24 Dihedral angle restraints: 19704 sinusoidal: 11136 harmonic: 8568 Sorted by residual: dihedral pdb=" C33 MC3 E 501 " pdb=" C31 MC3 E 501 " pdb=" C32 MC3 E 501 " pdb=" O2 MC3 E 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 K 501 " pdb=" C31 MC3 K 501 " pdb=" C32 MC3 K 501 " pdb=" O2 MC3 K 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 B 501 " pdb=" C31 MC3 B 501 " pdb=" C32 MC3 B 501 " pdb=" O2 MC3 B 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 19701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2112 0.053 - 0.106: 735 0.106 - 0.159: 129 0.159 - 0.213: 12 0.213 - 0.266: 24 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA ASN I 197 " pdb=" N ASN I 197 " pdb=" C ASN I 197 " pdb=" CB ASN I 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN F 197 " pdb=" N ASN F 197 " pdb=" C ASN F 197 " pdb=" CB ASN F 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN A 197 " pdb=" N ASN A 197 " pdb=" C ASN A 197 " pdb=" CB ASN A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3009 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.216 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " 0.014 2.00e-02 2.50e+03 pdb="HD21 ASN E 197 " 0.437 2.00e-02 2.50e+03 pdb="HD22 ASN E 197 " -0.434 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN C 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN C 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN C 197 " 0.433 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN L 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN L 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN L 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN L 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN L 197 " 0.433 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3769 2.24 - 2.83: 84805 2.83 - 3.42: 101264 3.42 - 4.01: 143201 4.01 - 4.60: 227331 Nonbonded interactions: 560370 Sorted by model distance: nonbonded pdb=" O TYR H 158 " pdb=" HD1 HIS H 161 " model vdw 1.650 2.450 nonbonded pdb=" O TYR I 158 " pdb=" HD1 HIS I 161 " model vdw 1.650 2.450 nonbonded pdb=" O TYR F 158 " pdb=" HD1 HIS F 161 " model vdw 1.650 2.450 nonbonded pdb=" O TYR E 158 " pdb=" HD1 HIS E 161 " model vdw 1.651 2.450 nonbonded pdb=" O TYR K 158 " pdb=" HD1 HIS K 161 " model vdw 1.651 2.450 ... (remaining 560365 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' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or n \ ame C24)))) selection = (chain 'B' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'C' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'D' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'E' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'F' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or n \ ame C24)))) selection = (chain 'H' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'I' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'J' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'K' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'L' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 32.640 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.010 0.072 21516 Z= 0.407 Angle : 1.288 16.685 28512 Z= 0.530 Chirality : 0.057 0.266 3012 Planarity : 0.006 0.055 3288 Dihedral : 14.519 176.875 8496 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.57 % Allowed : 6.29 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.40 (0.16), residues: 2256 helix: 3.16 (0.10), residues: 1704 sheet: 0.10 (0.46), residues: 132 loop : -1.18 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 192 TYR 0.014 0.003 TYR A 180 PHE 0.034 0.002 PHE C 202 TRP 0.013 0.002 TRP C 193 HIS 0.005 0.002 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00990 (21480) covalent geometry : angle 1.28747 (28440) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.29932 ( 72) hydrogen bonds : bond 0.09286 ( 1428) hydrogen bonds : angle 5.58017 ( 4212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 1.116 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: 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: symmetry clash REVERT: A 23 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6925 (mtt90) outliers start: 12 outliers final: 12 residues processed: 263 average time/residue: 0.9803 time to fit residues: 302.8173 Evaluate side-chains 223 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN E 15 ASN K 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122896 restraints weight = 57075.670| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.44 r_work: 0.3347 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21516 Z= 0.132 Angle : 0.549 4.733 28512 Z= 0.280 Chirality : 0.039 0.134 3012 Planarity : 0.004 0.042 3288 Dihedral : 13.067 171.205 4284 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.48 % Allowed : 9.05 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.83 (0.17), residues: 2256 helix: 3.42 (0.11), residues: 1716 sheet: 0.49 (0.44), residues: 132 loop : -1.01 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 192 TYR 0.009 0.002 TYR A 177 PHE 0.015 0.001 PHE E 202 TRP 0.007 0.001 TRP F 4 HIS 0.004 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00289 (21480) covalent geometry : angle 0.54853 (28440) SS BOND : bond 0.00084 ( 36) SS BOND : angle 0.76023 ( 72) hydrogen bonds : bond 0.04485 ( 1428) hydrogen bonds : angle 4.67205 ( 4212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.006 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: 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 outliers start: 31 outliers final: 30 residues processed: 253 average time/residue: 1.0569 time to fit residues: 312.8057 Evaluate side-chains 255 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117391 restraints weight = 57788.740| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.42 r_work: 0.3286 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21516 Z= 0.155 Angle : 0.522 5.537 28512 Z= 0.274 Chirality : 0.039 0.132 3012 Planarity : 0.004 0.036 3288 Dihedral : 12.322 154.037 4284 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.38 % Allowed : 9.00 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.85 (0.17), residues: 2256 helix: 3.48 (0.12), residues: 1728 sheet: -0.23 (0.38), residues: 132 loop : -1.10 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.011 0.002 TYR D 66 PHE 0.018 0.002 PHE J 202 TRP 0.007 0.001 TRP I 4 HIS 0.005 0.001 HIS J 98 Details of bonding type rmsd covalent geometry : bond 0.00369 (21480) covalent geometry : angle 0.52103 (28440) SS BOND : bond 0.00199 ( 36) SS BOND : angle 0.92877 ( 72) hydrogen bonds : bond 0.04379 ( 1428) hydrogen bonds : angle 4.52100 ( 4212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 1.029 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7289 (mtt90) REVERT: C 176 HIS cc_start: 0.8151 (t-90) cc_final: 0.7893 (t-170) REVERT: F 176 HIS cc_start: 0.8204 (t-90) cc_final: 0.7929 (t-170) REVERT: I 176 HIS cc_start: 0.8173 (t-90) cc_final: 0.7901 (t-170) REVERT: L 176 HIS cc_start: 0.8199 (t-90) cc_final: 0.7939 (t-170) outliers start: 50 outliers final: 36 residues processed: 256 average time/residue: 1.0695 time to fit residues: 319.6970 Evaluate side-chains 266 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS D 176 HIS G 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113513 restraints weight = 57666.748| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.42 r_work: 0.3246 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21516 Z= 0.222 Angle : 0.563 5.145 28512 Z= 0.298 Chirality : 0.042 0.141 3012 Planarity : 0.004 0.036 3288 Dihedral : 11.032 134.888 4284 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.05 % Allowed : 9.43 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.26 (0.17), residues: 2256 helix: 3.08 (0.12), residues: 1728 sheet: -0.79 (0.36), residues: 132 loop : -1.25 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.014 0.002 TYR A 66 PHE 0.022 0.002 PHE C 202 TRP 0.005 0.001 TRP A 4 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00547 (21480) covalent geometry : angle 0.56017 (28440) SS BOND : bond 0.00306 ( 36) SS BOND : angle 1.18729 ( 72) hydrogen bonds : bond 0.04671 ( 1428) hydrogen bonds : angle 4.60049 ( 4212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.896 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 HIS cc_start: 0.8276 (t-90) cc_final: 0.8038 (t-170) REVERT: D 183 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7122 (tpt170) outliers start: 43 outliers final: 39 residues processed: 263 average time/residue: 1.0606 time to fit residues: 325.3861 Evaluate side-chains 271 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS D 9 ASN E 176 HIS F 176 HIS G 9 ASN H 176 HIS I 176 HIS J 176 HIS K 176 HIS L 176 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115632 restraints weight = 57601.713| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.42 r_work: 0.3255 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21516 Z= 0.139 Angle : 0.484 4.421 28512 Z= 0.257 Chirality : 0.039 0.131 3012 Planarity : 0.003 0.033 3288 Dihedral : 10.057 117.214 4284 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.90 % Allowed : 8.57 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.41 (0.17), residues: 2256 helix: 3.20 (0.12), residues: 1728 sheet: -0.79 (0.35), residues: 132 loop : -1.25 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 33 TYR 0.011 0.002 TYR A 66 PHE 0.016 0.002 PHE K 202 TRP 0.005 0.001 TRP A 4 HIS 0.007 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00321 (21480) covalent geometry : angle 0.48211 (28440) SS BOND : bond 0.00194 ( 36) SS BOND : angle 0.93499 ( 72) hydrogen bonds : bond 0.04156 ( 1428) hydrogen bonds : angle 4.49154 ( 4212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 0.990 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: B 16 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7811 (mm-30) REVERT: B 23 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7449 (mtt90) REVERT: C 23 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7318 (mtt90) REVERT: D 23 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7585 (mtm-85) REVERT: E 23 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7449 (mtt90) REVERT: F 23 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7391 (mtt90) REVERT: H 23 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7480 (mtt90) REVERT: I 23 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7401 (mtt90) REVERT: J 23 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7459 (mtt-85) REVERT: K 23 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7540 (mtt-85) REVERT: L 23 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7378 (mtt90) outliers start: 61 outliers final: 37 residues processed: 284 average time/residue: 1.3093 time to fit residues: 422.2901 Evaluate side-chains 281 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 175 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 176 HIS C 95 HIS C 176 HIS D 9 ASN D 95 HIS E 176 HIS F 95 HIS F 176 HIS G 9 ASN H 176 HIS I 176 HIS J 95 HIS K 176 HIS L 95 HIS L 176 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114978 restraints weight = 57705.405| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.40 r_work: 0.3243 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21516 Z= 0.155 Angle : 0.500 4.365 28512 Z= 0.266 Chirality : 0.039 0.132 3012 Planarity : 0.005 0.063 3288 Dihedral : 9.518 104.852 4284 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.57 % Allowed : 8.95 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.29 (0.17), residues: 2256 helix: 3.12 (0.12), residues: 1728 sheet: -0.84 (0.35), residues: 132 loop : -1.29 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 101 TYR 0.011 0.002 TYR A 66 PHE 0.017 0.002 PHE A 202 TRP 0.005 0.001 TRP A 4 HIS 0.008 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00367 (21480) covalent geometry : angle 0.49807 (28440) SS BOND : bond 0.00206 ( 36) SS BOND : angle 0.98314 ( 72) hydrogen bonds : bond 0.04110 ( 1428) hydrogen bonds : angle 4.47122 ( 4212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.899 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 23 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7372 (mtt90) REVERT: B 23 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7482 (mtt90) REVERT: C 23 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7349 (mtt90) REVERT: D 23 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7611 (mtm-85) REVERT: D 183 ARG cc_start: 0.7679 (ttt180) cc_final: 0.7140 (tpt170) REVERT: E 23 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7475 (mtt90) REVERT: F 23 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7433 (mtt90) REVERT: G 23 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7500 (mtt-85) REVERT: H 23 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7512 (mtt90) REVERT: I 23 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7410 (mtt90) REVERT: J 23 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7499 (mtt-85) REVERT: K 23 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7576 (mtt-85) REVERT: L 23 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7400 (mtt90) outliers start: 54 outliers final: 40 residues processed: 275 average time/residue: 1.0764 time to fit residues: 345.5947 Evaluate side-chains 274 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 176 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 176 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 123 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 176 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 95 HIS E 176 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 ASN G 95 HIS H 95 HIS H 176 HIS I 95 HIS ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS K 176 HIS K 233 HIS ** L 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114896 restraints weight = 57314.961| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.40 r_work: 0.3263 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21516 Z= 0.151 Angle : 0.501 4.529 28512 Z= 0.273 Chirality : 0.039 0.131 3012 Planarity : 0.004 0.046 3288 Dihedral : 8.956 89.464 4284 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.24 % Allowed : 9.62 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.20 (0.17), residues: 2256 helix: 3.05 (0.12), residues: 1728 sheet: -0.89 (0.35), residues: 132 loop : -1.30 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 101 TYR 0.013 0.002 TYR I 177 PHE 0.016 0.002 PHE J 202 TRP 0.005 0.001 TRP I 4 HIS 0.016 0.002 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00344 (21480) covalent geometry : angle 0.49955 (28440) SS BOND : bond 0.00195 ( 36) SS BOND : angle 0.96038 ( 72) hydrogen bonds : bond 0.04156 ( 1428) hydrogen bonds : angle 4.50383 ( 4212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.053 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: A 23 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7369 (mtt90) REVERT: B 23 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7493 (mtt90) REVERT: C 23 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7379 (mtt90) REVERT: D 23 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7639 (mtm-85) REVERT: D 183 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7143 (tpt170) REVERT: E 23 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7485 (mtt90) REVERT: F 23 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7444 (mtt90) REVERT: G 23 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7502 (mtt-85) REVERT: I 23 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7419 (mtt90) REVERT: J 23 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7485 (mtt-85) REVERT: K 23 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7589 (mtt-85) REVERT: L 23 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7414 (mtt90) outliers start: 47 outliers final: 37 residues processed: 272 average time/residue: 1.0542 time to fit residues: 334.2982 Evaluate side-chains 282 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 17 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 166 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 212 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 9 ASN H 176 HIS I 176 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.163648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116469 restraints weight = 57206.629| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.41 r_work: 0.3277 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 21516 Z= 0.109 Angle : 0.455 4.217 28512 Z= 0.243 Chirality : 0.038 0.128 3012 Planarity : 0.004 0.038 3288 Dihedral : 8.402 70.588 4284 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.29 % Allowed : 9.90 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.48 (0.17), residues: 2256 helix: 3.27 (0.12), residues: 1728 sheet: -0.80 (0.35), residues: 132 loop : -1.30 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 101 TYR 0.009 0.001 TYR A 66 PHE 0.013 0.001 PHE C 202 TRP 0.005 0.001 TRP L 4 HIS 0.011 0.002 HIS I 176 Details of bonding type rmsd covalent geometry : bond 0.00241 (21480) covalent geometry : angle 0.45390 (28440) SS BOND : bond 0.00146 ( 36) SS BOND : angle 0.84271 ( 72) hydrogen bonds : bond 0.03733 ( 1428) hydrogen bonds : angle 4.36383 ( 4212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.990 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: A 23 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7308 (mtt90) REVERT: C 23 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7223 (mtt90) REVERT: D 23 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7549 (mtm-85) REVERT: E 23 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7430 (mtt90) REVERT: F 23 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7375 (mtt90) REVERT: G 23 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7430 (mtt-85) REVERT: I 23 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7341 (mtt90) REVERT: J 23 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7428 (mtt-85) REVERT: K 23 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7524 (mtt-85) REVERT: L 23 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7325 (mtt90) outliers start: 48 outliers final: 40 residues processed: 267 average time/residue: 1.0671 time to fit residues: 333.0708 Evaluate side-chains 279 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 176 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 150 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 176 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 9 ASN G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115781 restraints weight = 56974.118| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.44 r_work: 0.3222 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 21516 Z= 0.158 Angle : 0.507 9.771 28512 Z= 0.275 Chirality : 0.039 0.141 3012 Planarity : 0.004 0.034 3288 Dihedral : 8.564 64.760 4284 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.43 % Allowed : 10.10 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.27 (0.17), residues: 2256 helix: 3.11 (0.12), residues: 1728 sheet: -0.89 (0.35), residues: 132 loop : -1.32 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 101 TYR 0.011 0.002 TYR A 66 PHE 0.016 0.002 PHE K 202 TRP 0.005 0.001 TRP L 4 HIS 0.016 0.002 HIS L 176 Details of bonding type rmsd covalent geometry : bond 0.00370 (21480) covalent geometry : angle 0.50485 (28440) SS BOND : bond 0.00218 ( 36) SS BOND : angle 0.96970 ( 72) hydrogen bonds : bond 0.04084 ( 1428) hydrogen bonds : angle 4.45455 ( 4212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 0.929 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: A 23 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7326 (mtt90) REVERT: C 23 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7319 (mtt90) REVERT: D 23 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7573 (mtm-85) REVERT: D 183 ARG cc_start: 0.7689 (ttt180) cc_final: 0.7141 (tpt170) REVERT: E 23 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7429 (mtt90) REVERT: F 16 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7751 (mm-30) REVERT: F 23 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7407 (mtt90) REVERT: G 23 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7452 (mtt-85) REVERT: I 23 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7350 (mtt90) REVERT: J 23 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7445 (mtt-85) REVERT: K 23 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7525 (mtt-85) REVERT: L 23 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7336 (mtt90) outliers start: 51 outliers final: 36 residues processed: 269 average time/residue: 1.0745 time to fit residues: 337.0327 Evaluate side-chains 281 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 134 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 176 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS G 9 ASN G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116064 restraints weight = 56982.514| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.45 r_work: 0.3230 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21516 Z= 0.135 Angle : 0.473 4.261 28512 Z= 0.252 Chirality : 0.038 0.131 3012 Planarity : 0.004 0.032 3288 Dihedral : 8.477 59.118 4284 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.43 % Allowed : 10.10 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.40 (0.17), residues: 2256 helix: 3.21 (0.12), residues: 1728 sheet: -0.88 (0.35), residues: 132 loop : -1.33 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 101 TYR 0.010 0.002 TYR A 66 PHE 0.015 0.001 PHE J 202 TRP 0.005 0.001 TRP F 4 HIS 0.016 0.002 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00315 (21480) covalent geometry : angle 0.47110 (28440) SS BOND : bond 0.00183 ( 36) SS BOND : angle 0.91298 ( 72) hydrogen bonds : bond 0.03874 ( 1428) hydrogen bonds : angle 4.35435 ( 4212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 0.877 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: A 23 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7312 (mtt90) REVERT: C 23 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7329 (mtt90) REVERT: D 23 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7569 (mtm-85) REVERT: D 183 ARG cc_start: 0.7699 (ttt180) cc_final: 0.7142 (tpt170) REVERT: F 16 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7760 (mm-30) REVERT: F 23 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7401 (mtt90) REVERT: G 23 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7459 (mtt-85) REVERT: I 23 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7349 (mtt90) REVERT: J 23 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7442 (mtt-85) REVERT: K 23 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7514 (mtt-85) REVERT: L 23 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7335 (mtt90) outliers start: 51 outliers final: 39 residues processed: 277 average time/residue: 0.9827 time to fit residues: 318.3538 Evaluate side-chains 291 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 99 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 176 HIS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 HIS Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 176 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 91 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 176 HIS B 233 HIS C 176 HIS D 9 ASN E 176 HIS F 176 HIS F 233 HIS G 9 ASN G 233 HIS H 176 HIS I 176 HIS I 233 HIS J 233 HIS K 176 HIS K 233 HIS L 176 HIS L 233 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115808 restraints weight = 57259.537| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.45 r_work: 0.3245 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21516 Z= 0.146 Angle : 0.493 10.226 28512 Z= 0.264 Chirality : 0.039 0.130 3012 Planarity : 0.004 0.032 3288 Dihedral : 8.515 59.147 4284 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.52 % Allowed : 10.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2256 helix: 3.11 (0.12), residues: 1716 sheet: -0.88 (0.35), residues: 132 loop : -1.27 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 101 TYR 0.011 0.002 TYR A 66 PHE 0.016 0.002 PHE J 202 TRP 0.004 0.001 TRP F 4 HIS 0.017 0.002 HIS K 176 Details of bonding type rmsd covalent geometry : bond 0.00340 (21480) covalent geometry : angle 0.49092 (28440) SS BOND : bond 0.00198 ( 36) SS BOND : angle 0.93779 ( 72) hydrogen bonds : bond 0.03985 ( 1428) hydrogen bonds : angle 4.39560 ( 4212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13053.52 seconds wall clock time: 220 minutes 56.29 seconds (13256.29 seconds total)