Starting phenix.real_space_refine on Sat Jul 4 18:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbm_38223/07_2026/8xbm_38223.map" } resolution = 3.0 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= 0.040 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 120 5.16 5 C 15132 2.51 5 N 3576 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22860 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1858 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.03, per 1000 atoms: 0.13 Number of scatterers: 22860 At special positions: 0 Unit cell: (99.2673, 104.633, 192.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 36 15.00 O 3996 8.00 N 3576 7.00 C 15132 6.00 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 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 74.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 150 through 177 Processing helix chain 'A' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.783A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 86 through 114 removed outlier: 3.627A pdb=" N LEU B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 150 through 177 Processing helix chain 'B' and resid 202 through 238 removed outlier: 3.726A pdb=" N ASP B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 150 through 177 Processing helix chain 'C' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 34 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.783A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 86 through 114 removed outlier: 3.627A pdb=" N LEU D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 150 through 177 Processing helix chain 'D' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 34 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.783A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 150 through 177 Processing helix chain 'E' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 34 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 150 through 177 Processing helix chain 'F' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.783A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.580A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 Processing helix chain 'G' and resid 86 through 114 removed outlier: 3.627A pdb=" N LEU G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 150 through 177 Processing helix chain 'G' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP G 238 " --> pdb=" O LYS G 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 34 through 40 Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 45' Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 Processing helix chain 'H' and resid 86 through 114 removed outlier: 3.627A pdb=" N LEU H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 150 through 177 Processing helix chain 'H' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP H 238 " --> pdb=" O LYS H 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 34 through 40 Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 45' Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 Processing helix chain 'I' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 150 through 177 Processing helix chain 'I' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 34 through 40 Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.785A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 Processing helix chain 'J' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU J 90 " --> pdb=" O SER J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 150 through 177 Processing helix chain 'J' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP J 238 " --> pdb=" O LYS J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 34 through 40 Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.784A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 45' Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 Processing helix chain 'K' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 150 through 177 Processing helix chain 'K' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP K 238 " --> pdb=" O LYS K 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 19 through 32 Processing helix chain 'L' and resid 34 through 40 Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.783A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 45' Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.579A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 Processing helix chain 'L' and resid 86 through 114 removed outlier: 3.628A pdb=" N LEU L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 150 through 177 Processing helix chain 'L' and resid 202 through 238 removed outlier: 3.725A pdb=" N ASP L 238 " --> pdb=" O LYS L 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.714A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.714A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.714A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1548 hydrogen bonds defined for protein. 4608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3611 1.32 - 1.45: 6298 1.45 - 1.57: 13299 1.57 - 1.69: 48 1.69 - 1.81: 168 Bond restraints: 23424 Sorted by residual: bond pdb=" O4 PIO F 301 " pdb=" P4 PIO F 301 " ideal model delta sigma weight residual 1.710 1.617 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" O4 PIO J 301 " pdb=" P4 PIO J 301 " ideal model delta sigma weight residual 1.710 1.618 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O4 PIO E 301 " pdb=" P4 PIO E 301 " ideal model delta sigma weight residual 1.710 1.618 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O4 PIO G 301 " pdb=" P4 PIO G 301 " ideal model delta sigma weight residual 1.710 1.618 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O4 PIO B 301 " pdb=" P4 PIO B 301 " ideal model delta sigma weight residual 1.710 1.618 0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 23419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 30523 1.17 - 2.35: 772 2.35 - 3.52: 189 3.52 - 4.70: 88 4.70 - 5.87: 48 Bond angle restraints: 31620 Sorted by residual: angle pdb=" C2A PIO E 301 " pdb=" C1A PIO E 301 " pdb=" O2C PIO E 301 " ideal model delta sigma weight residual 110.66 116.53 -5.87 3.00e+00 1.11e-01 3.83e+00 angle pdb=" C2A PIO L 301 " pdb=" C1A PIO L 301 " pdb=" O2C PIO L 301 " ideal model delta sigma weight residual 110.66 116.53 -5.87 3.00e+00 1.11e-01 3.83e+00 angle pdb=" C2A PIO D 301 " pdb=" C1A PIO D 301 " pdb=" O2C PIO D 301 " ideal model delta sigma weight residual 110.66 116.53 -5.87 3.00e+00 1.11e-01 3.83e+00 angle pdb=" C2A PIO F 301 " pdb=" C1A PIO F 301 " pdb=" O2C PIO F 301 " ideal model delta sigma weight residual 110.66 116.52 -5.86 3.00e+00 1.11e-01 3.81e+00 angle pdb=" C2A PIO H 301 " pdb=" C1A PIO H 301 " pdb=" O2C PIO H 301 " ideal model delta sigma weight residual 110.66 116.52 -5.86 3.00e+00 1.11e-01 3.81e+00 ... (remaining 31615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12783 17.14 - 34.27: 717 34.27 - 51.41: 180 51.41 - 68.54: 36 68.54 - 85.68: 12 Dihedral angle restraints: 13728 sinusoidal: 5772 harmonic: 7956 Sorted by residual: dihedral pdb=" CA ARG E 76 " pdb=" CB ARG E 76 " pdb=" CG ARG E 76 " pdb=" CD ARG E 76 " ideal model delta sinusoidal sigma weight residual 180.00 134.67 45.33 3 1.50e+01 4.44e-03 8.15e+00 dihedral pdb=" CA ARG D 76 " pdb=" CB ARG D 76 " pdb=" CG ARG D 76 " pdb=" CD ARG D 76 " ideal model delta sinusoidal sigma weight residual 180.00 134.67 45.33 3 1.50e+01 4.44e-03 8.15e+00 dihedral pdb=" CA ARG K 76 " pdb=" CB ARG K 76 " pdb=" CG ARG K 76 " pdb=" CD ARG K 76 " ideal model delta sinusoidal sigma weight residual 180.00 134.68 45.32 3 1.50e+01 4.44e-03 8.15e+00 ... (remaining 13725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2939 0.049 - 0.098: 518 0.098 - 0.147: 59 0.147 - 0.196: 0 0.196 - 0.245: 24 Chirality restraints: 3540 Sorted by residual: chirality pdb=" C1 PIO L 301 " pdb=" C2 PIO L 301 " pdb=" C6 PIO L 301 " pdb=" O1 PIO L 301 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 PIO G 301 " pdb=" C2 PIO G 301 " pdb=" C6 PIO G 301 " pdb=" O1 PIO G 301 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 PIO J 301 " pdb=" C2 PIO J 301 " pdb=" C6 PIO J 301 " pdb=" O1 PIO J 301 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3537 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 190 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.82e-01 pdb=" N PRO G 191 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO G 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 191 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 190 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.76e-01 pdb=" N PRO H 191 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO H 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 191 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 190 " 0.014 5.00e-02 4.00e+02 2.05e-02 6.75e-01 pdb=" N PRO C 191 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " 0.010 5.00e-02 4.00e+02 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4432 2.78 - 3.31: 22405 3.31 - 3.84: 37501 3.84 - 4.37: 37267 4.37 - 4.90: 69203 Nonbonded interactions: 170808 Sorted by model distance: nonbonded pdb=" OH TYR C 155 " pdb=" OE2 GLU C 227 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR J 155 " pdb=" OE2 GLU J 227 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR D 155 " pdb=" OE2 GLU D 227 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR E 155 " pdb=" OE2 GLU E 227 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR B 155 " pdb=" OE2 GLU B 227 " model vdw 2.246 3.040 ... (remaining 170803 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 23460 Z= 0.247 Angle : 0.538 5.873 31692 Z= 0.244 Chirality : 0.040 0.245 3540 Planarity : 0.002 0.021 3744 Dihedral : 11.718 85.680 8484 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.96 % Allowed : 5.39 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.17), residues: 2676 helix: 3.43 (0.11), residues: 1920 sheet: 2.27 (0.47), residues: 132 loop : -1.78 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 189 TYR 0.008 0.001 TYR D 155 PHE 0.006 0.001 PHE C 52 TRP 0.004 0.001 TRP L 78 HIS 0.001 0.000 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.25 (23424) covalent geometry : angle 0.53776 / 0.24 (31620) SS BOND : bond 0.00152 / 0.09 ( 36) SS BOND : angle 0.59394 / 0.43 ( 72) hydrogen bonds : bond 0.08908 / 6.04 ( 1548) hydrogen bonds : angle 3.36786 / 2.37 ( 4608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 530 time to evaluate : 0.922 Fit side-chains REVERT: A 17 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.5278 (p90) REVERT: A 93 LEU cc_start: 0.8554 (tm) cc_final: 0.8075 (tm) REVERT: A 229 PHE cc_start: 0.7995 (t80) cc_final: 0.7747 (t80) REVERT: B 17 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.4985 (p90) REVERT: B 93 LEU cc_start: 0.8556 (tm) cc_final: 0.8094 (tm) REVERT: B 229 PHE cc_start: 0.8082 (t80) cc_final: 0.7833 (t80) REVERT: C 17 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.4945 (p90) REVERT: C 93 LEU cc_start: 0.8434 (tm) cc_final: 0.8037 (tm) REVERT: D 17 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.5252 (p90) REVERT: D 93 LEU cc_start: 0.8550 (tm) cc_final: 0.8073 (tm) REVERT: D 229 PHE cc_start: 0.8004 (t80) cc_final: 0.7755 (t80) REVERT: E 17 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.4983 (p90) REVERT: E 93 LEU cc_start: 0.8556 (tm) cc_final: 0.8094 (tm) REVERT: E 229 PHE cc_start: 0.8080 (t80) cc_final: 0.7832 (t80) REVERT: F 17 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.4909 (p90) REVERT: F 93 LEU cc_start: 0.8418 (tm) cc_final: 0.8016 (tm) REVERT: G 17 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.4991 (p90) REVERT: G 93 LEU cc_start: 0.8534 (tm) cc_final: 0.8078 (tm) REVERT: G 229 PHE cc_start: 0.8116 (t80) cc_final: 0.7876 (t80) REVERT: H 17 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.4945 (p90) REVERT: H 93 LEU cc_start: 0.8420 (tm) cc_final: 0.8019 (tm) REVERT: I 17 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.5258 (p90) REVERT: I 93 LEU cc_start: 0.8553 (tm) cc_final: 0.8076 (tm) REVERT: I 229 PHE cc_start: 0.7995 (t80) cc_final: 0.7747 (t80) REVERT: J 17 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.4984 (p90) REVERT: J 93 LEU cc_start: 0.8557 (tm) cc_final: 0.8094 (tm) REVERT: J 229 PHE cc_start: 0.8119 (t80) cc_final: 0.7880 (t80) REVERT: K 17 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.4908 (p90) REVERT: K 93 LEU cc_start: 0.8418 (tm) cc_final: 0.8015 (tm) REVERT: L 17 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.5260 (p90) REVERT: L 93 LEU cc_start: 0.8554 (tm) cc_final: 0.8071 (tm) REVERT: L 229 PHE cc_start: 0.7996 (t80) cc_final: 0.7747 (t80) outliers start: 48 outliers final: 0 residues processed: 554 average time/residue: 0.6300 time to fit residues: 398.3030 Evaluate side-chains 332 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 320 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain L residue 17 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 142 HIS A 173 GLN B 81 GLN C 81 GLN C 173 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS D 173 GLN E 81 GLN F 81 GLN F 173 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 173 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS I 173 GLN J 81 GLN K 81 GLN K 173 GLN L 81 GLN L 173 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.142338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100038 restraints weight = 38440.228| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.50 r_work: 0.3309 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23460 Z= 0.122 Angle : 0.526 5.194 31692 Z= 0.273 Chirality : 0.037 0.164 3540 Planarity : 0.004 0.053 3744 Dihedral : 8.835 61.377 3144 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.98 % Allowed : 10.54 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.17), residues: 2676 helix: 3.59 (0.11), residues: 1920 sheet: 2.01 (0.46), residues: 132 loop : -1.78 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 153 TYR 0.009 0.001 TYR E 230 PHE 0.020 0.001 PHE A 233 TRP 0.004 0.001 TRP L 4 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (23424) covalent geometry : angle 0.52647 / 0.27 (31620) SS BOND : bond 0.00064 / 0.04 ( 36) SS BOND : angle 0.39065 / 0.29 ( 72) hydrogen bonds : bond 0.03888 / 2.59 ( 1548) hydrogen bonds : angle 2.81396 / 1.99 ( 4608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 389 time to evaluate : 0.692 Fit side-chains REVERT: A 17 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5226 (p90) REVERT: A 93 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8092 (tm) REVERT: B 17 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.5048 (p90) REVERT: B 93 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8116 (tm) REVERT: C 17 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.4911 (p90) REVERT: C 93 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8023 (tm) REVERT: C 135 PHE cc_start: 0.6117 (t80) cc_final: 0.5607 (t80) REVERT: C 140 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6330 (mp0) REVERT: D 17 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.5180 (p90) REVERT: D 93 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8086 (tm) REVERT: E 17 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.5048 (p90) REVERT: E 93 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8112 (tm) REVERT: F 17 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.4829 (p90) REVERT: F 93 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8023 (tm) REVERT: F 135 PHE cc_start: 0.6114 (t80) cc_final: 0.5597 (t80) REVERT: F 140 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6319 (mp0) REVERT: G 17 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.4995 (p90) REVERT: G 93 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8139 (tm) REVERT: H 17 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.4820 (p90) REVERT: H 93 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8023 (tm) REVERT: H 135 PHE cc_start: 0.6116 (t80) cc_final: 0.5603 (t80) REVERT: H 140 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6323 (mp0) REVERT: I 17 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.5235 (p90) REVERT: I 47 ASP cc_start: 0.9199 (p0) cc_final: 0.8997 (p0) REVERT: I 93 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8074 (tm) REVERT: J 17 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5049 (p90) REVERT: J 93 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8112 (tm) REVERT: K 17 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.4833 (p90) REVERT: K 93 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8023 (tm) REVERT: K 135 PHE cc_start: 0.6114 (t80) cc_final: 0.5601 (t80) REVERT: K 140 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6326 (mp0) REVERT: L 17 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.5219 (p90) REVERT: L 93 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8069 (tm) outliers start: 122 outliers final: 51 residues processed: 460 average time/residue: 0.5946 time to fit residues: 314.1040 Evaluate side-chains 409 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 334 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 30 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Chi-restraints excluded: chain L residue 238 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 258 optimal weight: 0.3980 chunk 242 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 81 GLN L 57 GLN L 81 GLN L 142 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100208 restraints weight = 38639.668| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.49 r_work: 0.3314 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23460 Z= 0.117 Angle : 0.523 7.320 31692 Z= 0.276 Chirality : 0.037 0.183 3540 Planarity : 0.004 0.039 3744 Dihedral : 8.394 54.736 3144 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.49 % Allowed : 13.28 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.60 (0.17), residues: 2676 helix: 3.55 (0.11), residues: 1920 sheet: 2.07 (0.46), residues: 132 loop : -1.68 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 153 TYR 0.009 0.001 TYR D 155 PHE 0.012 0.001 PHE J 232 TRP 0.005 0.001 TRP C 45 HIS 0.002 0.000 HIS G 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (23424) covalent geometry : angle 0.52374 / 0.28 (31620) SS BOND : bond 0.00058 / 0.04 ( 36) SS BOND : angle 0.35165 / 0.26 ( 72) hydrogen bonds : bond 0.03622 / 2.41 ( 1548) hydrogen bonds : angle 2.72646 / 1.93 ( 4608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 408 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.5281 (p90) REVERT: A 93 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8035 (tm) REVERT: A 139 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6034 (tp) REVERT: A 140 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: A 153 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7108 (ptt-90) REVERT: A 231 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7318 (p) REVERT: B 17 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.5041 (p90) REVERT: B 93 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8102 (tm) REVERT: B 139 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.5943 (tp) REVERT: C 17 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.4896 (p90) REVERT: C 48 GLU cc_start: 0.8854 (pm20) cc_final: 0.8643 (pm20) REVERT: C 93 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8004 (tm) REVERT: D 17 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5238 (p90) REVERT: D 93 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8069 (tm) REVERT: D 139 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6043 (tp) REVERT: D 140 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5660 (mp0) REVERT: D 153 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7195 (ptt-90) REVERT: D 231 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7327 (p) REVERT: E 17 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.5029 (p90) REVERT: E 93 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8101 (tm) REVERT: E 139 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.5937 (tp) REVERT: F 17 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.4878 (p90) REVERT: F 48 GLU cc_start: 0.8860 (pm20) cc_final: 0.8645 (pm20) REVERT: F 93 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7982 (tm) REVERT: G 17 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.5097 (p90) REVERT: G 93 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8103 (tm) REVERT: H 17 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.4869 (p90) REVERT: H 48 GLU cc_start: 0.8859 (pm20) cc_final: 0.8648 (pm20) REVERT: H 93 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8009 (tm) REVERT: I 17 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.5333 (p90) REVERT: I 93 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8030 (tm) REVERT: I 139 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6063 (tp) REVERT: I 140 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5689 (mp0) REVERT: I 153 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7108 (ptt-90) REVERT: I 231 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7302 (p) REVERT: J 17 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.5043 (p90) REVERT: J 93 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8101 (tm) REVERT: J 139 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.5960 (tp) REVERT: K 17 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.4885 (p90) REVERT: K 48 GLU cc_start: 0.8852 (pm20) cc_final: 0.8640 (pm20) REVERT: K 93 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7983 (tm) REVERT: L 17 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.5327 (p90) REVERT: L 93 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8105 (tm) REVERT: L 139 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6053 (tp) REVERT: L 140 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5686 (mp0) REVERT: L 231 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7330 (p) outliers start: 110 outliers final: 41 residues processed: 470 average time/residue: 0.5976 time to fit residues: 321.7822 Evaluate side-chains 448 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 368 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 30 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 135 PHE Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 240 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 224 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.140930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098818 restraints weight = 38549.611| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.47 r_work: 0.3288 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23460 Z= 0.140 Angle : 0.533 5.018 31692 Z= 0.282 Chirality : 0.037 0.168 3540 Planarity : 0.003 0.023 3744 Dihedral : 8.364 56.374 3144 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.55 % Allowed : 15.24 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.17), residues: 2676 helix: 3.55 (0.11), residues: 1920 sheet: 1.97 (0.46), residues: 132 loop : -1.70 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 153 TYR 0.008 0.001 TYR D 155 PHE 0.022 0.001 PHE D 135 TRP 0.004 0.001 TRP I 4 HIS 0.001 0.000 HIS K 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (23424) covalent geometry : angle 0.53309 / 0.28 (31620) SS BOND : bond 0.00077 / 0.05 ( 36) SS BOND : angle 0.35553 / 0.26 ( 72) hydrogen bonds : bond 0.03966 / 2.63 ( 1548) hydrogen bonds : angle 2.76193 / 1.95 ( 4608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 354 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.5353 (p90) REVERT: A 93 LEU cc_start: 0.8517 (tm) cc_final: 0.8093 (tm) REVERT: A 140 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5524 (mp0) REVERT: A 153 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7172 (ptt-90) REVERT: B 17 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.5204 (p90) REVERT: B 93 LEU cc_start: 0.8626 (tm) cc_final: 0.8111 (tm) REVERT: C 17 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.4912 (p90) REVERT: C 67 ASP cc_start: 0.9103 (t70) cc_final: 0.8656 (t0) REVERT: C 93 LEU cc_start: 0.8393 (tm) cc_final: 0.8008 (tm) REVERT: D 17 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.5304 (p90) REVERT: D 93 LEU cc_start: 0.8516 (tm) cc_final: 0.8012 (tm) REVERT: D 140 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5479 (mp0) REVERT: D 153 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7203 (ptt-90) REVERT: E 17 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5186 (p90) REVERT: E 93 LEU cc_start: 0.8627 (tm) cc_final: 0.8109 (tm) REVERT: F 17 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.4899 (p90) REVERT: F 67 ASP cc_start: 0.9096 (t70) cc_final: 0.8640 (t0) REVERT: F 93 LEU cc_start: 0.8395 (tm) cc_final: 0.8019 (tm) REVERT: G 17 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.5258 (p90) REVERT: G 93 LEU cc_start: 0.8604 (tm) cc_final: 0.8096 (tm) REVERT: H 17 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.4879 (p90) REVERT: H 67 ASP cc_start: 0.9101 (t70) cc_final: 0.8654 (t0) REVERT: H 93 LEU cc_start: 0.8394 (tm) cc_final: 0.8013 (tm) REVERT: I 17 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.5364 (p90) REVERT: I 93 LEU cc_start: 0.8530 (tm) cc_final: 0.8110 (tm) REVERT: I 140 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5525 (mp0) REVERT: I 153 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7179 (ptt-90) REVERT: J 17 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.5200 (p90) REVERT: J 93 LEU cc_start: 0.8624 (tm) cc_final: 0.8107 (tm) REVERT: K 17 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.4885 (p90) REVERT: K 48 GLU cc_start: 0.8890 (pm20) cc_final: 0.8661 (pm20) REVERT: K 67 ASP cc_start: 0.9098 (t70) cc_final: 0.8649 (t0) REVERT: K 93 LEU cc_start: 0.8390 (tm) cc_final: 0.8015 (tm) REVERT: L 17 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.5366 (p90) REVERT: L 93 LEU cc_start: 0.8541 (tm) cc_final: 0.8117 (tm) REVERT: L 140 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5523 (mp0) outliers start: 87 outliers final: 46 residues processed: 403 average time/residue: 0.5406 time to fit residues: 253.8903 Evaluate side-chains 433 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 371 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN B 81 GLN C 81 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 81 GLN J 81 GLN K 81 GLN L 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.140835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098670 restraints weight = 38238.625| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.45 r_work: 0.3285 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23460 Z= 0.139 Angle : 0.544 5.688 31692 Z= 0.287 Chirality : 0.037 0.172 3540 Planarity : 0.003 0.024 3744 Dihedral : 8.477 58.894 3144 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.74 % Allowed : 15.16 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.17), residues: 2676 helix: 3.54 (0.11), residues: 1920 sheet: 1.88 (0.46), residues: 132 loop : -1.67 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 153 TYR 0.006 0.001 TYR B 155 PHE 0.017 0.001 PHE D 135 TRP 0.004 0.001 TRP D 4 HIS 0.002 0.000 HIS F 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (23424) covalent geometry : angle 0.54415 / 0.29 (31620) SS BOND : bond 0.00085 / 0.06 ( 36) SS BOND : angle 0.35186 / 0.26 ( 72) hydrogen bonds : bond 0.04005 / 2.66 ( 1548) hydrogen bonds : angle 2.77582 / 1.97 ( 4608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 383 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.5356 (p90) REVERT: A 93 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8113 (tm) REVERT: A 139 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6540 (tp) REVERT: A 140 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: A 153 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7196 (ptt-90) REVERT: B 17 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.5266 (p90) REVERT: B 93 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8105 (tm) REVERT: C 17 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.4905 (p90) REVERT: C 48 GLU cc_start: 0.8918 (pm20) cc_final: 0.8684 (pm20) REVERT: C 67 ASP cc_start: 0.9121 (t70) cc_final: 0.8679 (t0) REVERT: C 93 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8009 (tm) REVERT: D 17 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.5316 (p90) REVERT: D 93 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8040 (tm) REVERT: D 139 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6443 (tp) REVERT: D 140 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5714 (mm-30) REVERT: D 153 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7185 (ptt-90) REVERT: E 17 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.5260 (p90) REVERT: E 93 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8101 (tm) REVERT: F 17 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.4867 (p90) REVERT: F 48 GLU cc_start: 0.8915 (pm20) cc_final: 0.8677 (pm20) REVERT: F 67 ASP cc_start: 0.9116 (t70) cc_final: 0.8666 (t0) REVERT: F 93 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8015 (tm) REVERT: G 17 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.5287 (p90) REVERT: G 93 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8110 (tm) REVERT: H 17 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.4863 (p90) REVERT: H 48 GLU cc_start: 0.8905 (pm20) cc_final: 0.8673 (pm20) REVERT: H 67 ASP cc_start: 0.9122 (t70) cc_final: 0.8677 (t0) REVERT: H 93 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8012 (tm) REVERT: I 17 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5352 (p90) REVERT: I 93 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8119 (tm) REVERT: I 139 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6535 (tp) REVERT: I 140 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: I 153 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7157 (ptt-90) REVERT: J 17 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.5270 (p90) REVERT: J 93 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8108 (tm) REVERT: K 17 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.4865 (p90) REVERT: K 48 GLU cc_start: 0.8902 (pm20) cc_final: 0.8672 (pm20) REVERT: K 67 ASP cc_start: 0.9121 (t70) cc_final: 0.8672 (t0) REVERT: K 93 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8003 (tm) REVERT: L 17 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.5342 (p90) REVERT: L 48 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: L 93 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8111 (tm) REVERT: L 139 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6516 (tp) REVERT: L 140 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5548 (mp0) outliers start: 116 outliers final: 52 residues processed: 440 average time/residue: 0.5932 time to fit residues: 300.9998 Evaluate side-chains 423 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 338 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 30 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098960 restraints weight = 38554.083| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.47 r_work: 0.3290 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23460 Z= 0.130 Angle : 0.552 5.794 31692 Z= 0.290 Chirality : 0.037 0.172 3540 Planarity : 0.003 0.044 3744 Dihedral : 8.611 59.362 3144 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.82 % Allowed : 15.28 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.17), residues: 2676 helix: 3.57 (0.11), residues: 1920 sheet: 1.86 (0.46), residues: 132 loop : -1.67 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 153 TYR 0.007 0.001 TYR K 155 PHE 0.029 0.001 PHE I 135 TRP 0.004 0.001 TRP D 4 HIS 0.002 0.000 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (23424) covalent geometry : angle 0.55212 / 0.29 (31620) SS BOND : bond 0.00081 / 0.05 ( 36) SS BOND : angle 0.35757 / 0.27 ( 72) hydrogen bonds : bond 0.03899 / 2.59 ( 1548) hydrogen bonds : angle 2.75705 / 1.95 ( 4608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 355 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.5323 (p90) REVERT: A 48 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: A 93 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8108 (tm) REVERT: A 139 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.6748 (tp) REVERT: A 140 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5641 (mp0) REVERT: A 153 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7110 (ptt-90) REVERT: B 17 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.5345 (p90) REVERT: B 93 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8097 (tm) REVERT: B 153 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7005 (ptt-90) REVERT: C 17 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.4905 (p90) REVERT: C 48 GLU cc_start: 0.8928 (pm20) cc_final: 0.8691 (pm20) REVERT: C 93 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8002 (tm) REVERT: D 17 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.5302 (p90) REVERT: D 48 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: D 93 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8092 (tm) REVERT: D 139 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.6679 (tp) REVERT: D 140 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: D 153 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7160 (ptt-90) REVERT: E 17 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5331 (p90) REVERT: E 93 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8089 (tm) REVERT: E 153 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7022 (ptt-90) REVERT: F 17 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.4909 (p90) REVERT: F 48 GLU cc_start: 0.8936 (pm20) cc_final: 0.8697 (pm20) REVERT: F 93 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8008 (tm) REVERT: G 17 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.5340 (p90) REVERT: G 93 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8095 (tm) REVERT: G 153 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7006 (ptt-90) REVERT: H 17 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.4904 (p90) REVERT: H 48 GLU cc_start: 0.8912 (pm20) cc_final: 0.8677 (pm20) REVERT: H 93 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8004 (tm) REVERT: I 17 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.5314 (p90) REVERT: I 48 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: I 93 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8103 (tm) REVERT: I 139 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6682 (tp) REVERT: I 140 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: I 153 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7132 (ptt-90) REVERT: J 17 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.5351 (p90) REVERT: J 93 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8092 (tm) REVERT: J 153 ARG cc_start: 0.7543 (mtm110) cc_final: 0.7012 (ptt-90) REVERT: K 17 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.4907 (p90) REVERT: K 48 GLU cc_start: 0.8912 (pm20) cc_final: 0.8681 (pm20) REVERT: K 93 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7999 (tm) REVERT: L 17 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5249 (p90) REVERT: L 48 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: L 93 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8085 (tm) REVERT: L 139 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6752 (tp) REVERT: L 140 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5627 (mp0) outliers start: 118 outliers final: 51 residues processed: 407 average time/residue: 0.5804 time to fit residues: 273.4409 Evaluate side-chains 438 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 158 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099320 restraints weight = 38529.294| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.47 r_work: 0.3300 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23460 Z= 0.125 Angle : 0.557 5.601 31692 Z= 0.292 Chirality : 0.037 0.165 3540 Planarity : 0.003 0.047 3744 Dihedral : 8.567 59.924 3144 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.37 % Allowed : 16.54 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.17), residues: 2676 helix: 3.61 (0.11), residues: 1920 sheet: 1.85 (0.46), residues: 132 loop : -1.66 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 153 TYR 0.006 0.001 TYR B 155 PHE 0.022 0.001 PHE I 135 TRP 0.004 0.001 TRP L 4 HIS 0.001 0.000 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (23424) covalent geometry : angle 0.55727 / 0.29 (31620) SS BOND : bond 0.00079 / 0.05 ( 36) SS BOND : angle 0.35908 / 0.27 ( 72) hydrogen bonds : bond 0.03765 / 2.50 ( 1548) hydrogen bonds : angle 2.73880 / 1.94 ( 4608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 374 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5299 (p90) REVERT: A 48 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: A 93 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8100 (tm) REVERT: A 139 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.6774 (tp) REVERT: A 140 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5599 (mp0) REVERT: A 153 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7096 (ptt-90) REVERT: B 17 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.5354 (p90) REVERT: B 93 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8121 (tm) REVERT: B 153 ARG cc_start: 0.7500 (mtm110) cc_final: 0.7002 (ptt-90) REVERT: C 17 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.4882 (p90) REVERT: C 48 GLU cc_start: 0.8913 (pm20) cc_final: 0.8687 (pm20) REVERT: C 67 ASP cc_start: 0.9116 (t70) cc_final: 0.8663 (t0) REVERT: C 93 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (tm) REVERT: D 17 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.5329 (p90) REVERT: D 48 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: D 93 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8095 (tm) REVERT: D 139 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6775 (tp) REVERT: D 140 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: D 153 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7167 (ptt-90) REVERT: E 17 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.5338 (p90) REVERT: E 93 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8111 (tm) REVERT: E 153 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7016 (ptt-90) REVERT: F 17 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.4891 (p90) REVERT: F 48 GLU cc_start: 0.8924 (pm20) cc_final: 0.8692 (pm20) REVERT: F 67 ASP cc_start: 0.9099 (t70) cc_final: 0.8636 (t0) REVERT: F 93 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8010 (tm) REVERT: G 17 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.5344 (p90) REVERT: G 93 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8114 (tm) REVERT: G 153 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7004 (ptt-90) REVERT: H 17 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.4883 (p90) REVERT: H 48 GLU cc_start: 0.8909 (pm20) cc_final: 0.8684 (pm20) REVERT: H 67 ASP cc_start: 0.9108 (t70) cc_final: 0.8648 (t0) REVERT: H 93 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8013 (tm) REVERT: I 17 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.5304 (p90) REVERT: I 48 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: I 93 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8100 (tm) REVERT: I 139 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.6779 (tp) REVERT: I 140 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: I 153 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7120 (ptt-90) REVERT: J 17 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.5344 (p90) REVERT: J 93 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8107 (tm) REVERT: J 153 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7011 (ptt-90) REVERT: K 17 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.4883 (p90) REVERT: K 48 GLU cc_start: 0.8899 (pm20) cc_final: 0.8675 (pm20) REVERT: K 67 ASP cc_start: 0.9095 (t70) cc_final: 0.8632 (t0) REVERT: K 93 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8004 (tm) REVERT: L 17 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.5225 (p90) REVERT: L 48 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: L 93 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8080 (tm) REVERT: L 139 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.6785 (tp) REVERT: L 140 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5592 (mp0) outliers start: 107 outliers final: 56 residues processed: 415 average time/residue: 0.5941 time to fit residues: 284.6691 Evaluate side-chains 439 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 347 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 30 PHE Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 183 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 81 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 57 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.141225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099322 restraints weight = 38305.326| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23460 Z= 0.131 Angle : 0.575 6.662 31692 Z= 0.300 Chirality : 0.036 0.167 3540 Planarity : 0.003 0.049 3744 Dihedral : 8.344 57.512 3144 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.98 % Allowed : 16.83 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.17), residues: 2676 helix: 3.63 (0.11), residues: 1920 sheet: 1.85 (0.46), residues: 132 loop : -1.65 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 153 TYR 0.009 0.001 TYR A 155 PHE 0.020 0.001 PHE I 135 TRP 0.004 0.001 TRP E 4 HIS 0.002 0.000 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (23424) covalent geometry : angle 0.57558 / 0.30 (31620) SS BOND : bond 0.00080 / 0.05 ( 36) SS BOND : angle 0.35969 / 0.27 ( 72) hydrogen bonds : bond 0.03757 / 2.50 ( 1548) hydrogen bonds : angle 2.73470 / 1.93 ( 4608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 352 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5251 (p90) REVERT: A 48 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: A 93 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8084 (tm) REVERT: A 140 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5372 (mp0) REVERT: A 153 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7130 (ptt-90) REVERT: B 17 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.5342 (p90) REVERT: B 93 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8163 (tm) REVERT: B 153 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7017 (ptt-90) REVERT: C 17 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.4976 (p90) REVERT: C 48 GLU cc_start: 0.8927 (pm20) cc_final: 0.8697 (pm20) REVERT: C 67 ASP cc_start: 0.9112 (t70) cc_final: 0.8646 (t0) REVERT: C 93 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8009 (tm) REVERT: C 125 MET cc_start: 0.4999 (pmm) cc_final: 0.4669 (tmt) REVERT: D 17 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5297 (p90) REVERT: D 48 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: D 93 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8085 (tm) REVERT: D 140 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5717 (mp0) REVERT: D 153 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7147 (ptt-90) REVERT: E 17 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.5333 (p90) REVERT: E 93 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8150 (tm) REVERT: E 153 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7030 (ptt-90) REVERT: F 17 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.4970 (p90) REVERT: F 48 GLU cc_start: 0.8927 (pm20) cc_final: 0.8693 (pm20) REVERT: F 67 ASP cc_start: 0.9097 (t70) cc_final: 0.8623 (t0) REVERT: F 93 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8017 (tm) REVERT: F 125 MET cc_start: 0.4953 (pmm) cc_final: 0.4682 (tmt) REVERT: G 17 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.5420 (p90) REVERT: G 93 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8194 (tm) REVERT: G 153 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7030 (ptt-90) REVERT: H 17 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.4962 (p90) REVERT: H 48 GLU cc_start: 0.8919 (pm20) cc_final: 0.8689 (pm20) REVERT: H 67 ASP cc_start: 0.9113 (t70) cc_final: 0.8645 (t0) REVERT: H 93 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7999 (tm) REVERT: H 125 MET cc_start: 0.5027 (pmm) cc_final: 0.4691 (tmt) REVERT: I 17 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5237 (p90) REVERT: I 48 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: I 93 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8081 (tm) REVERT: I 140 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5365 (mp0) REVERT: I 153 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7131 (ptt-90) REVERT: J 17 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.5344 (p90) REVERT: J 93 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8154 (tm) REVERT: J 153 ARG cc_start: 0.7517 (mtm110) cc_final: 0.7034 (ptt-90) REVERT: K 17 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.4963 (p90) REVERT: K 48 GLU cc_start: 0.8912 (pm20) cc_final: 0.8687 (pm20) REVERT: K 67 ASP cc_start: 0.9109 (t70) cc_final: 0.8637 (t0) REVERT: K 93 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8012 (tm) REVERT: K 125 MET cc_start: 0.4953 (pmm) cc_final: 0.4691 (tmt) REVERT: L 17 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.5233 (p90) REVERT: L 48 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: L 93 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8068 (tm) REVERT: L 140 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5366 (mp0) outliers start: 122 outliers final: 60 residues processed: 401 average time/residue: 0.5978 time to fit residues: 276.4718 Evaluate side-chains 447 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 355 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 60 optimal weight: 0.0040 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN B 81 GLN C 57 GLN C 81 GLN D 57 GLN D 81 GLN E 81 GLN F 57 GLN F 81 GLN H 57 GLN H 81 GLN I 57 GLN I 81 GLN J 81 GLN K 57 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101119 restraints weight = 38724.944| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.47 r_work: 0.3333 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23460 Z= 0.121 Angle : 0.573 6.956 31692 Z= 0.300 Chirality : 0.036 0.159 3540 Planarity : 0.003 0.044 3744 Dihedral : 7.994 53.770 3144 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.37 % Allowed : 17.65 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.17), residues: 2676 helix: 3.65 (0.11), residues: 1932 sheet: 1.84 (0.46), residues: 132 loop : -1.51 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 153 TYR 0.006 0.001 TYR B 155 PHE 0.020 0.001 PHE L 135 TRP 0.004 0.001 TRP J 4 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23424) covalent geometry : angle 0.57357 / 0.30 (31620) SS BOND : bond 0.00078 / 0.05 ( 36) SS BOND : angle 0.39419 / 0.29 ( 72) hydrogen bonds : bond 0.03251 / 2.17 ( 1548) hydrogen bonds : angle 2.68855 / 1.89 ( 4608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 355 time to evaluate : 0.914 Fit side-chains REVERT: A 15 GLN cc_start: 0.7546 (pp30) cc_final: 0.7314 (pp30) REVERT: A 17 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.5230 (p90) REVERT: A 48 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: A 93 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8068 (tm) REVERT: A 140 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5366 (mp0) REVERT: B 17 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.5328 (p90) REVERT: B 93 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8194 (tm) REVERT: B 153 ARG cc_start: 0.7465 (mtm110) cc_final: 0.7018 (ptt-90) REVERT: C 17 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.5032 (p90) REVERT: C 48 GLU cc_start: 0.8909 (pm20) cc_final: 0.8699 (pm20) REVERT: C 93 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7993 (tm) REVERT: D 15 GLN cc_start: 0.7556 (pp30) cc_final: 0.7321 (pp30) REVERT: D 17 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.5187 (p90) REVERT: D 48 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: D 93 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8102 (tm) REVERT: D 140 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5310 (mp0) REVERT: E 17 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5314 (p90) REVERT: E 93 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8158 (tm) REVERT: E 153 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7033 (ptt-90) REVERT: F 17 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.5035 (p90) REVERT: F 48 GLU cc_start: 0.8916 (pm20) cc_final: 0.8702 (pm20) REVERT: F 93 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7977 (tm) REVERT: G 17 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.5439 (p90) REVERT: G 93 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8179 (tm) REVERT: G 153 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7038 (ptt-90) REVERT: H 17 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.5033 (p90) REVERT: H 48 GLU cc_start: 0.8902 (pm20) cc_final: 0.8690 (pm20) REVERT: H 93 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7996 (tm) REVERT: I 15 GLN cc_start: 0.7541 (pp30) cc_final: 0.7309 (pp30) REVERT: I 17 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.5233 (p90) REVERT: I 48 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: I 93 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8099 (tm) REVERT: I 140 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5363 (mp0) REVERT: I 153 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7109 (ptt-90) REVERT: J 17 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.5333 (p90) REVERT: J 93 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8189 (tm) REVERT: J 153 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7027 (ptt-90) REVERT: K 17 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.5034 (p90) REVERT: K 48 GLU cc_start: 0.8889 (pm20) cc_final: 0.8683 (pm20) REVERT: K 93 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7979 (tm) REVERT: L 15 GLN cc_start: 0.7575 (pp30) cc_final: 0.7343 (pp30) REVERT: L 17 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.5240 (p90) REVERT: L 48 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8715 (pm20) REVERT: L 93 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8055 (tm) REVERT: L 140 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5422 (mp0) outliers start: 107 outliers final: 41 residues processed: 402 average time/residue: 0.5792 time to fit residues: 269.6369 Evaluate side-chains 398 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 325 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 252 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN B 81 GLN C 81 GLN D 81 GLN E 81 GLN F 81 GLN G 81 GLN H 81 GLN I 81 GLN J 81 GLN K 81 GLN L 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100273 restraints weight = 38729.101| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.47 r_work: 0.3321 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23460 Z= 0.125 Angle : 0.577 6.895 31692 Z= 0.302 Chirality : 0.036 0.165 3540 Planarity : 0.003 0.044 3744 Dihedral : 7.865 51.384 3144 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.55 % Allowed : 18.30 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.17), residues: 2676 helix: 3.64 (0.11), residues: 1932 sheet: 1.83 (0.46), residues: 132 loop : -1.47 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 153 TYR 0.006 0.001 TYR B 155 PHE 0.017 0.001 PHE A 135 TRP 0.004 0.001 TRP F 45 HIS 0.002 0.000 HIS F 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (23424) covalent geometry : angle 0.57713 / 0.30 (31620) SS BOND : bond 0.00074 / 0.05 ( 36) SS BOND : angle 0.36214 / 0.27 ( 72) hydrogen bonds : bond 0.03415 / 2.27 ( 1548) hydrogen bonds : angle 2.68355 / 1.89 ( 4608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 0.921 Fit side-chains REVERT: A 17 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.5221 (p90) REVERT: A 48 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 93 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8080 (tm) REVERT: A 140 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5394 (mp0) REVERT: A 141 GLU cc_start: 0.6741 (mp0) cc_final: 0.6526 (mp0) REVERT: B 17 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.5297 (p90) REVERT: B 93 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8175 (tm) REVERT: B 153 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7035 (ptt-90) REVERT: B 230 TYR cc_start: 0.8303 (t80) cc_final: 0.8054 (t80) REVERT: C 17 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.4956 (p90) REVERT: C 93 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8007 (tm) REVERT: D 17 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.5171 (p90) REVERT: D 48 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: D 93 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8070 (tm) REVERT: D 140 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5370 (mp0) REVERT: D 141 GLU cc_start: 0.6825 (mp0) cc_final: 0.6612 (mp0) REVERT: E 17 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.5292 (p90) REVERT: E 93 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8168 (tm) REVERT: E 153 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7047 (ptt-90) REVERT: E 230 TYR cc_start: 0.8303 (t80) cc_final: 0.8048 (t80) REVERT: F 17 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.4962 (p90) REVERT: F 48 GLU cc_start: 0.8892 (pm20) cc_final: 0.8692 (pm20) REVERT: F 93 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8011 (tm) REVERT: G 17 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.5353 (p90) REVERT: G 93 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8189 (tm) REVERT: G 153 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7046 (ptt-90) REVERT: H 17 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.4962 (p90) REVERT: H 93 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8008 (tm) REVERT: I 17 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.5231 (p90) REVERT: I 48 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: I 93 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8080 (tm) REVERT: I 140 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5428 (mp0) REVERT: I 153 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7105 (ptt-90) REVERT: J 17 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.5300 (p90) REVERT: J 93 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8171 (tm) REVERT: J 153 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7047 (ptt-90) REVERT: J 230 TYR cc_start: 0.8301 (t80) cc_final: 0.8049 (t80) REVERT: K 17 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.4968 (p90) REVERT: K 93 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8005 (tm) REVERT: L 17 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.5234 (p90) REVERT: L 93 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8073 (tm) REVERT: L 140 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5433 (mp0) outliers start: 87 outliers final: 41 residues processed: 379 average time/residue: 0.5345 time to fit residues: 237.2187 Evaluate side-chains 416 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 30 PHE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 30 PHE Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain I residue 140 GLU Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 17 TYR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain K residue 17 TYR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 30 PHE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 168 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 0.0670 chunk 130 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 60 optimal weight: 0.0060 chunk 155 optimal weight: 8.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 81 GLN C 81 GLN D 57 GLN D 81 GLN F 81 GLN G 81 GLN H 81 GLN I 57 GLN I 81 GLN K 81 GLN L 57 GLN L 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101168 restraints weight = 38781.632| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.46 r_work: 0.3332 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23460 Z= 0.124 Angle : 0.591 7.106 31692 Z= 0.309 Chirality : 0.036 0.168 3540 Planarity : 0.003 0.045 3744 Dihedral : 7.754 49.546 3144 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.43 % Allowed : 18.79 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.17), residues: 2676 helix: 3.64 (0.11), residues: 1932 sheet: 1.83 (0.46), residues: 132 loop : -1.46 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 153 TYR 0.006 0.001 TYR E 155 PHE 0.017 0.001 PHE A 135 TRP 0.004 0.001 TRP K 4 HIS 0.001 0.000 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (23424) covalent geometry : angle 0.59132 / 0.31 (31620) SS BOND : bond 0.00069 / 0.05 ( 36) SS BOND : angle 0.37300 / 0.28 ( 72) hydrogen bonds : bond 0.03248 / 2.16 ( 1548) hydrogen bonds : angle 2.66399 / 1.88 ( 4608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7710.18 seconds wall clock time: 132 minutes 24.71 seconds (7944.71 seconds total)