Starting phenix.real_space_refine on Thu May 29 16:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgg_38322/05_2025/8xgg_38322.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.132 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 S 156 5.16 5 C 11292 2.51 5 N 2532 2.21 5 O 2748 1.98 5 H 15972 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32700 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2657 Classifications: {'peptide': 165} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 6, 68 Unusual residues: {'HE2': 1, 'MC3': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'MC3:plan-2': 5, 'MC3:plan-1': 5} Unresolved non-hydrogen planarities: 34 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" CAABHE2 A 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 A 406 " occ=0.84 residue: pdb=" CAABHE2 C 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 C 406 " occ=0.84 residue: pdb=" CAABHE2 B 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 B 406 " occ=0.84 residue: pdb=" CAABHE2 D 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 D 406 " occ=0.84 residue: pdb=" CAABHE2 E 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 E 406 " occ=0.84 residue: pdb=" CAABHE2 F 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 F 406 " occ=0.84 residue: pdb=" CAABHE2 G 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 G 406 " occ=0.84 residue: pdb=" CAABHE2 H 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 H 406 " occ=0.84 residue: pdb=" CAABHE2 I 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 I 406 " occ=0.84 residue: pdb=" CAABHE2 J 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 J 406 " occ=0.84 residue: pdb=" CAABHE2 K 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 K 406 " occ=0.84 residue: pdb=" CAABHE2 L 406 " occ=0.84 ... (5 atoms not shown) pdb=" OABBHE2 L 406 " occ=0.84 Time building chain proxies: 8.66, per 1000 atoms: 0.26 Number of scatterers: 32700 At special positions: 0 Unit cell: (99.68, 101.92, 151.2, 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 156 16.00 O 2748 8.00 N 2532 7.00 C 11292 6.00 H 15972 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 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: 7.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 74.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.656A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.103A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL C 45 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 274 removed outlier: 3.644A pdb=" N ILE C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 removed outlier: 3.741A pdb=" N VAL B 45 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 274 removed outlier: 3.646A pdb=" N ILE B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL D 45 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 removed outlier: 3.741A pdb=" N VAL E 45 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.105A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 removed outlier: 3.741A pdb=" N VAL F 45 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 45' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 101 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE F 263 " --> pdb=" O ALA F 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL G 45 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 42 through 45' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE G 263 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL H 45 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 42 through 45' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU H 91 " --> pdb=" O CYS H 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE H 263 " --> pdb=" O ALA H 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 41 removed outlier: 4.105A pdb=" N ARG I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL I 45 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 45' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE I 263 " --> pdb=" O ALA I 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 45 removed outlier: 3.741A pdb=" N VAL J 45 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 42 through 45' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.630A pdb=" N LEU J 91 " --> pdb=" O CYS J 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 101 " --> pdb=" O SER J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE J 263 " --> pdb=" O ALA J 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 41 removed outlier: 4.104A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL K 45 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 42 through 45' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 274 removed outlier: 3.645A pdb=" N ILE K 263 " --> pdb=" O ALA K 259 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.103A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 45 removed outlier: 3.740A pdb=" N VAL L 45 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU L 91 " --> pdb=" O CYS L 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 274 removed outlier: 3.644A pdb=" N ILE L 263 " --> pdb=" O ALA L 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.662A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.661A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.662A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3276 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: 10.46 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15936 1.03 - 1.23: 240 1.23 - 1.43: 6780 1.43 - 1.63: 9852 1.63 - 1.82: 204 Bond restraints: 33012 Sorted by residual: bond pdb=" C37 MC3 K 405 " pdb=" C38 MC3 K 405 " ideal model delta sigma weight residual 1.524 1.493 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C37 MC3 B 405 " pdb=" C38 MC3 B 405 " ideal model delta sigma weight residual 1.524 1.493 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C37 MC3 L 405 " pdb=" C38 MC3 L 405 " ideal model delta sigma weight residual 1.524 1.493 0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C37 MC3 J 405 " pdb=" C38 MC3 J 405 " ideal model delta sigma weight residual 1.524 1.493 0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C37 MC3 G 405 " pdb=" C38 MC3 G 405 " ideal model delta sigma weight residual 1.524 1.493 0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 33007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 56426 1.45 - 2.90: 2118 2.90 - 4.35: 112 4.35 - 5.80: 108 5.80 - 7.25: 72 Bond angle restraints: 58836 Sorted by residual: angle pdb=" N GLY I 262 " pdb=" CA GLY I 262 " pdb=" C GLY I 262 " ideal model delta sigma weight residual 112.73 115.73 -3.00 1.20e+00 6.94e-01 6.25e+00 angle pdb=" N GLY H 262 " pdb=" CA GLY H 262 " pdb=" C GLY H 262 " ideal model delta sigma weight residual 112.73 115.72 -2.99 1.20e+00 6.94e-01 6.21e+00 angle pdb=" N GLY C 262 " pdb=" CA GLY C 262 " pdb=" C GLY C 262 " ideal model delta sigma weight residual 112.73 115.71 -2.98 1.20e+00 6.94e-01 6.18e+00 angle pdb=" N GLY L 262 " pdb=" CA GLY L 262 " pdb=" C GLY L 262 " ideal model delta sigma weight residual 112.73 115.70 -2.97 1.20e+00 6.94e-01 6.13e+00 angle pdb=" N GLY F 262 " pdb=" CA GLY F 262 " pdb=" C GLY F 262 " ideal model delta sigma weight residual 112.73 115.70 -2.97 1.20e+00 6.94e-01 6.13e+00 ... (remaining 58831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 14004 16.87 - 33.73: 1345 33.73 - 50.60: 467 50.60 - 67.46: 132 67.46 - 84.33: 24 Dihedral angle restraints: 15972 sinusoidal: 8712 harmonic: 7260 Sorted by residual: dihedral pdb=" CB GLU E 241 " pdb=" CG GLU E 241 " pdb=" CD GLU E 241 " pdb=" OE1 GLU E 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.33 -84.33 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CB GLU F 241 " pdb=" CG GLU F 241 " pdb=" CD GLU F 241 " pdb=" OE1 GLU F 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.32 -84.32 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CB GLU G 241 " pdb=" CG GLU G 241 " pdb=" CD GLU G 241 " pdb=" OE1 GLU G 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.30 -84.30 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 15969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1523 0.027 - 0.053: 508 0.053 - 0.080: 410 0.080 - 0.107: 138 0.107 - 0.134: 25 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA VAL E 225 " pdb=" N VAL E 225 " pdb=" C VAL E 225 " pdb=" CB VAL E 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL C 225 " pdb=" N VAL C 225 " pdb=" C VAL C 225 " pdb=" CB VAL C 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL L 225 " pdb=" N VAL L 225 " pdb=" C VAL L 225 " pdb=" CB VAL L 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2601 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 246 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO E 247 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 246 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO I 247 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 247 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 247 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 246 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO L 247 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.023 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 4801 2.29 - 2.86: 68581 2.86 - 3.44: 76733 3.44 - 4.02: 104419 4.02 - 4.60: 158305 Nonbonded interactions: 412839 Sorted by model distance: nonbonded pdb=" O SER L 245 " pdb=" HZ2 LYS L 250 " model vdw 1.707 2.450 nonbonded pdb=" O SER B 245 " pdb=" HZ2 LYS B 250 " model vdw 1.707 2.450 nonbonded pdb=" O SER F 245 " pdb=" HZ2 LYS F 250 " model vdw 1.707 2.450 nonbonded pdb=" O SER I 245 " pdb=" HZ2 LYS I 250 " model vdw 1.707 2.450 nonbonded pdb=" O SER E 245 " pdb=" HZ2 LYS E 250 " model vdw 1.707 2.450 ... (remaining 412834 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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=0.84 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: 0.840 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: 0.570 Extract box with map and model: 1.230 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 55.440 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17076 Z= 0.173 Angle : 0.841 7.245 22908 Z= 0.426 Chirality : 0.041 0.134 2604 Planarity : 0.005 0.041 2736 Dihedral : 15.472 84.326 6336 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.67 % Allowed : 14.00 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.17), residues: 1932 helix: 2.02 (0.13), residues: 1320 sheet: 1.07 (0.36), residues: 120 loop : -1.39 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 79 HIS 0.005 0.001 HIS I 274 PHE 0.005 0.001 PHE G 205 TYR 0.008 0.001 TYR K 67 ARG 0.003 0.001 ARG L 197 Details of bonding type rmsd hydrogen bonds : bond 0.13268 ( 1104) hydrogen bonds : angle 4.18399 ( 3276) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.23922 ( 72) covalent geometry : bond 0.00331 (17040) covalent geometry : angle 0.83961 (22836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 2.751 Fit side-chains REVERT: A 21 MET cc_start: 0.5398 (tpt) cc_final: 0.5141 (tpt) REVERT: A 43 GLU cc_start: 0.7503 (tp30) cc_final: 0.7192 (tp30) REVERT: C 43 GLU cc_start: 0.7545 (tp30) cc_final: 0.7270 (tp30) REVERT: B 21 MET cc_start: 0.5517 (tpt) cc_final: 0.4808 (ttt) REVERT: B 43 GLU cc_start: 0.7615 (tp30) cc_final: 0.7251 (tp30) REVERT: D 21 MET cc_start: 0.5221 (tpt) cc_final: 0.4942 (tpt) REVERT: D 43 GLU cc_start: 0.7499 (tp30) cc_final: 0.7202 (tp30) REVERT: E 21 MET cc_start: 0.5578 (tpt) cc_final: 0.4847 (ttt) REVERT: E 43 GLU cc_start: 0.7611 (tp30) cc_final: 0.7255 (tp30) REVERT: F 43 GLU cc_start: 0.7554 (tp30) cc_final: 0.7278 (tp30) REVERT: G 21 MET cc_start: 0.5311 (tpt) cc_final: 0.5047 (tpt) REVERT: G 43 GLU cc_start: 0.7504 (tp30) cc_final: 0.7198 (tp30) REVERT: H 21 MET cc_start: 0.5586 (tpt) cc_final: 0.4854 (ttt) REVERT: H 43 GLU cc_start: 0.7610 (tp30) cc_final: 0.7252 (tp30) REVERT: I 43 GLU cc_start: 0.7546 (tp30) cc_final: 0.7279 (tp30) REVERT: J 21 MET cc_start: 0.5211 (tpt) cc_final: 0.4976 (tpt) REVERT: J 43 GLU cc_start: 0.7506 (tp30) cc_final: 0.7201 (tp30) REVERT: K 21 MET cc_start: 0.5681 (tpt) cc_final: 0.4930 (ttt) REVERT: K 43 GLU cc_start: 0.7615 (tp30) cc_final: 0.7252 (tp30) REVERT: L 43 GLU cc_start: 0.7549 (tp30) cc_final: 0.7272 (tp30) outliers start: 12 outliers final: 0 residues processed: 283 average time/residue: 0.5293 time to fit residues: 233.0905 Evaluate side-chains 228 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.191358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135621 restraints weight = 43660.468| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.82 r_work: 0.3459 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17076 Z= 0.227 Angle : 0.616 4.642 22908 Z= 0.333 Chirality : 0.043 0.128 2604 Planarity : 0.004 0.025 2736 Dihedral : 8.962 51.233 2772 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.89 % Allowed : 13.56 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.18), residues: 1932 helix: 2.84 (0.13), residues: 1332 sheet: 1.60 (0.44), residues: 120 loop : -0.71 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP K 79 HIS 0.001 0.000 HIS H 75 PHE 0.020 0.001 PHE A 53 TYR 0.013 0.002 TYR H 67 ARG 0.003 0.001 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.07798 ( 1104) hydrogen bonds : angle 3.41288 ( 3276) SS BOND : bond 0.00263 ( 36) SS BOND : angle 1.29232 ( 72) covalent geometry : bond 0.00552 (17040) covalent geometry : angle 0.61234 (22836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5333 (tpt) cc_final: 0.4397 (ttt) REVERT: A 43 GLU cc_start: 0.7967 (tp30) cc_final: 0.7460 (tp30) REVERT: A 210 GLU cc_start: 0.7173 (tp30) cc_final: 0.6890 (tp30) REVERT: A 211 ILE cc_start: 0.8069 (mt) cc_final: 0.7845 (mt) REVERT: A 271 GLU cc_start: 0.6605 (tp30) cc_final: 0.6334 (tp30) REVERT: C 207 ASN cc_start: 0.8095 (m-40) cc_final: 0.7729 (t0) REVERT: B 21 MET cc_start: 0.5553 (tpt) cc_final: 0.4758 (ttt) REVERT: B 43 GLU cc_start: 0.7998 (tp30) cc_final: 0.7415 (tp30) REVERT: D 21 MET cc_start: 0.5211 (tpt) cc_final: 0.4201 (ttt) REVERT: D 43 GLU cc_start: 0.7942 (tp30) cc_final: 0.7460 (tp30) REVERT: D 210 GLU cc_start: 0.7185 (tp30) cc_final: 0.6907 (tp30) REVERT: D 211 ILE cc_start: 0.8076 (mt) cc_final: 0.7843 (mt) REVERT: E 21 MET cc_start: 0.5567 (tpt) cc_final: 0.4785 (ttt) REVERT: E 43 GLU cc_start: 0.7975 (tp30) cc_final: 0.7398 (tp30) REVERT: E 271 GLU cc_start: 0.6580 (tp30) cc_final: 0.6303 (tp30) REVERT: F 207 ASN cc_start: 0.8094 (m-40) cc_final: 0.7716 (t0) REVERT: G 21 MET cc_start: 0.5193 (tpt) cc_final: 0.4179 (ttt) REVERT: G 43 GLU cc_start: 0.7953 (tp30) cc_final: 0.7464 (tp30) REVERT: G 210 GLU cc_start: 0.7184 (tp30) cc_final: 0.6904 (tp30) REVERT: G 211 ILE cc_start: 0.8076 (mt) cc_final: 0.7845 (mt) REVERT: G 271 GLU cc_start: 0.6575 (tp30) cc_final: 0.6293 (tp30) REVERT: H 21 MET cc_start: 0.5570 (tpt) cc_final: 0.4789 (ttt) REVERT: H 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7395 (tp30) REVERT: H 271 GLU cc_start: 0.6583 (tp30) cc_final: 0.6307 (tp30) REVERT: I 207 ASN cc_start: 0.8095 (m-40) cc_final: 0.7716 (t0) REVERT: J 21 MET cc_start: 0.5189 (tpt) cc_final: 0.4175 (ttt) REVERT: J 43 GLU cc_start: 0.7958 (tp30) cc_final: 0.7479 (tp30) REVERT: J 210 GLU cc_start: 0.7182 (tp30) cc_final: 0.6893 (tp30) REVERT: J 211 ILE cc_start: 0.8062 (mt) cc_final: 0.7836 (mt) REVERT: J 271 GLU cc_start: 0.6554 (tp30) cc_final: 0.6265 (tp30) REVERT: K 21 MET cc_start: 0.5558 (tpt) cc_final: 0.4767 (ttt) REVERT: K 43 GLU cc_start: 0.7987 (tp30) cc_final: 0.7402 (tp30) REVERT: L 207 ASN cc_start: 0.8100 (m-40) cc_final: 0.7730 (t0) outliers start: 16 outliers final: 8 residues processed: 254 average time/residue: 0.5429 time to fit residues: 213.0881 Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 32 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN E 207 ASN H 207 ASN K 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.189799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135272 restraints weight = 43833.590| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.76 r_work: 0.3459 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17076 Z= 0.152 Angle : 0.512 4.180 22908 Z= 0.270 Chirality : 0.040 0.122 2604 Planarity : 0.003 0.026 2736 Dihedral : 8.395 54.657 2772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.67 % Allowed : 14.72 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.19), residues: 1932 helix: 3.32 (0.13), residues: 1332 sheet: 1.82 (0.45), residues: 120 loop : -0.63 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.001 0.000 HIS E 75 PHE 0.013 0.001 PHE I 33 TYR 0.011 0.001 TYR J 67 ARG 0.003 0.000 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.06696 ( 1104) hydrogen bonds : angle 3.14055 ( 3276) SS BOND : bond 0.00178 ( 36) SS BOND : angle 0.89396 ( 72) covalent geometry : bond 0.00335 (17040) covalent geometry : angle 0.51040 (22836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5361 (tpt) cc_final: 0.4295 (ttt) REVERT: A 43 GLU cc_start: 0.8067 (tp30) cc_final: 0.7352 (tp30) REVERT: A 210 GLU cc_start: 0.7288 (tp30) cc_final: 0.6940 (tp30) REVERT: A 211 ILE cc_start: 0.8215 (mt) cc_final: 0.7990 (mt) REVERT: C 43 GLU cc_start: 0.7867 (tp30) cc_final: 0.7263 (tp30) REVERT: C 207 ASN cc_start: 0.8108 (m-40) cc_final: 0.7685 (t0) REVERT: B 43 GLU cc_start: 0.7936 (tp30) cc_final: 0.7274 (tp30) REVERT: D 21 MET cc_start: 0.5371 (tpt) cc_final: 0.4323 (ttt) REVERT: D 43 GLU cc_start: 0.8056 (tp30) cc_final: 0.7371 (tp30) REVERT: D 210 GLU cc_start: 0.7312 (tp30) cc_final: 0.6950 (tp30) REVERT: D 211 ILE cc_start: 0.8204 (mt) cc_final: 0.7966 (mt) REVERT: E 43 GLU cc_start: 0.7939 (tp30) cc_final: 0.7287 (tp30) REVERT: F 43 GLU cc_start: 0.7828 (tp30) cc_final: 0.7233 (tp30) REVERT: F 207 ASN cc_start: 0.8105 (m-40) cc_final: 0.7667 (t0) REVERT: G 21 MET cc_start: 0.5290 (tpt) cc_final: 0.4205 (ttt) REVERT: G 43 GLU cc_start: 0.8048 (tp30) cc_final: 0.7364 (tp30) REVERT: G 210 GLU cc_start: 0.7295 (tp30) cc_final: 0.6935 (tp30) REVERT: G 211 ILE cc_start: 0.8202 (mt) cc_final: 0.7969 (mt) REVERT: H 43 GLU cc_start: 0.7941 (tp30) cc_final: 0.7299 (tp30) REVERT: I 43 GLU cc_start: 0.7838 (tp30) cc_final: 0.7235 (tp30) REVERT: I 207 ASN cc_start: 0.8116 (m-40) cc_final: 0.7678 (t0) REVERT: J 21 MET cc_start: 0.5406 (tpt) cc_final: 0.4376 (ttt) REVERT: J 43 GLU cc_start: 0.8068 (tp30) cc_final: 0.7354 (tp30) REVERT: J 210 GLU cc_start: 0.7298 (tp30) cc_final: 0.6943 (tp30) REVERT: J 211 ILE cc_start: 0.8220 (mt) cc_final: 0.7984 (mt) REVERT: K 43 GLU cc_start: 0.7943 (tp30) cc_final: 0.7279 (tp30) REVERT: L 43 GLU cc_start: 0.7834 (tp30) cc_final: 0.7245 (tp30) REVERT: L 207 ASN cc_start: 0.8118 (m-40) cc_final: 0.7688 (t0) outliers start: 12 outliers final: 8 residues processed: 206 average time/residue: 0.5193 time to fit residues: 170.3347 Evaluate side-chains 207 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain L residue 204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN E 207 ASN G 207 ASN H 207 ASN K 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.187177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132950 restraints weight = 44474.433| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.75 r_work: 0.3438 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17076 Z= 0.157 Angle : 0.512 4.300 22908 Z= 0.271 Chirality : 0.041 0.178 2604 Planarity : 0.003 0.025 2736 Dihedral : 8.529 58.363 2772 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.33 % Allowed : 14.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.19), residues: 1932 helix: 3.31 (0.13), residues: 1332 sheet: 1.67 (0.46), residues: 120 loop : -0.52 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.001 0.000 HIS G 274 PHE 0.011 0.001 PHE E 53 TYR 0.010 0.001 TYR D 67 ARG 0.003 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.06436 ( 1104) hydrogen bonds : angle 3.11173 ( 3276) SS BOND : bond 0.00137 ( 36) SS BOND : angle 0.87141 ( 72) covalent geometry : bond 0.00368 (17040) covalent geometry : angle 0.51049 (22836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5401 (tpt) cc_final: 0.4345 (ttt) REVERT: A 43 GLU cc_start: 0.8060 (tp30) cc_final: 0.7380 (tp30) REVERT: A 211 ILE cc_start: 0.8205 (mt) cc_final: 0.7971 (mt) REVERT: C 43 GLU cc_start: 0.7807 (tp30) cc_final: 0.7209 (tp30) REVERT: C 207 ASN cc_start: 0.8107 (m-40) cc_final: 0.7657 (t0) REVERT: B 52 MET cc_start: 0.8448 (mmt) cc_final: 0.8040 (mmt) REVERT: D 21 MET cc_start: 0.5583 (tpt) cc_final: 0.4526 (ttt) REVERT: D 43 GLU cc_start: 0.8088 (tp30) cc_final: 0.7394 (tp30) REVERT: D 211 ILE cc_start: 0.8207 (mt) cc_final: 0.7961 (mt) REVERT: E 52 MET cc_start: 0.8435 (mmt) cc_final: 0.8023 (mmt) REVERT: F 43 GLU cc_start: 0.7800 (tp30) cc_final: 0.7193 (tp30) REVERT: F 207 ASN cc_start: 0.8102 (m-40) cc_final: 0.7645 (t0) REVERT: G 21 MET cc_start: 0.5395 (tpt) cc_final: 0.4346 (ttt) REVERT: G 43 GLU cc_start: 0.8078 (tp30) cc_final: 0.7396 (tp30) REVERT: H 52 MET cc_start: 0.8443 (mmt) cc_final: 0.8034 (mmt) REVERT: I 43 GLU cc_start: 0.7828 (tp30) cc_final: 0.7224 (tp30) REVERT: I 207 ASN cc_start: 0.8098 (m-40) cc_final: 0.7638 (t0) REVERT: J 21 MET cc_start: 0.5386 (tpt) cc_final: 0.4339 (ttt) REVERT: J 43 GLU cc_start: 0.8087 (tp30) cc_final: 0.7409 (tp30) REVERT: K 52 MET cc_start: 0.8419 (mmt) cc_final: 0.8001 (mmt) REVERT: L 43 GLU cc_start: 0.7797 (tp30) cc_final: 0.7218 (tp30) REVERT: L 207 ASN cc_start: 0.8105 (m-40) cc_final: 0.7653 (t0) outliers start: 6 outliers final: 2 residues processed: 202 average time/residue: 0.4961 time to fit residues: 159.9670 Evaluate side-chains 200 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain G residue 207 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131036 restraints weight = 44504.943| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.74 r_work: 0.3411 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17076 Z= 0.179 Angle : 0.531 4.479 22908 Z= 0.281 Chirality : 0.041 0.185 2604 Planarity : 0.003 0.022 2736 Dihedral : 8.547 59.953 2772 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.39 % Allowed : 15.28 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.19), residues: 1932 helix: 3.29 (0.13), residues: 1332 sheet: 1.32 (0.48), residues: 120 loop : -0.47 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 79 HIS 0.002 0.001 HIS E 75 PHE 0.013 0.001 PHE E 53 TYR 0.011 0.002 TYR K 67 ARG 0.003 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.06572 ( 1104) hydrogen bonds : angle 3.11776 ( 3276) SS BOND : bond 0.00178 ( 36) SS BOND : angle 1.00427 ( 72) covalent geometry : bond 0.00428 (17040) covalent geometry : angle 0.52898 (22836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5460 (tpt) cc_final: 0.4409 (ttt) REVERT: A 43 GLU cc_start: 0.8217 (tp30) cc_final: 0.7475 (tp30) REVERT: C 43 GLU cc_start: 0.7945 (tp30) cc_final: 0.7319 (tp30) REVERT: C 207 ASN cc_start: 0.8224 (m-40) cc_final: 0.7739 (t0) REVERT: B 52 MET cc_start: 0.8489 (mmt) cc_final: 0.8051 (mmt) REVERT: D 21 MET cc_start: 0.5565 (tpt) cc_final: 0.4528 (ttt) REVERT: D 43 GLU cc_start: 0.8192 (tp30) cc_final: 0.7430 (tp30) REVERT: E 52 MET cc_start: 0.8464 (mmt) cc_final: 0.8018 (mmt) REVERT: F 43 GLU cc_start: 0.7954 (tp30) cc_final: 0.7315 (tp30) REVERT: F 207 ASN cc_start: 0.8218 (m-40) cc_final: 0.7730 (t0) REVERT: G 21 MET cc_start: 0.5560 (tpt) cc_final: 0.4522 (ttt) REVERT: G 43 GLU cc_start: 0.8184 (tp30) cc_final: 0.7433 (tp30) REVERT: H 52 MET cc_start: 0.8470 (mmt) cc_final: 0.8023 (mmt) REVERT: I 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7334 (tp30) REVERT: I 207 ASN cc_start: 0.8226 (m-40) cc_final: 0.7735 (t0) REVERT: J 21 MET cc_start: 0.5547 (tpt) cc_final: 0.4520 (ttt) REVERT: J 43 GLU cc_start: 0.8194 (tp30) cc_final: 0.7448 (tp30) REVERT: K 52 MET cc_start: 0.8455 (mmt) cc_final: 0.8004 (mmt) REVERT: L 43 GLU cc_start: 0.7974 (tp30) cc_final: 0.7348 (tp30) REVERT: L 207 ASN cc_start: 0.8229 (m-40) cc_final: 0.7744 (t0) outliers start: 7 outliers final: 1 residues processed: 209 average time/residue: 0.5079 time to fit residues: 170.2650 Evaluate side-chains 206 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.184116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130383 restraints weight = 44969.876| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.75 r_work: 0.3412 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17076 Z= 0.158 Angle : 0.513 4.402 22908 Z= 0.267 Chirality : 0.041 0.222 2604 Planarity : 0.003 0.023 2736 Dihedral : 8.119 55.413 2772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.67 % Allowed : 14.67 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.19), residues: 1932 helix: 3.30 (0.13), residues: 1344 sheet: 1.11 (0.50), residues: 120 loop : -0.37 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 79 HIS 0.002 0.001 HIS B 75 PHE 0.011 0.001 PHE B 53 TYR 0.011 0.001 TYR D 67 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.06205 ( 1104) hydrogen bonds : angle 3.08348 ( 3276) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.93953 ( 72) covalent geometry : bond 0.00379 (17040) covalent geometry : angle 0.51099 (22836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5611 (tpt) cc_final: 0.4592 (ttt) REVERT: A 43 GLU cc_start: 0.8247 (tp30) cc_final: 0.7492 (tp30) REVERT: C 43 GLU cc_start: 0.8035 (tp30) cc_final: 0.7443 (tp30) REVERT: C 207 ASN cc_start: 0.8198 (m-40) cc_final: 0.7666 (t0) REVERT: C 211 ILE cc_start: 0.8243 (mt) cc_final: 0.7965 (mt) REVERT: B 52 MET cc_start: 0.8496 (mmt) cc_final: 0.8030 (mmt) REVERT: D 43 GLU cc_start: 0.8232 (tp30) cc_final: 0.7466 (tp30) REVERT: E 52 MET cc_start: 0.8490 (mmt) cc_final: 0.8026 (mmt) REVERT: F 43 GLU cc_start: 0.8016 (tp30) cc_final: 0.7420 (tp30) REVERT: F 207 ASN cc_start: 0.8184 (m-40) cc_final: 0.7708 (t0) REVERT: G 43 GLU cc_start: 0.8229 (tp30) cc_final: 0.7473 (tp30) REVERT: H 52 MET cc_start: 0.8483 (mmt) cc_final: 0.8014 (mmt) REVERT: I 43 GLU cc_start: 0.8029 (tp30) cc_final: 0.7443 (tp30) REVERT: I 207 ASN cc_start: 0.8241 (m-40) cc_final: 0.7752 (t0) REVERT: J 43 GLU cc_start: 0.8234 (tp30) cc_final: 0.7485 (tp30) REVERT: K 52 MET cc_start: 0.8479 (mmt) cc_final: 0.8005 (mmt) REVERT: L 43 GLU cc_start: 0.8020 (tp30) cc_final: 0.7437 (tp30) REVERT: L 207 ASN cc_start: 0.8199 (m-40) cc_final: 0.7667 (t0) REVERT: L 211 ILE cc_start: 0.8245 (mt) cc_final: 0.7970 (mt) outliers start: 12 outliers final: 5 residues processed: 223 average time/residue: 0.5040 time to fit residues: 180.9575 Evaluate side-chains 199 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 137 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129307 restraints weight = 44857.959| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.74 r_work: 0.3399 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17076 Z= 0.153 Angle : 0.506 4.462 22908 Z= 0.264 Chirality : 0.041 0.130 2604 Planarity : 0.003 0.024 2736 Dihedral : 7.775 58.801 2772 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.56 % Allowed : 15.17 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.19), residues: 1932 helix: 3.39 (0.13), residues: 1344 sheet: 1.13 (0.51), residues: 120 loop : -0.32 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.002 0.001 HIS E 75 PHE 0.010 0.001 PHE K 53 TYR 0.011 0.001 TYR J 67 ARG 0.002 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.05939 ( 1104) hydrogen bonds : angle 3.05169 ( 3276) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.94206 ( 72) covalent geometry : bond 0.00368 (17040) covalent geometry : angle 0.50421 (22836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8224 (tp30) cc_final: 0.7531 (tp30) REVERT: C 43 GLU cc_start: 0.8086 (tp30) cc_final: 0.7474 (tp30) REVERT: C 207 ASN cc_start: 0.8177 (m-40) cc_final: 0.7588 (t0) REVERT: C 211 ILE cc_start: 0.7963 (mt) cc_final: 0.7689 (mt) REVERT: B 52 MET cc_start: 0.8462 (mmt) cc_final: 0.7993 (mmt) REVERT: B 69 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7899 (tpp80) REVERT: D 43 GLU cc_start: 0.8196 (tp30) cc_final: 0.7519 (tp30) REVERT: E 52 MET cc_start: 0.8463 (mmt) cc_final: 0.7991 (mmt) REVERT: E 69 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7895 (tpp80) REVERT: E 272 LEU cc_start: 0.6804 (tt) cc_final: 0.6565 (tp) REVERT: F 43 GLU cc_start: 0.8078 (tp30) cc_final: 0.7459 (tp30) REVERT: F 207 ASN cc_start: 0.8185 (m-40) cc_final: 0.7583 (t0) REVERT: F 211 ILE cc_start: 0.8214 (mt) cc_final: 0.7932 (mt) REVERT: G 43 GLU cc_start: 0.8183 (tp30) cc_final: 0.7505 (tp30) REVERT: H 52 MET cc_start: 0.8456 (mmt) cc_final: 0.7984 (mmt) REVERT: H 69 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7892 (tpp80) REVERT: H 272 LEU cc_start: 0.6821 (tt) cc_final: 0.6577 (tp) REVERT: I 43 GLU cc_start: 0.8085 (tp30) cc_final: 0.7477 (tp30) REVERT: I 207 ASN cc_start: 0.8203 (m-40) cc_final: 0.7596 (t0) REVERT: I 211 ILE cc_start: 0.8224 (mt) cc_final: 0.7940 (mt) REVERT: J 43 GLU cc_start: 0.8199 (tp30) cc_final: 0.7520 (tp30) REVERT: K 52 MET cc_start: 0.8454 (mmt) cc_final: 0.7974 (mmt) REVERT: K 69 ARG cc_start: 0.8134 (tpp-160) cc_final: 0.7893 (tpp80) REVERT: L 43 GLU cc_start: 0.8063 (tp30) cc_final: 0.7457 (tp30) REVERT: L 207 ASN cc_start: 0.8194 (m-40) cc_final: 0.7593 (t0) REVERT: L 211 ILE cc_start: 0.7963 (mt) cc_final: 0.7688 (mt) outliers start: 10 outliers final: 5 residues processed: 216 average time/residue: 0.5061 time to fit residues: 175.8211 Evaluate side-chains 214 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 148 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 187 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.184296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131526 restraints weight = 44903.822| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.73 r_work: 0.3422 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17076 Z= 0.109 Angle : 0.468 4.223 22908 Z= 0.242 Chirality : 0.039 0.128 2604 Planarity : 0.003 0.023 2736 Dihedral : 7.296 57.518 2772 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.44 % Allowed : 15.39 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.19), residues: 1932 helix: 3.51 (0.13), residues: 1344 sheet: 1.21 (0.51), residues: 120 loop : -0.24 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.002 0.000 HIS F 274 PHE 0.007 0.001 PHE H 53 TYR 0.010 0.001 TYR D 67 ARG 0.001 0.000 ARG J 197 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 1104) hydrogen bonds : angle 3.01415 ( 3276) SS BOND : bond 0.00064 ( 36) SS BOND : angle 0.77373 ( 72) covalent geometry : bond 0.00239 (17040) covalent geometry : angle 0.46627 (22836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8190 (tp30) cc_final: 0.7511 (tp30) REVERT: C 43 GLU cc_start: 0.8078 (tp30) cc_final: 0.7458 (tp30) REVERT: C 207 ASN cc_start: 0.8159 (m-40) cc_final: 0.7560 (t0) REVERT: C 211 ILE cc_start: 0.8170 (mt) cc_final: 0.7886 (mt) REVERT: C 254 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7213 (tt) REVERT: B 52 MET cc_start: 0.8484 (mmt) cc_final: 0.8019 (mmt) REVERT: B 69 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7970 (tpp80) REVERT: D 43 GLU cc_start: 0.8186 (tp30) cc_final: 0.7502 (tp30) REVERT: E 52 MET cc_start: 0.8486 (mmt) cc_final: 0.8020 (mmt) REVERT: E 69 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7886 (tpp80) REVERT: F 43 GLU cc_start: 0.8066 (tp30) cc_final: 0.7431 (tp30) REVERT: F 207 ASN cc_start: 0.8164 (m-40) cc_final: 0.7562 (t0) REVERT: F 211 ILE cc_start: 0.8188 (mt) cc_final: 0.7907 (mt) REVERT: F 254 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7204 (tt) REVERT: G 43 GLU cc_start: 0.8171 (tp30) cc_final: 0.7520 (tp30) REVERT: H 52 MET cc_start: 0.8467 (mmt) cc_final: 0.7995 (mmt) REVERT: H 69 ARG cc_start: 0.8179 (tpp-160) cc_final: 0.7885 (tpp80) REVERT: I 43 GLU cc_start: 0.8086 (tp30) cc_final: 0.7453 (tp30) REVERT: I 207 ASN cc_start: 0.8193 (m-40) cc_final: 0.7585 (t0) REVERT: I 211 ILE cc_start: 0.8211 (mt) cc_final: 0.7922 (mt) REVERT: I 254 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7207 (tt) REVERT: J 43 GLU cc_start: 0.8176 (tp30) cc_final: 0.7536 (tp30) REVERT: K 52 MET cc_start: 0.8459 (mmt) cc_final: 0.7985 (mmt) REVERT: K 69 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7891 (tpp80) REVERT: L 43 GLU cc_start: 0.8056 (tp30) cc_final: 0.7428 (tp30) REVERT: L 207 ASN cc_start: 0.8184 (m-40) cc_final: 0.7582 (t0) REVERT: L 211 ILE cc_start: 0.8197 (mt) cc_final: 0.7915 (mt) REVERT: L 254 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7204 (tt) outliers start: 8 outliers final: 4 residues processed: 210 average time/residue: 0.5315 time to fit residues: 178.4950 Evaluate side-chains 210 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 56 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.182838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130135 restraints weight = 45003.852| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.73 r_work: 0.3405 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17076 Z= 0.132 Angle : 0.489 4.442 22908 Z= 0.253 Chirality : 0.040 0.132 2604 Planarity : 0.003 0.024 2736 Dihedral : 7.091 50.240 2772 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.67 % Allowed : 15.06 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.19), residues: 1932 helix: 3.53 (0.13), residues: 1344 sheet: 1.14 (0.52), residues: 120 loop : -0.19 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.002 0.001 HIS B 274 PHE 0.010 0.001 PHE B 53 TYR 0.010 0.001 TYR A 67 ARG 0.002 0.000 ARG I 197 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 1104) hydrogen bonds : angle 3.02842 ( 3276) SS BOND : bond 0.00121 ( 36) SS BOND : angle 0.86642 ( 72) covalent geometry : bond 0.00316 (17040) covalent geometry : angle 0.48781 (22836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8281 (tp30) cc_final: 0.7602 (tp30) REVERT: C 43 GLU cc_start: 0.8197 (tp30) cc_final: 0.7516 (tp30) REVERT: C 207 ASN cc_start: 0.8180 (m-40) cc_final: 0.7577 (t0) REVERT: C 211 ILE cc_start: 0.8203 (mt) cc_final: 0.7937 (mt) REVERT: C 254 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7249 (tt) REVERT: B 52 MET cc_start: 0.8504 (mmt) cc_final: 0.8060 (mmt) REVERT: B 69 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7980 (tpp80) REVERT: D 21 MET cc_start: 0.5536 (tpt) cc_final: 0.5298 (tpt) REVERT: D 43 GLU cc_start: 0.8253 (tp30) cc_final: 0.7579 (tp30) REVERT: E 52 MET cc_start: 0.8491 (mmt) cc_final: 0.8039 (mmt) REVERT: E 69 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7968 (tpp80) REVERT: F 43 GLU cc_start: 0.8183 (tp30) cc_final: 0.7522 (tp30) REVERT: F 207 ASN cc_start: 0.8182 (m-40) cc_final: 0.7577 (t0) REVERT: F 211 ILE cc_start: 0.8232 (mt) cc_final: 0.7970 (mt) REVERT: F 254 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7149 (tt) REVERT: G 43 GLU cc_start: 0.8249 (tp30) cc_final: 0.7573 (tp30) REVERT: H 52 MET cc_start: 0.8487 (mmt) cc_final: 0.8035 (mmt) REVERT: H 69 ARG cc_start: 0.8187 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: I 43 GLU cc_start: 0.8198 (tp30) cc_final: 0.7527 (tp30) REVERT: I 207 ASN cc_start: 0.8187 (m-40) cc_final: 0.7575 (t0) REVERT: I 211 ILE cc_start: 0.8219 (mt) cc_final: 0.7956 (mt) REVERT: I 254 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7151 (tt) REVERT: J 43 GLU cc_start: 0.8262 (tp30) cc_final: 0.7582 (tp30) REVERT: K 52 MET cc_start: 0.8487 (mmt) cc_final: 0.8031 (mmt) REVERT: K 69 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7970 (tpp80) REVERT: L 43 GLU cc_start: 0.8171 (tp30) cc_final: 0.7513 (tp30) REVERT: L 207 ASN cc_start: 0.8190 (m-40) cc_final: 0.7582 (t0) REVERT: L 211 ILE cc_start: 0.8199 (mt) cc_final: 0.7934 (mt) REVERT: L 254 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7229 (tt) outliers start: 12 outliers final: 4 residues processed: 220 average time/residue: 0.5194 time to fit residues: 183.0949 Evaluate side-chains 215 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.182241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129465 restraints weight = 44924.499| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.74 r_work: 0.3399 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17076 Z= 0.139 Angle : 0.493 4.449 22908 Z= 0.255 Chirality : 0.040 0.127 2604 Planarity : 0.003 0.024 2736 Dihedral : 7.091 49.729 2772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.83 % Allowed : 15.33 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.19), residues: 1932 helix: 3.51 (0.13), residues: 1344 sheet: 1.01 (0.51), residues: 120 loop : -0.12 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE H 53 TYR 0.011 0.001 TYR D 67 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 1104) hydrogen bonds : angle 3.06075 ( 3276) SS BOND : bond 0.00128 ( 36) SS BOND : angle 0.88816 ( 72) covalent geometry : bond 0.00335 (17040) covalent geometry : angle 0.49141 (22836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5447 (tpt) cc_final: 0.5060 (tpt) REVERT: A 43 GLU cc_start: 0.8300 (tp30) cc_final: 0.7617 (tp30) REVERT: C 43 GLU cc_start: 0.8212 (tp30) cc_final: 0.7514 (tp30) REVERT: C 207 ASN cc_start: 0.8154 (m-40) cc_final: 0.7461 (t0) REVERT: C 211 ILE cc_start: 0.8187 (mt) cc_final: 0.7940 (mt) REVERT: C 254 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7168 (tt) REVERT: C 269 LEU cc_start: 0.7165 (mt) cc_final: 0.6924 (mt) REVERT: B 52 MET cc_start: 0.8521 (mmt) cc_final: 0.8010 (mmt) REVERT: B 69 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7891 (tpp80) REVERT: D 21 MET cc_start: 0.5446 (tpt) cc_final: 0.5209 (tpt) REVERT: D 43 GLU cc_start: 0.8275 (tp30) cc_final: 0.7597 (tp30) REVERT: E 52 MET cc_start: 0.8518 (mmt) cc_final: 0.8006 (mmt) REVERT: E 69 ARG cc_start: 0.8149 (tpp-160) cc_final: 0.7945 (tpp80) REVERT: F 43 GLU cc_start: 0.8199 (tp30) cc_final: 0.7521 (tp30) REVERT: F 207 ASN cc_start: 0.8160 (m-40) cc_final: 0.7546 (t0) REVERT: F 211 ILE cc_start: 0.8218 (mt) cc_final: 0.7981 (mt) REVERT: F 254 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7148 (tt) REVERT: G 21 MET cc_start: 0.5427 (tpt) cc_final: 0.5188 (tpt) REVERT: G 43 GLU cc_start: 0.8281 (tp30) cc_final: 0.7592 (tp30) REVERT: H 52 MET cc_start: 0.8508 (mmt) cc_final: 0.7992 (mmt) REVERT: H 69 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7887 (tpp80) REVERT: I 43 GLU cc_start: 0.8210 (tp30) cc_final: 0.7533 (tp30) REVERT: I 207 ASN cc_start: 0.8162 (m-40) cc_final: 0.7548 (t0) REVERT: I 211 ILE cc_start: 0.8215 (mt) cc_final: 0.7975 (mt) REVERT: I 254 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7161 (tt) REVERT: J 21 MET cc_start: 0.5439 (tpt) cc_final: 0.5202 (tpt) REVERT: J 43 GLU cc_start: 0.8288 (tp30) cc_final: 0.7603 (tp30) REVERT: K 52 MET cc_start: 0.8501 (mmt) cc_final: 0.7980 (mmt) REVERT: K 69 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7887 (tpp80) REVERT: L 43 GLU cc_start: 0.8187 (tp30) cc_final: 0.7510 (tp30) REVERT: L 207 ASN cc_start: 0.8156 (m-40) cc_final: 0.7462 (t0) REVERT: L 211 ILE cc_start: 0.8186 (mt) cc_final: 0.7937 (mt) REVERT: L 254 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7165 (tt) REVERT: L 269 LEU cc_start: 0.7166 (mt) cc_final: 0.6924 (mt) outliers start: 15 outliers final: 7 residues processed: 238 average time/residue: 0.4903 time to fit residues: 188.1087 Evaluate side-chains 231 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129218 restraints weight = 44860.842| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.74 r_work: 0.3400 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17076 Z= 0.137 Angle : 0.493 4.430 22908 Z= 0.255 Chirality : 0.040 0.130 2604 Planarity : 0.003 0.024 2736 Dihedral : 7.065 55.090 2772 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.50 % Allowed : 15.94 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.19), residues: 1932 helix: 3.54 (0.13), residues: 1344 sheet: 0.98 (0.52), residues: 120 loop : -0.10 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS F 274 PHE 0.010 0.001 PHE H 53 TYR 0.010 0.001 TYR J 67 ARG 0.002 0.000 ARG H 197 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 1104) hydrogen bonds : angle 3.07224 ( 3276) SS BOND : bond 0.00125 ( 36) SS BOND : angle 0.87884 ( 72) covalent geometry : bond 0.00331 (17040) covalent geometry : angle 0.49112 (22836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15451.04 seconds wall clock time: 264 minutes 58.41 seconds (15898.41 seconds total)