Starting phenix.real_space_refine on Fri Jun 27 23:25:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgg_38322/06_2025/8xgg_38322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgg_38322/06_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_38322/06_2025/8xgg_38322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgg_38322/06_2025/8xgg_38322.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgg_38322/06_2025/8xgg_38322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgg_38322/06_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-5710/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: 9.39, per 1000 atoms: 0.29 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: 9.08 Conformation dependent library (CDL) restraints added in 2.4 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: 2.22 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: 11.34 Time building geometry restraints manager: 10.99 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: 0.17 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 1.250 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 59.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.740 ------------------------------------------------------------------------------- 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 : 2.272 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: 0.5182 time to fit residues: 228.8608 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 : 2.190 ------------------------------------------------------------------------------- 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 = 0.191298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135553 restraints weight = 43663.854| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.82 r_work: 0.3457 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17076 Z= 0.230 Angle : 0.615 4.312 22908 Z= 0.333 Chirality : 0.043 0.129 2604 Planarity : 0.004 0.025 2736 Dihedral : 8.956 51.225 2772 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 13.83 % 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: 2.93 (0.18), residues: 1932 helix: 2.84 (0.13), residues: 1332 sheet: 1.62 (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 E 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 0.000 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.07788 ( 1104) hydrogen bonds : angle 3.41331 ( 3276) SS BOND : bond 0.00276 ( 36) SS BOND : angle 1.31550 ( 72) covalent geometry : bond 0.00550 (17040) covalent geometry : angle 0.61134 (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: 15 poor density : 243 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5337 (tpt) cc_final: 0.4397 (ttt) REVERT: A 43 GLU cc_start: 0.8004 (tp30) cc_final: 0.7471 (tp30) REVERT: A 210 GLU cc_start: 0.7180 (tp30) cc_final: 0.6908 (tp30) REVERT: A 211 ILE cc_start: 0.8070 (mt) cc_final: 0.7841 (mt) REVERT: A 271 GLU cc_start: 0.6606 (tp30) cc_final: 0.6340 (tp30) REVERT: C 207 ASN cc_start: 0.8097 (m-40) cc_final: 0.7731 (t0) REVERT: B 21 MET cc_start: 0.5566 (tpt) cc_final: 0.4778 (ttt) REVERT: B 43 GLU cc_start: 0.7995 (tp30) cc_final: 0.7412 (tp30) REVERT: D 21 MET cc_start: 0.5220 (tpt) cc_final: 0.4208 (ttt) REVERT: D 43 GLU cc_start: 0.7939 (tp30) cc_final: 0.7460 (tp30) REVERT: D 210 GLU cc_start: 0.7200 (tp30) cc_final: 0.6919 (tp30) REVERT: D 211 ILE cc_start: 0.8076 (mt) cc_final: 0.7844 (mt) REVERT: E 21 MET cc_start: 0.5570 (tpt) cc_final: 0.4790 (ttt) REVERT: E 43 GLU cc_start: 0.7972 (tp30) cc_final: 0.7395 (tp30) REVERT: E 271 GLU cc_start: 0.6582 (tp30) cc_final: 0.6306 (tp30) REVERT: F 207 ASN cc_start: 0.8094 (m-40) cc_final: 0.7716 (t0) REVERT: G 21 MET cc_start: 0.5195 (tpt) cc_final: 0.4181 (ttt) REVERT: G 43 GLU cc_start: 0.7951 (tp30) cc_final: 0.7463 (tp30) REVERT: G 210 GLU cc_start: 0.7187 (tp30) cc_final: 0.6905 (tp30) REVERT: G 211 ILE cc_start: 0.8077 (mt) cc_final: 0.7845 (mt) REVERT: G 271 GLU cc_start: 0.6578 (tp30) cc_final: 0.6295 (tp30) REVERT: H 21 MET cc_start: 0.5571 (tpt) cc_final: 0.4792 (ttt) REVERT: H 43 GLU cc_start: 0.7966 (tp30) cc_final: 0.7396 (tp30) REVERT: H 271 GLU cc_start: 0.6585 (tp30) cc_final: 0.6311 (tp30) REVERT: I 207 ASN cc_start: 0.8100 (m-40) cc_final: 0.7720 (t0) REVERT: J 21 MET cc_start: 0.5191 (tpt) cc_final: 0.4175 (ttt) REVERT: J 43 GLU cc_start: 0.7996 (tp30) cc_final: 0.7491 (tp30) REVERT: J 210 GLU cc_start: 0.7188 (tp30) cc_final: 0.6899 (tp30) REVERT: J 211 ILE cc_start: 0.8064 (mt) cc_final: 0.7838 (mt) REVERT: J 271 GLU cc_start: 0.6556 (tp30) cc_final: 0.6267 (tp30) REVERT: K 21 MET cc_start: 0.5561 (tpt) cc_final: 0.4770 (ttt) REVERT: K 43 GLU cc_start: 0.7985 (tp30) cc_final: 0.7401 (tp30) REVERT: L 207 ASN cc_start: 0.8105 (m-40) cc_final: 0.7734 (t0) outliers start: 15 outliers final: 7 residues processed: 255 average time/residue: 0.5535 time to fit residues: 218.4655 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 : 2.253 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 32 optimal weight: 8.9990 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: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.190104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135499 restraints weight = 43833.115| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.77 r_work: 0.3461 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 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 = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2832 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= 0.148 Angle : 0.511 4.159 22908 Z= 0.269 Chirality : 0.040 0.122 2604 Planarity : 0.003 0.023 2736 Dihedral : 8.421 54.468 2772 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.67 % Allowed : 14.78 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.49 (0.19), residues: 1932 helix: 3.30 (0.13), residues: 1332 sheet: 1.83 (0.46), residues: 120 loop : -0.62 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.001 0.000 HIS C 274 PHE 0.014 0.001 PHE F 33 TYR 0.011 0.001 TYR H 218 ARG 0.003 0.000 ARG J 206 Details of bonding type rmsd hydrogen bonds : bond 0.06755 ( 1104) hydrogen bonds : angle 3.15369 ( 3276) SS BOND : bond 0.00151 ( 36) SS BOND : angle 0.89878 ( 72) covalent geometry : bond 0.00332 (17040) covalent geometry : angle 0.50909 (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 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5348 (tpt) cc_final: 0.4288 (ttt) REVERT: A 43 GLU cc_start: 0.8040 (tp30) cc_final: 0.7362 (tp30) REVERT: A 210 GLU cc_start: 0.7279 (tp30) cc_final: 0.6923 (tp30) REVERT: A 211 ILE cc_start: 0.8188 (mt) cc_final: 0.7957 (mt) REVERT: C 43 GLU cc_start: 0.7858 (tp30) cc_final: 0.7277 (tp30) REVERT: C 207 ASN cc_start: 0.8115 (m-40) cc_final: 0.7708 (t0) REVERT: B 43 GLU cc_start: 0.7939 (tp30) cc_final: 0.7284 (tp30) REVERT: D 21 MET cc_start: 0.5358 (tpt) cc_final: 0.4313 (ttt) REVERT: D 43 GLU cc_start: 0.8038 (tp30) cc_final: 0.7492 (tp30) REVERT: D 210 GLU cc_start: 0.7302 (tp30) cc_final: 0.6942 (tp30) REVERT: D 211 ILE cc_start: 0.8193 (mt) cc_final: 0.7956 (mt) REVERT: E 43 GLU cc_start: 0.7938 (tp30) cc_final: 0.7291 (tp30) REVERT: F 43 GLU cc_start: 0.7834 (tp30) cc_final: 0.7239 (tp30) REVERT: F 207 ASN cc_start: 0.8112 (m-40) cc_final: 0.7692 (t0) REVERT: G 21 MET cc_start: 0.5326 (tpt) cc_final: 0.4257 (ttt) REVERT: G 43 GLU cc_start: 0.8039 (tp30) cc_final: 0.7366 (tp30) REVERT: G 85 MET cc_start: 0.7378 (tpt) cc_final: 0.7178 (tpp) REVERT: G 210 GLU cc_start: 0.7280 (tp30) cc_final: 0.6920 (tp30) REVERT: G 211 ILE cc_start: 0.8185 (mt) cc_final: 0.7953 (mt) REVERT: H 43 GLU cc_start: 0.7935 (tp30) cc_final: 0.7295 (tp30) REVERT: I 43 GLU cc_start: 0.7856 (tp30) cc_final: 0.7264 (tp30) REVERT: I 207 ASN cc_start: 0.8118 (m-40) cc_final: 0.7700 (t0) REVERT: J 21 MET cc_start: 0.5334 (tpt) cc_final: 0.4261 (ttt) REVERT: J 43 GLU cc_start: 0.8041 (tp30) cc_final: 0.7364 (tp30) REVERT: J 210 GLU cc_start: 0.7290 (tp30) cc_final: 0.6936 (tp30) REVERT: J 211 ILE cc_start: 0.8196 (mt) cc_final: 0.7961 (mt) REVERT: K 43 GLU cc_start: 0.7941 (tp30) cc_final: 0.7285 (tp30) REVERT: L 43 GLU cc_start: 0.7835 (tp30) cc_final: 0.7256 (tp30) REVERT: L 207 ASN cc_start: 0.8124 (m-40) cc_final: 0.7712 (t0) outliers start: 12 outliers final: 8 residues processed: 203 average time/residue: 0.5175 time to fit residues: 167.5751 Evaluate side-chains 203 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 2.512 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.184540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130057 restraints weight = 44758.783| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.76 r_work: 0.3399 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- 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 = 0.92 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 = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17076 Z= 0.215 Angle : 0.573 4.649 22908 Z= 0.305 Chirality : 0.043 0.185 2604 Planarity : 0.004 0.026 2736 Dihedral : 8.941 59.204 2772 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.44 % Allowed : 14.61 % Favored : 84.94 % 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: 3.29 (0.19), residues: 1932 helix: 3.15 (0.13), residues: 1332 sheet: 1.24 (0.48), residues: 120 loop : -0.54 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 79 HIS 0.002 0.000 HIS B 75 PHE 0.015 0.001 PHE K 53 TYR 0.012 0.002 TYR H 67 ARG 0.004 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.07242 ( 1104) hydrogen bonds : angle 3.20419 ( 3276) SS BOND : bond 0.00227 ( 36) SS BOND : angle 1.16696 ( 72) covalent geometry : bond 0.00532 (17040) covalent geometry : angle 0.56970 (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 215 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5417 (tpt) cc_final: 0.4362 (ttt) REVERT: A 43 GLU cc_start: 0.8099 (tp30) cc_final: 0.7404 (tp30) REVERT: A 211 ILE cc_start: 0.8228 (mt) cc_final: 0.7984 (mt) REVERT: C 207 ASN cc_start: 0.8216 (m-40) cc_final: 0.7763 (t0) REVERT: D 21 MET cc_start: 0.5432 (tpt) cc_final: 0.4376 (ttt) REVERT: D 43 GLU cc_start: 0.8106 (tp30) cc_final: 0.7412 (tp30) REVERT: F 43 GLU cc_start: 0.7924 (tp30) cc_final: 0.7278 (tp30) REVERT: F 207 ASN cc_start: 0.8207 (m-40) cc_final: 0.7750 (t0) REVERT: G 21 MET cc_start: 0.5393 (tpt) cc_final: 0.4327 (ttt) REVERT: G 43 GLU cc_start: 0.8099 (tp30) cc_final: 0.7410 (tp30) REVERT: G 211 ILE cc_start: 0.8238 (mt) cc_final: 0.7995 (mt) REVERT: I 43 GLU cc_start: 0.7943 (tp30) cc_final: 0.7315 (tp30) REVERT: I 207 ASN cc_start: 0.8125 (m-40) cc_final: 0.7660 (t0) REVERT: J 21 MET cc_start: 0.5402 (tpt) cc_final: 0.4338 (ttt) REVERT: J 43 GLU cc_start: 0.8109 (tp30) cc_final: 0.7419 (tp30) REVERT: L 207 ASN cc_start: 0.8220 (m-40) cc_final: 0.7763 (t0) outliers start: 8 outliers final: 2 residues processed: 207 average time/residue: 0.5376 time to fit residues: 179.6319 Evaluate side-chains 203 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain I residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.182104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128484 restraints weight = 44804.026| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.73 r_work: 0.3383 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17076 Z= 0.200 Angle : 0.563 4.621 22908 Z= 0.296 Chirality : 0.043 0.179 2604 Planarity : 0.003 0.026 2736 Dihedral : 8.766 56.963 2772 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.22 % Allowed : 14.17 % 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: 3.35 (0.19), residues: 1932 helix: 3.23 (0.13), residues: 1332 sheet: 1.04 (0.51), residues: 120 loop : -0.54 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 79 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.001 PHE B 53 TYR 0.012 0.002 TYR H 67 ARG 0.004 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.06974 ( 1104) hydrogen bonds : angle 3.23313 ( 3276) SS BOND : bond 0.00212 ( 36) SS BOND : angle 1.18862 ( 72) covalent geometry : bond 0.00490 (17040) covalent geometry : angle 0.56031 (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 253 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5524 (tpt) cc_final: 0.4526 (ttt) REVERT: A 43 GLU cc_start: 0.8249 (tp30) cc_final: 0.7583 (tp30) REVERT: C 43 GLU cc_start: 0.8098 (tp30) cc_final: 0.7481 (tp30) REVERT: C 207 ASN cc_start: 0.8215 (m-40) cc_final: 0.7683 (t0) REVERT: C 211 ILE cc_start: 0.8113 (mt) cc_final: 0.7830 (mt) REVERT: D 43 GLU cc_start: 0.8248 (tp30) cc_final: 0.7499 (tp30) REVERT: F 43 GLU cc_start: 0.8078 (tp30) cc_final: 0.7459 (tp30) REVERT: F 207 ASN cc_start: 0.8240 (m-40) cc_final: 0.7714 (t0) REVERT: F 211 ILE cc_start: 0.8100 (mt) cc_final: 0.7823 (mt) REVERT: G 43 GLU cc_start: 0.8226 (tp30) cc_final: 0.7557 (tp30) REVERT: H 52 MET cc_start: 0.8511 (mmt) cc_final: 0.8051 (mmt) REVERT: I 43 GLU cc_start: 0.8089 (tp30) cc_final: 0.7481 (tp30) REVERT: I 207 ASN cc_start: 0.8252 (m-40) cc_final: 0.7711 (t0) REVERT: I 211 ILE cc_start: 0.8107 (mt) cc_final: 0.7828 (mt) REVERT: J 21 MET cc_start: 0.5626 (tpt) cc_final: 0.4597 (ttt) REVERT: J 43 GLU cc_start: 0.8235 (tp30) cc_final: 0.7568 (tp30) REVERT: J 85 MET cc_start: 0.7529 (tpt) cc_final: 0.7229 (tpp) REVERT: L 43 GLU cc_start: 0.8076 (tp30) cc_final: 0.7465 (tp30) REVERT: L 207 ASN cc_start: 0.8208 (m-40) cc_final: 0.7686 (t0) REVERT: L 211 ILE cc_start: 0.8089 (mt) cc_final: 0.7808 (mt) outliers start: 22 outliers final: 6 residues processed: 247 average time/residue: 0.4976 time to fit residues: 199.0180 Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain K residue 254 LEU 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: 1.9990 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 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: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.181908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128771 restraints weight = 45114.487| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.75 r_work: 0.3388 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17076 Z= 0.162 Angle : 0.521 4.397 22908 Z= 0.273 Chirality : 0.041 0.208 2604 Planarity : 0.003 0.025 2736 Dihedral : 8.366 59.814 2772 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.50 % Allowed : 15.61 % Favored : 83.89 % 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: 3.49 (0.19), residues: 1932 helix: 3.25 (0.13), residues: 1344 sheet: 1.07 (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 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 53 TYR 0.012 0.002 TYR J 67 ARG 0.002 0.000 ARG L 206 Details of bonding type rmsd hydrogen bonds : bond 0.06369 ( 1104) hydrogen bonds : angle 3.17451 ( 3276) SS BOND : bond 0.00138 ( 36) SS BOND : angle 1.01820 ( 72) covalent geometry : bond 0.00389 (17040) covalent geometry : angle 0.51831 (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 219 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5678 (tpt) cc_final: 0.4661 (ttt) REVERT: A 43 GLU cc_start: 0.8221 (tp30) cc_final: 0.7540 (tp30) REVERT: C 43 GLU cc_start: 0.8097 (tp30) cc_final: 0.7470 (tp30) REVERT: C 207 ASN cc_start: 0.8182 (m-40) cc_final: 0.7600 (t0) REVERT: C 211 ILE cc_start: 0.8116 (mt) cc_final: 0.7849 (mt) REVERT: B 52 MET cc_start: 0.8501 (mmt) cc_final: 0.7988 (mmt) REVERT: B 69 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7963 (tpp80) REVERT: D 43 GLU cc_start: 0.8214 (tp30) cc_final: 0.7533 (tp30) REVERT: E 52 MET cc_start: 0.8479 (mmt) cc_final: 0.7952 (mmt) REVERT: E 69 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7971 (tpp80) REVERT: F 43 GLU cc_start: 0.8078 (tp30) cc_final: 0.7438 (tp30) REVERT: F 207 ASN cc_start: 0.8185 (m-40) cc_final: 0.7607 (t0) REVERT: F 211 ILE cc_start: 0.8114 (mt) cc_final: 0.7854 (mt) REVERT: G 43 GLU cc_start: 0.8185 (tp30) cc_final: 0.7514 (tp30) REVERT: H 52 MET cc_start: 0.8487 (mmt) cc_final: 0.7966 (mmt) REVERT: H 69 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7957 (tpp80) REVERT: I 43 GLU cc_start: 0.8095 (tp30) cc_final: 0.7460 (tp30) REVERT: I 207 ASN cc_start: 0.8199 (m-40) cc_final: 0.7613 (t0) REVERT: I 211 ILE cc_start: 0.8128 (mt) cc_final: 0.7863 (mt) REVERT: J 43 GLU cc_start: 0.8208 (tp30) cc_final: 0.7538 (tp30) REVERT: J 85 MET cc_start: 0.7544 (tpt) cc_final: 0.7252 (tpp) REVERT: K 52 MET cc_start: 0.8481 (mmt) cc_final: 0.7956 (mmt) REVERT: K 69 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7962 (tpp80) REVERT: L 43 GLU cc_start: 0.8072 (tp30) cc_final: 0.7447 (tp30) REVERT: L 207 ASN cc_start: 0.8205 (m-40) cc_final: 0.7622 (t0) REVERT: L 211 ILE cc_start: 0.8128 (mt) cc_final: 0.7864 (mt) outliers start: 9 outliers final: 8 residues processed: 216 average time/residue: 0.6839 time to fit residues: 244.0924 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 : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain K residue 209 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: 1.9990 chunk 137 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.183176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130413 restraints weight = 44742.143| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.73 r_work: 0.3414 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17076 Z= 0.121 Angle : 0.476 4.228 22908 Z= 0.248 Chirality : 0.040 0.144 2604 Planarity : 0.003 0.026 2736 Dihedral : 7.514 55.411 2772 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.67 % Allowed : 15.22 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.74 (0.19), residues: 1932 helix: 3.45 (0.13), residues: 1344 sheet: 1.24 (0.52), residues: 120 loop : -0.30 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.002 0.001 HIS L 274 PHE 0.008 0.001 PHE I 33 TYR 0.010 0.001 TYR G 67 ARG 0.002 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 1104) hydrogen bonds : angle 3.04842 ( 3276) SS BOND : bond 0.00076 ( 36) SS BOND : angle 0.81644 ( 72) covalent geometry : bond 0.00272 (17040) covalent geometry : angle 0.47475 (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 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8201 (tp30) cc_final: 0.7540 (tp30) REVERT: C 43 GLU cc_start: 0.8181 (tp30) cc_final: 0.7516 (tp30) REVERT: C 207 ASN cc_start: 0.8162 (m-40) cc_final: 0.7569 (t0) REVERT: C 211 ILE cc_start: 0.8052 (mt) cc_final: 0.7806 (mt) REVERT: C 254 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7224 (tt) REVERT: B 52 MET cc_start: 0.8467 (mmt) cc_final: 0.7939 (mmt) REVERT: B 69 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7905 (tpp80) REVERT: D 43 GLU cc_start: 0.8237 (tp30) cc_final: 0.7581 (tp30) REVERT: E 52 MET cc_start: 0.8472 (mmt) cc_final: 0.7943 (mmt) REVERT: F 43 GLU cc_start: 0.8179 (tp30) cc_final: 0.7505 (tp30) REVERT: F 207 ASN cc_start: 0.8168 (m-40) cc_final: 0.7577 (t0) REVERT: F 211 ILE cc_start: 0.8083 (mt) cc_final: 0.7844 (mt) REVERT: F 254 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7220 (tt) REVERT: G 21 MET cc_start: 0.5727 (tpt) cc_final: 0.4761 (ttt) REVERT: G 43 GLU cc_start: 0.8239 (tp30) cc_final: 0.7575 (tp30) REVERT: H 52 MET cc_start: 0.8458 (mmt) cc_final: 0.7930 (mmt) REVERT: H 69 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7893 (tpp80) REVERT: I 43 GLU cc_start: 0.8183 (tp30) cc_final: 0.7508 (tp30) REVERT: I 207 ASN cc_start: 0.8195 (m-40) cc_final: 0.7596 (t0) REVERT: I 211 ILE cc_start: 0.8094 (mt) cc_final: 0.7848 (mt) REVERT: I 254 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7220 (tt) REVERT: J 21 MET cc_start: 0.5725 (tpt) cc_final: 0.4759 (ttt) REVERT: J 43 GLU cc_start: 0.8258 (tp30) cc_final: 0.7600 (tp30) REVERT: J 85 MET cc_start: 0.7531 (tpt) cc_final: 0.7235 (tpp) REVERT: K 52 MET cc_start: 0.8451 (mmt) cc_final: 0.7917 (mmt) REVERT: K 69 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7891 (tpp80) REVERT: L 43 GLU cc_start: 0.8165 (tp30) cc_final: 0.7494 (tp30) REVERT: L 207 ASN cc_start: 0.8183 (m-40) cc_final: 0.7589 (t0) REVERT: L 211 ILE cc_start: 0.8064 (mt) cc_final: 0.7823 (mt) REVERT: L 254 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7227 (tt) outliers start: 12 outliers final: 4 residues processed: 224 average time/residue: 0.4925 time to fit residues: 178.0010 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 : 2.402 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 148 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131646 restraints weight = 44804.627| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.74 r_work: 0.3424 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17076 Z= 0.109 Angle : 0.464 4.195 22908 Z= 0.240 Chirality : 0.039 0.130 2604 Planarity : 0.003 0.025 2736 Dihedral : 6.952 57.967 2772 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.89 % Allowed : 15.33 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.55 (0.13), residues: 1344 sheet: 1.21 (0.52), residues: 120 loop : -0.31 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.003 0.001 HIS G 274 PHE 0.007 0.001 PHE I 33 TYR 0.009 0.001 TYR J 67 ARG 0.005 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 1104) hydrogen bonds : angle 3.03411 ( 3276) SS BOND : bond 0.00057 ( 36) SS BOND : angle 0.78547 ( 72) covalent geometry : bond 0.00244 (17040) covalent geometry : angle 0.46310 (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 226 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5609 (tpt) cc_final: 0.4711 (ttt) REVERT: A 43 GLU cc_start: 0.8256 (tp30) cc_final: 0.7575 (tp30) REVERT: C 43 GLU cc_start: 0.8181 (tp30) cc_final: 0.7489 (tp30) REVERT: C 207 ASN cc_start: 0.8155 (m-40) cc_final: 0.7548 (t0) REVERT: C 211 ILE cc_start: 0.8095 (mt) cc_final: 0.7851 (mt) REVERT: C 254 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7213 (tt) REVERT: B 52 MET cc_start: 0.8484 (mmt) cc_final: 0.8010 (mmt) REVERT: B 69 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7979 (tpp80) REVERT: D 21 MET cc_start: 0.5524 (tpt) cc_final: 0.5296 (tpt) REVERT: D 43 GLU cc_start: 0.8258 (tp30) cc_final: 0.7577 (tp30) REVERT: E 52 MET cc_start: 0.8485 (mmt) cc_final: 0.8011 (mmt) REVERT: F 43 GLU cc_start: 0.8190 (tp30) cc_final: 0.7495 (tp30) REVERT: F 207 ASN cc_start: 0.8153 (m-40) cc_final: 0.7548 (t0) REVERT: F 211 ILE cc_start: 0.8096 (mt) cc_final: 0.7852 (mt) REVERT: F 254 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7222 (tt) REVERT: G 43 GLU cc_start: 0.8239 (tp30) cc_final: 0.7559 (tp30) REVERT: H 52 MET cc_start: 0.8470 (mmt) cc_final: 0.7986 (mmt) REVERT: H 69 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: I 43 GLU cc_start: 0.8207 (tp30) cc_final: 0.7504 (tp30) REVERT: I 207 ASN cc_start: 0.8180 (m-40) cc_final: 0.7564 (t0) REVERT: I 211 ILE cc_start: 0.8109 (mt) cc_final: 0.7866 (mt) REVERT: I 254 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7218 (tt) REVERT: J 43 GLU cc_start: 0.8249 (tp30) cc_final: 0.7578 (tp30) REVERT: J 85 MET cc_start: 0.7512 (tpt) cc_final: 0.7260 (tpp) REVERT: K 52 MET cc_start: 0.8466 (mmt) cc_final: 0.7983 (mmt) REVERT: K 69 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7968 (tpp80) REVERT: L 43 GLU cc_start: 0.8158 (tp30) cc_final: 0.7468 (tp30) REVERT: L 207 ASN cc_start: 0.8165 (m-40) cc_final: 0.7559 (t0) REVERT: L 211 ILE cc_start: 0.8070 (mt) cc_final: 0.7823 (mt) REVERT: L 254 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7223 (tt) outliers start: 16 outliers final: 6 residues processed: 221 average time/residue: 0.5606 time to fit residues: 201.9096 Evaluate side-chains 214 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 207 ASN 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: 0.1980 chunk 176 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 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: 0.4478 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.186032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134015 restraints weight = 44635.014| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.74 r_work: 0.3454 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17076 Z= 0.090 Angle : 0.440 4.084 22908 Z= 0.226 Chirality : 0.038 0.130 2604 Planarity : 0.003 0.025 2736 Dihedral : 6.140 54.630 2772 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.44 % Allowed : 15.94 % Favored : 83.61 % 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: 4.05 (0.19), residues: 1932 helix: 3.79 (0.13), residues: 1332 sheet: 0.63 (0.51), residues: 132 loop : -0.22 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP K 79 HIS 0.002 0.001 HIS E 274 PHE 0.007 0.001 PHE I 33 TYR 0.007 0.001 TYR C 67 ARG 0.001 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 1104) hydrogen bonds : angle 2.96032 ( 3276) SS BOND : bond 0.00027 ( 36) SS BOND : angle 0.65340 ( 72) covalent geometry : bond 0.00186 (17040) covalent geometry : angle 0.43912 (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 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 5.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8246 (tp30) cc_final: 0.7562 (tp30) REVERT: C 43 GLU cc_start: 0.8130 (tp30) cc_final: 0.7429 (tp30) REVERT: C 207 ASN cc_start: 0.8144 (m-40) cc_final: 0.7519 (t0) REVERT: C 211 ILE cc_start: 0.8020 (mt) cc_final: 0.7786 (mt) REVERT: C 254 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7183 (tt) REVERT: B 52 MET cc_start: 0.8496 (mmt) cc_final: 0.8013 (mmt) REVERT: B 69 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7887 (tpp80) REVERT: D 21 MET cc_start: 0.5485 (tpt) cc_final: 0.5258 (tpt) REVERT: D 43 GLU cc_start: 0.8220 (tp30) cc_final: 0.7528 (tp30) REVERT: E 52 MET cc_start: 0.8483 (mmt) cc_final: 0.7993 (mmt) REVERT: F 43 GLU cc_start: 0.8148 (tp30) cc_final: 0.7435 (tp30) REVERT: F 207 ASN cc_start: 0.8149 (m-40) cc_final: 0.7527 (t0) REVERT: F 211 ILE cc_start: 0.8038 (mt) cc_final: 0.7804 (mt) REVERT: F 254 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7177 (tt) REVERT: G 43 GLU cc_start: 0.8220 (tp30) cc_final: 0.7524 (tp30) REVERT: H 52 MET cc_start: 0.8464 (mmt) cc_final: 0.7978 (mmt) REVERT: H 69 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7876 (tpp80) REVERT: I 43 GLU cc_start: 0.8137 (tp30) cc_final: 0.7434 (tp30) REVERT: I 254 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7171 (tt) REVERT: J 43 GLU cc_start: 0.8229 (tp30) cc_final: 0.7561 (tp30) REVERT: J 85 MET cc_start: 0.7502 (tpt) cc_final: 0.7292 (tpp) REVERT: K 52 MET cc_start: 0.8463 (mmt) cc_final: 0.7969 (mmt) REVERT: K 69 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7863 (tpp80) REVERT: L 43 GLU cc_start: 0.8129 (tp30) cc_final: 0.7425 (tp30) REVERT: L 207 ASN cc_start: 0.8156 (m-40) cc_final: 0.7533 (t0) REVERT: L 211 ILE cc_start: 0.7996 (mt) cc_final: 0.7747 (mt) REVERT: L 254 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7171 (tt) outliers start: 8 outliers final: 4 residues processed: 222 average time/residue: 0.9412 time to fit residues: 345.4504 Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 6.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I 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: 0.7980 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.183392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131040 restraints weight = 44824.302| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.74 r_work: 0.3424 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 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 = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4681 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= 0.127 Angle : 0.477 4.459 22908 Z= 0.245 Chirality : 0.039 0.129 2604 Planarity : 0.003 0.024 2736 Dihedral : 6.317 51.261 2772 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.61 % Allowed : 16.44 % Favored : 82.94 % 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: 4.03 (0.19), residues: 1932 helix: 3.69 (0.13), residues: 1344 sheet: 1.13 (0.53), residues: 120 loop : -0.20 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.001 0.001 HIS F 274 PHE 0.009 0.001 PHE E 53 TYR 0.009 0.001 TYR J 67 ARG 0.002 0.000 ARG I 206 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 1104) hydrogen bonds : angle 3.02350 ( 3276) SS BOND : bond 0.00112 ( 36) SS BOND : angle 0.84905 ( 72) covalent geometry : bond 0.00310 (17040) covalent geometry : angle 0.47521 (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 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8315 (tp30) cc_final: 0.7628 (tp30) REVERT: C 43 GLU cc_start: 0.8165 (tp30) cc_final: 0.7441 (tp30) REVERT: C 254 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7182 (tt) REVERT: C 269 LEU cc_start: 0.7288 (mt) cc_final: 0.7023 (mt) REVERT: B 52 MET cc_start: 0.8539 (mmt) cc_final: 0.8068 (mmt) REVERT: B 69 ARG cc_start: 0.8149 (tpp-160) cc_final: 0.7940 (tpp80) REVERT: D 21 MET cc_start: 0.5512 (tpt) cc_final: 0.5279 (tpt) REVERT: D 43 GLU cc_start: 0.8287 (tp30) cc_final: 0.7593 (tp30) REVERT: E 52 MET cc_start: 0.8532 (mmt) cc_final: 0.8055 (mmt) REVERT: F 43 GLU cc_start: 0.8187 (tp30) cc_final: 0.7461 (tp30) REVERT: F 254 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7184 (tt) REVERT: G 21 MET cc_start: 0.5411 (tpt) cc_final: 0.5171 (tpt) REVERT: G 43 GLU cc_start: 0.8310 (tp30) cc_final: 0.7605 (tp30) REVERT: H 52 MET cc_start: 0.8511 (mmt) cc_final: 0.8039 (mmt) REVERT: H 69 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7936 (tpp80) REVERT: I 43 GLU cc_start: 0.8190 (tp30) cc_final: 0.7464 (tp30) REVERT: I 207 ASN cc_start: 0.8108 (m-40) cc_final: 0.7615 (t0) REVERT: I 254 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7193 (tt) REVERT: J 21 MET cc_start: 0.5505 (tpt) cc_final: 0.5266 (tpt) REVERT: J 43 GLU cc_start: 0.8308 (tp30) cc_final: 0.7614 (tp30) REVERT: K 52 MET cc_start: 0.8510 (mmt) cc_final: 0.8025 (mmt) REVERT: K 69 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7928 (tpp80) REVERT: L 43 GLU cc_start: 0.8174 (tp30) cc_final: 0.7452 (tp30) REVERT: L 211 ILE cc_start: 0.8048 (mt) cc_final: 0.7844 (mt) REVERT: L 254 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7200 (tt) outliers start: 11 outliers final: 7 residues processed: 214 average time/residue: 0.6394 time to fit residues: 224.6184 Evaluate side-chains 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain K residue 87 CYS 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: 0.8980 chunk 12 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.184290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132219 restraints weight = 44718.130| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.72 r_work: 0.3435 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17076 Z= 0.103 Angle : 0.451 4.232 22908 Z= 0.232 Chirality : 0.039 0.130 2604 Planarity : 0.003 0.024 2736 Dihedral : 6.124 51.834 2772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.56 % Allowed : 16.50 % Favored : 82.94 % 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: 4.05 (0.19), residues: 1932 helix: 3.72 (0.13), residues: 1344 sheet: 0.49 (0.51), residues: 132 loop : -0.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.002 0.000 HIS L 274 PHE 0.007 0.001 PHE I 33 TYR 0.009 0.001 TYR J 67 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 1104) hydrogen bonds : angle 3.00848 ( 3276) SS BOND : bond 0.00075 ( 36) SS BOND : angle 0.72528 ( 72) covalent geometry : bond 0.00231 (17040) covalent geometry : angle 0.45021 (22836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16836.95 seconds wall clock time: 295 minutes 50.24 seconds (17750.24 seconds total)