Starting phenix.real_space_refine on Tue Aug 26 01:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgg_38322/08_2025/8xgg_38322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgg_38322/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xgg_38322/08_2025/8xgg_38322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgg_38322/08_2025/8xgg_38322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xgg_38322/08_2025/8xgg_38322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgg_38322/08_2025/8xgg_38322.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 5, 'MC3:plan-2': 5} Unresolved non-hydrogen planarities: 34 Restraints were copied for chains: C, B, D, E, F, G, H, I, J, K, 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: 2.95, per 1000 atoms: 0.09 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 D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 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 D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 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 D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 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: 2.78 Conformation dependent library (CDL) restraints added in 873.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 6.87 Time building geometry restraints manager: 3.87 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.160 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.130 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG L 197 TYR 0.008 0.001 TYR K 67 PHE 0.005 0.001 PHE G 205 TRP 0.003 0.001 TRP G 79 HIS 0.005 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00331 (17040) covalent geometry : angle 0.83961 (22836) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.23922 ( 72) hydrogen bonds : bond 0.13268 ( 1104) hydrogen bonds : angle 4.18399 ( 3276) *********************** 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 : 0.577 Fit side-chains REVERT: A 21 MET cc_start: 0.5398 (tpt) cc_final: 0.5144 (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: 0.7269 (tp30) REVERT: B 21 MET cc_start: 0.5517 (tpt) cc_final: 0.4811 (ttt) REVERT: B 43 GLU cc_start: 0.7615 (tp30) cc_final: 0.7250 (tp30) REVERT: D 21 MET cc_start: 0.5221 (tpt) cc_final: 0.4945 (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: 0.4851 (ttt) REVERT: E 43 GLU cc_start: 0.7611 (tp30) cc_final: 0.7253 (tp30) REVERT: F 43 GLU cc_start: 0.7554 (tp30) cc_final: 0.7277 (tp30) REVERT: G 21 MET cc_start: 0.5311 (tpt) cc_final: 0.5050 (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: 0.4857 (ttt) REVERT: H 43 GLU cc_start: 0.7610 (tp30) cc_final: 0.7250 (tp30) REVERT: I 43 GLU cc_start: 0.7546 (tp30) cc_final: 0.7278 (tp30) REVERT: J 21 MET cc_start: 0.5211 (tpt) cc_final: 0.4979 (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: 0.4933 (ttt) REVERT: K 43 GLU cc_start: 0.7615 (tp30) cc_final: 0.7250 (tp30) REVERT: L 43 GLU cc_start: 0.7549 (tp30) cc_final: 0.7271 (tp30) outliers start: 12 outliers final: 0 residues processed: 283 average time/residue: 0.2278 time to fit residues: 101.9775 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 : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.196581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141255 restraints weight = 43833.632| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.84 r_work: 0.3525 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1858 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 : 0.548 4.205 22908 Z= 0.294 Chirality : 0.040 0.124 2604 Planarity : 0.003 0.024 2736 Dihedral : 8.662 51.070 2772 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.44 % Allowed : 13.39 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.18), residues: 1932 helix: 3.04 (0.13), residues: 1332 sheet: 2.09 (0.43), residues: 120 loop : -0.81 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 233 TYR 0.012 0.002 TYR E 67 PHE 0.014 0.001 PHE A 53 TRP 0.005 0.002 TRP H 79 HIS 0.001 0.000 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00365 (17040) covalent geometry : angle 0.54638 (22836) SS BOND : bond 0.00170 ( 36) SS BOND : angle 0.96936 ( 72) hydrogen bonds : bond 0.06967 ( 1104) hydrogen bonds : angle 3.33126 ( 3276) *********************** 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 244 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5248 (tpt) cc_final: 0.4299 (ttt) REVERT: A 43 GLU cc_start: 0.8067 (tp30) cc_final: 0.7476 (tp30) REVERT: A 210 GLU cc_start: 0.7145 (tp30) cc_final: 0.6843 (tp30) REVERT: A 271 GLU cc_start: 0.6542 (tp30) cc_final: 0.6255 (tp30) REVERT: C 43 GLU cc_start: 0.7914 (tp30) cc_final: 0.7396 (tp30) REVERT: B 21 MET cc_start: 0.5539 (tpt) cc_final: 0.4737 (ttt) REVERT: B 43 GLU cc_start: 0.8015 (tp30) cc_final: 0.7434 (tp30) REVERT: D 21 MET cc_start: 0.5131 (tpt) cc_final: 0.4110 (ttt) REVERT: D 43 GLU cc_start: 0.8048 (tp30) cc_final: 0.7497 (tp30) REVERT: D 210 GLU cc_start: 0.7160 (tp30) cc_final: 0.6852 (tp30) REVERT: E 21 MET cc_start: 0.5552 (tpt) cc_final: 0.4768 (ttt) REVERT: E 43 GLU cc_start: 0.8007 (tp30) cc_final: 0.7422 (tp30) REVERT: E 271 GLU cc_start: 0.6437 (tp30) cc_final: 0.6123 (tp30) REVERT: F 43 GLU cc_start: 0.7895 (tp30) cc_final: 0.7293 (tp30) REVERT: F 271 GLU cc_start: 0.6749 (tp30) cc_final: 0.6547 (tp30) REVERT: G 21 MET cc_start: 0.5204 (tpt) cc_final: 0.4236 (ttt) REVERT: G 43 GLU cc_start: 0.8055 (tp30) cc_final: 0.7484 (tp30) REVERT: G 210 GLU cc_start: 0.7158 (tp30) cc_final: 0.6848 (tp30) REVERT: G 271 GLU cc_start: 0.6515 (tp30) cc_final: 0.6218 (tp30) REVERT: H 21 MET cc_start: 0.5553 (tpt) cc_final: 0.4766 (ttt) REVERT: H 43 GLU cc_start: 0.7990 (tp30) cc_final: 0.7422 (tp30) REVERT: H 271 GLU cc_start: 0.6473 (tp30) cc_final: 0.6165 (tp30) REVERT: I 43 GLU cc_start: 0.7902 (tp30) cc_final: 0.7301 (tp30) REVERT: I 271 GLU cc_start: 0.6739 (tp30) cc_final: 0.6536 (tp30) REVERT: J 21 MET cc_start: 0.5261 (tpt) cc_final: 0.4333 (ttt) REVERT: J 43 GLU cc_start: 0.8036 (tp30) cc_final: 0.7477 (tp30) REVERT: J 210 GLU cc_start: 0.7158 (tp30) cc_final: 0.6847 (tp30) REVERT: J 271 GLU cc_start: 0.6497 (tp30) cc_final: 0.6197 (tp30) REVERT: K 21 MET cc_start: 0.5539 (tpt) cc_final: 0.4737 (ttt) REVERT: K 43 GLU cc_start: 0.8019 (tp30) cc_final: 0.7429 (tp30) REVERT: L 43 GLU cc_start: 0.7909 (tp30) cc_final: 0.7313 (tp30) outliers start: 8 outliers final: 8 residues processed: 240 average time/residue: 0.2338 time to fit residues: 86.9438 Evaluate side-chains 210 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.196058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141147 restraints weight = 43438.103| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.83 r_work: 0.3531 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2376 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= 0.118 Angle : 0.470 3.930 22908 Z= 0.250 Chirality : 0.039 0.120 2604 Planarity : 0.002 0.021 2736 Dihedral : 7.488 52.749 2772 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.44 % Allowed : 14.11 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.73 (0.18), residues: 1932 helix: 3.48 (0.13), residues: 1332 sheet: 2.25 (0.44), residues: 120 loop : -0.64 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 69 TYR 0.010 0.001 TYR K 67 PHE 0.012 0.001 PHE F 33 TRP 0.002 0.001 TRP K 79 HIS 0.001 0.000 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00241 (17040) covalent geometry : angle 0.46918 (22836) SS BOND : bond 0.00063 ( 36) SS BOND : angle 0.77569 ( 72) hydrogen bonds : bond 0.06023 ( 1104) hydrogen bonds : angle 3.05785 ( 3276) *********************** 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 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 212 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5378 (tpt) cc_final: 0.4395 (ttt) REVERT: A 43 GLU cc_start: 0.7912 (tp30) cc_final: 0.7435 (tp30) REVERT: A 210 GLU cc_start: 0.7196 (tp30) cc_final: 0.6809 (tp30) REVERT: A 211 ILE cc_start: 0.7985 (mt) cc_final: 0.7765 (mt) REVERT: A 271 GLU cc_start: 0.6708 (tp30) cc_final: 0.6472 (tp30) REVERT: C 43 GLU cc_start: 0.7785 (tp30) cc_final: 0.7207 (tp30) REVERT: C 207 ASN cc_start: 0.8055 (m-40) cc_final: 0.7674 (t0) REVERT: B 21 MET cc_start: 0.5426 (tpt) cc_final: 0.4590 (ttt) REVERT: B 43 GLU cc_start: 0.7923 (tp30) cc_final: 0.7348 (tp30) REVERT: B 52 MET cc_start: 0.8243 (mmt) cc_final: 0.7948 (mmt) REVERT: D 21 MET cc_start: 0.5246 (tpt) cc_final: 0.4177 (ttt) REVERT: D 43 GLU cc_start: 0.7924 (tp30) cc_final: 0.7441 (tp30) REVERT: D 210 GLU cc_start: 0.7223 (tp30) cc_final: 0.6843 (tp30) REVERT: D 211 ILE cc_start: 0.7996 (mt) cc_final: 0.7756 (mt) REVERT: E 21 MET cc_start: 0.5440 (tpt) cc_final: 0.4616 (ttt) REVERT: E 43 GLU cc_start: 0.7901 (tp30) cc_final: 0.7335 (tp30) REVERT: F 43 GLU cc_start: 0.7775 (tp30) cc_final: 0.7204 (tp30) REVERT: F 271 GLU cc_start: 0.6726 (tp30) cc_final: 0.6490 (tp30) REVERT: G 21 MET cc_start: 0.5380 (tpt) cc_final: 0.4376 (ttt) REVERT: G 43 GLU cc_start: 0.7923 (tp30) cc_final: 0.7448 (tp30) REVERT: G 210 GLU cc_start: 0.7193 (tp30) cc_final: 0.6817 (tp30) REVERT: G 211 ILE cc_start: 0.7978 (mt) cc_final: 0.7741 (mt) REVERT: G 271 GLU cc_start: 0.6637 (tp30) cc_final: 0.6384 (tp30) REVERT: H 21 MET cc_start: 0.5441 (tpt) cc_final: 0.4609 (ttt) REVERT: H 43 GLU cc_start: 0.7915 (tp30) cc_final: 0.7342 (tp30) REVERT: I 43 GLU cc_start: 0.7785 (tp30) cc_final: 0.7213 (tp30) REVERT: I 271 GLU cc_start: 0.6724 (tp30) cc_final: 0.6495 (tp30) REVERT: J 21 MET cc_start: 0.5377 (tpt) cc_final: 0.4379 (ttt) REVERT: J 43 GLU cc_start: 0.7929 (tp30) cc_final: 0.7450 (tp30) REVERT: J 210 GLU cc_start: 0.7204 (tp30) cc_final: 0.6815 (tp30) REVERT: J 211 ILE cc_start: 0.7994 (mt) cc_final: 0.7761 (mt) REVERT: J 271 GLU cc_start: 0.6620 (tp30) cc_final: 0.6372 (tp30) REVERT: K 21 MET cc_start: 0.5429 (tpt) cc_final: 0.4593 (ttt) REVERT: K 43 GLU cc_start: 0.7912 (tp30) cc_final: 0.7345 (tp30) REVERT: L 43 GLU cc_start: 0.7767 (tp30) cc_final: 0.7191 (tp30) REVERT: L 207 ASN cc_start: 0.8045 (m-40) cc_final: 0.7666 (t0) outliers start: 8 outliers final: 8 residues processed: 212 average time/residue: 0.2145 time to fit residues: 73.0731 Evaluate side-chains 209 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 167 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.185888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131300 restraints weight = 44158.322| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.76 r_work: 0.3415 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17076 Z= 0.220 Angle : 0.580 4.707 22908 Z= 0.313 Chirality : 0.044 0.187 2604 Planarity : 0.004 0.026 2736 Dihedral : 8.461 54.355 2772 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.33 % Allowed : 14.22 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.18), residues: 1932 helix: 3.12 (0.13), residues: 1332 sheet: 1.55 (0.46), residues: 120 loop : -0.51 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 233 TYR 0.011 0.002 TYR K 67 PHE 0.018 0.001 PHE B 53 TRP 0.006 0.002 TRP E 79 HIS 0.001 0.000 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00546 (17040) covalent geometry : angle 0.57764 (22836) SS BOND : bond 0.00245 ( 36) SS BOND : angle 1.12539 ( 72) hydrogen bonds : bond 0.07220 ( 1104) hydrogen bonds : angle 3.15214 ( 3276) *********************** 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 226 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5352 (tpt) cc_final: 0.4258 (ttt) REVERT: A 43 GLU cc_start: 0.8028 (tp30) cc_final: 0.7347 (tp30) REVERT: A 210 GLU cc_start: 0.7265 (tp30) cc_final: 0.6940 (tp30) REVERT: A 211 ILE cc_start: 0.8205 (mt) cc_final: 0.7962 (mt) REVERT: C 207 ASN cc_start: 0.8090 (m-40) cc_final: 0.7641 (t0) REVERT: B 21 MET cc_start: 0.5455 (tpt) cc_final: 0.4589 (ttt) REVERT: B 43 GLU cc_start: 0.7986 (tp30) cc_final: 0.7353 (tp30) REVERT: D 21 MET cc_start: 0.5495 (tpt) cc_final: 0.4465 (ttt) REVERT: D 43 GLU cc_start: 0.8069 (tp30) cc_final: 0.7392 (tp30) REVERT: D 210 GLU cc_start: 0.7283 (tp30) cc_final: 0.6949 (tp30) REVERT: D 211 ILE cc_start: 0.8192 (mt) cc_final: 0.7949 (mt) REVERT: E 43 GLU cc_start: 0.7996 (tp30) cc_final: 0.7365 (tp30) REVERT: F 43 GLU cc_start: 0.7815 (tp30) cc_final: 0.7206 (tp30) REVERT: F 207 ASN cc_start: 0.8092 (m-40) cc_final: 0.7633 (t0) REVERT: G 21 MET cc_start: 0.5380 (tpt) cc_final: 0.4333 (ttt) REVERT: G 43 GLU cc_start: 0.8070 (tp30) cc_final: 0.7382 (tp30) REVERT: G 210 GLU cc_start: 0.7257 (tp30) cc_final: 0.6923 (tp30) REVERT: G 211 ILE cc_start: 0.8193 (mt) cc_final: 0.7954 (mt) REVERT: H 43 GLU cc_start: 0.7998 (tp30) cc_final: 0.7382 (tp30) REVERT: I 43 GLU cc_start: 0.7834 (tp30) cc_final: 0.7227 (tp30) REVERT: I 207 ASN cc_start: 0.8095 (m-40) cc_final: 0.7635 (t0) REVERT: I 257 MET cc_start: 0.7878 (mmm) cc_final: 0.7618 (mmm) REVERT: J 21 MET cc_start: 0.5489 (tpt) cc_final: 0.4459 (ttt) REVERT: J 43 GLU cc_start: 0.8062 (tp30) cc_final: 0.7373 (tp30) REVERT: J 87 CYS cc_start: 0.8374 (m) cc_final: 0.7987 (m) REVERT: J 210 GLU cc_start: 0.7268 (tp30) cc_final: 0.6938 (tp30) REVERT: J 211 ILE cc_start: 0.8211 (mt) cc_final: 0.7968 (mt) REVERT: K 21 MET cc_start: 0.5449 (tpt) cc_final: 0.4579 (ttt) REVERT: K 43 GLU cc_start: 0.8013 (tp30) cc_final: 0.7378 (tp30) REVERT: L 43 GLU cc_start: 0.7816 (tp30) cc_final: 0.7215 (tp30) REVERT: L 207 ASN cc_start: 0.8095 (m-40) cc_final: 0.7641 (t0) outliers start: 24 outliers final: 8 residues processed: 214 average time/residue: 0.2212 time to fit residues: 76.1099 Evaluate side-chains 205 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L 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: 2.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.189853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136137 restraints weight = 44074.452| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.76 r_work: 0.3476 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17076 Z= 0.110 Angle : 0.461 4.439 22908 Z= 0.242 Chirality : 0.039 0.196 2604 Planarity : 0.003 0.037 2736 Dihedral : 7.644 59.346 2772 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.61 % Allowed : 14.39 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.19), residues: 1932 helix: 3.51 (0.13), residues: 1332 sheet: 2.02 (0.48), residues: 120 loop : -0.50 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 206 TYR 0.010 0.001 TYR K 67 PHE 0.008 0.001 PHE E 33 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.000 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00222 (17040) covalent geometry : angle 0.46013 (22836) SS BOND : bond 0.00068 ( 36) SS BOND : angle 0.69437 ( 72) hydrogen bonds : bond 0.05529 ( 1104) hydrogen bonds : angle 2.97519 ( 3276) *********************** 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 213 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5430 (tpt) cc_final: 0.4395 (ttt) REVERT: A 43 GLU cc_start: 0.8003 (tp30) cc_final: 0.7332 (tp30) REVERT: A 211 ILE cc_start: 0.8172 (mt) cc_final: 0.7934 (mt) REVERT: C 43 GLU cc_start: 0.7843 (tp30) cc_final: 0.7179 (tp30) REVERT: C 207 ASN cc_start: 0.8100 (m-40) cc_final: 0.7640 (t0) REVERT: B 52 MET cc_start: 0.8392 (mmt) cc_final: 0.7980 (mmt) REVERT: D 21 MET cc_start: 0.5502 (tpt) cc_final: 0.4424 (ttt) REVERT: D 43 GLU cc_start: 0.8058 (tp30) cc_final: 0.7362 (tp30) REVERT: D 211 ILE cc_start: 0.8202 (mt) cc_final: 0.7957 (mt) REVERT: E 52 MET cc_start: 0.8350 (mmt) cc_final: 0.7927 (mmt) REVERT: F 43 GLU cc_start: 0.7841 (tp30) cc_final: 0.7141 (tp30) REVERT: F 207 ASN cc_start: 0.8085 (m-40) cc_final: 0.7614 (t0) REVERT: F 257 MET cc_start: 0.7907 (mmm) cc_final: 0.7559 (mmm) REVERT: G 21 MET cc_start: 0.5500 (tpt) cc_final: 0.4427 (ttt) REVERT: G 43 GLU cc_start: 0.8062 (tp30) cc_final: 0.7363 (tp30) REVERT: G 211 ILE cc_start: 0.8178 (mt) cc_final: 0.7937 (mt) REVERT: H 52 MET cc_start: 0.8353 (mmt) cc_final: 0.7929 (mmt) REVERT: I 43 GLU cc_start: 0.7856 (tp30) cc_final: 0.7166 (tp30) REVERT: I 207 ASN cc_start: 0.8087 (m-40) cc_final: 0.7613 (t0) REVERT: I 257 MET cc_start: 0.7878 (mmm) cc_final: 0.7536 (mmm) REVERT: J 21 MET cc_start: 0.5485 (tpt) cc_final: 0.4418 (ttt) REVERT: J 43 GLU cc_start: 0.8073 (tp30) cc_final: 0.7383 (tp30) REVERT: J 211 ILE cc_start: 0.8188 (mt) cc_final: 0.7946 (mt) REVERT: K 52 MET cc_start: 0.8339 (mmt) cc_final: 0.7911 (mmt) REVERT: L 43 GLU cc_start: 0.7857 (tp30) cc_final: 0.7214 (tp30) REVERT: L 207 ASN cc_start: 0.8088 (m-40) cc_final: 0.7623 (t0) REVERT: L 257 MET cc_start: 0.7890 (mmm) cc_final: 0.7543 (mmm) outliers start: 11 outliers final: 7 residues processed: 202 average time/residue: 0.2186 time to fit residues: 71.4185 Evaluate side-chains 205 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain D residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain K residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.183849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129885 restraints weight = 44627.134| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.74 r_work: 0.3403 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17076 Z= 0.182 Angle : 0.543 4.663 22908 Z= 0.286 Chirality : 0.042 0.229 2604 Planarity : 0.003 0.025 2736 Dihedral : 8.296 58.266 2772 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.59 (0.19), residues: 1932 helix: 3.37 (0.13), residues: 1332 sheet: 1.17 (0.51), residues: 120 loop : -0.35 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 233 TYR 0.011 0.001 TYR A 67 PHE 0.016 0.001 PHE B 53 TRP 0.005 0.002 TRP H 79 HIS 0.003 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (17040) covalent geometry : angle 0.54012 (22836) SS BOND : bond 0.00210 ( 36) SS BOND : angle 1.05618 ( 72) hydrogen bonds : bond 0.06438 ( 1104) hydrogen bonds : angle 3.07526 ( 3276) *********************** 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 221 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5535 (tpt) cc_final: 0.4545 (ttt) REVERT: A 43 GLU cc_start: 0.8245 (tp30) cc_final: 0.7455 (tp30) REVERT: C 43 GLU cc_start: 0.8038 (tp30) cc_final: 0.7420 (tp30) REVERT: C 207 ASN cc_start: 0.8221 (m-40) cc_final: 0.7674 (t0) REVERT: C 211 ILE cc_start: 0.8152 (mt) cc_final: 0.7844 (mt) REVERT: D 43 GLU cc_start: 0.8244 (tp30) cc_final: 0.7473 (tp30) REVERT: D 211 ILE cc_start: 0.8186 (mt) cc_final: 0.7959 (mt) REVERT: F 43 GLU cc_start: 0.8011 (tp30) cc_final: 0.7399 (tp30) REVERT: F 207 ASN cc_start: 0.8213 (m-40) cc_final: 0.7651 (t0) REVERT: F 211 ILE cc_start: 0.8140 (mt) cc_final: 0.7812 (mt) REVERT: F 257 MET cc_start: 0.7874 (mmm) cc_final: 0.7556 (mmm) REVERT: G 21 MET cc_start: 0.5602 (tpt) cc_final: 0.4563 (ttt) REVERT: G 43 GLU cc_start: 0.8237 (tp30) cc_final: 0.7465 (tp30) REVERT: I 43 GLU cc_start: 0.8031 (tp30) cc_final: 0.7432 (tp30) REVERT: I 207 ASN cc_start: 0.8225 (m-40) cc_final: 0.7732 (t0) REVERT: I 257 MET cc_start: 0.7891 (mmm) cc_final: 0.7578 (mmm) REVERT: J 21 MET cc_start: 0.5597 (tpt) cc_final: 0.4565 (ttt) REVERT: J 43 GLU cc_start: 0.8251 (tp30) cc_final: 0.7484 (tp30) REVERT: J 211 ILE cc_start: 0.8192 (mt) cc_final: 0.7972 (mt) REVERT: L 43 GLU cc_start: 0.8029 (tp30) cc_final: 0.7430 (tp30) REVERT: L 207 ASN cc_start: 0.8228 (m-40) cc_final: 0.7674 (t0) REVERT: L 211 ILE cc_start: 0.8148 (mt) cc_final: 0.7845 (mt) REVERT: L 257 MET cc_start: 0.7880 (mmm) cc_final: 0.7561 (mmm) outliers start: 8 outliers final: 8 residues processed: 217 average time/residue: 0.2129 time to fit residues: 74.9452 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain K residue 87 CYS 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 0 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.183348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130028 restraints weight = 44506.935| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.72 r_work: 0.3405 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17076 Z= 0.157 Angle : 0.507 4.452 22908 Z= 0.264 Chirality : 0.041 0.127 2604 Planarity : 0.003 0.024 2736 Dihedral : 7.982 53.365 2772 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.50 % Allowed : 14.94 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.67 (0.19), residues: 1932 helix: 3.35 (0.13), residues: 1344 sheet: 1.16 (0.52), residues: 120 loop : -0.17 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 246 TYR 0.012 0.002 TYR E 67 PHE 0.011 0.001 PHE B 53 TRP 0.003 0.001 TRP H 79 HIS 0.002 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00372 (17040) covalent geometry : angle 0.50548 (22836) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.94484 ( 72) hydrogen bonds : bond 0.06004 ( 1104) hydrogen bonds : angle 3.03602 ( 3276) *********************** 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 218 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8225 (tp30) cc_final: 0.7539 (tp30) REVERT: C 43 GLU cc_start: 0.8047 (tp30) cc_final: 0.7423 (tp30) REVERT: C 207 ASN cc_start: 0.8163 (m-40) cc_final: 0.7574 (t0) REVERT: C 211 ILE cc_start: 0.8075 (mt) cc_final: 0.7810 (mt) REVERT: B 52 MET cc_start: 0.8434 (mmt) cc_final: 0.7980 (mmt) REVERT: B 69 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7916 (tpp80) REVERT: B 272 LEU cc_start: 0.6858 (tt) cc_final: 0.6600 (tp) REVERT: D 43 GLU cc_start: 0.8219 (tp30) cc_final: 0.7532 (tp30) REVERT: E 52 MET cc_start: 0.8426 (mmt) cc_final: 0.7975 (mmt) REVERT: E 69 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7903 (tpp80) REVERT: E 272 LEU cc_start: 0.6827 (tt) cc_final: 0.6596 (tp) REVERT: F 43 GLU cc_start: 0.8020 (tp30) cc_final: 0.7413 (tp30) REVERT: F 207 ASN cc_start: 0.8159 (m-40) cc_final: 0.7589 (t0) REVERT: F 211 ILE cc_start: 0.8041 (mt) cc_final: 0.7765 (mt) REVERT: F 257 MET cc_start: 0.7832 (mmm) cc_final: 0.7513 (mmm) REVERT: G 43 GLU cc_start: 0.8202 (tp30) cc_final: 0.7524 (tp30) REVERT: H 52 MET cc_start: 0.8414 (mmt) cc_final: 0.7960 (mmt) REVERT: H 69 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7904 (tpp80) REVERT: H 272 LEU cc_start: 0.6815 (tt) cc_final: 0.6579 (tp) REVERT: I 43 GLU cc_start: 0.8044 (tp30) cc_final: 0.7435 (tp30) REVERT: I 207 ASN cc_start: 0.8173 (m-40) cc_final: 0.7580 (t0) REVERT: I 211 ILE cc_start: 0.8142 (mt) cc_final: 0.7868 (mt) REVERT: I 257 MET cc_start: 0.7833 (mmm) cc_final: 0.7517 (mmm) REVERT: J 43 GLU cc_start: 0.8226 (tp30) cc_final: 0.7542 (tp30) REVERT: K 52 MET cc_start: 0.8414 (mmt) cc_final: 0.7958 (mmt) REVERT: K 69 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7908 (tpp80) REVERT: K 272 LEU cc_start: 0.6857 (tt) cc_final: 0.6604 (tp) REVERT: L 43 GLU cc_start: 0.8009 (tp30) cc_final: 0.7409 (tp30) REVERT: L 207 ASN cc_start: 0.8184 (m-40) cc_final: 0.7589 (t0) REVERT: L 211 ILE cc_start: 0.8053 (mt) cc_final: 0.7786 (mt) REVERT: L 257 MET cc_start: 0.7843 (mmm) cc_final: 0.7523 (mmm) outliers start: 9 outliers final: 9 residues processed: 213 average time/residue: 0.2121 time to fit residues: 73.2963 Evaluate side-chains 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain K residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.185594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132646 restraints weight = 44401.097| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.73 r_work: 0.3437 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4097 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= 0.099 Angle : 0.449 4.110 22908 Z= 0.233 Chirality : 0.039 0.133 2604 Planarity : 0.003 0.023 2736 Dihedral : 7.120 55.945 2772 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.33 % Allowed : 15.11 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.19), residues: 1932 helix: 3.55 (0.13), residues: 1344 sheet: 1.25 (0.52), residues: 120 loop : -0.11 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.009 0.001 TYR A 67 PHE 0.006 0.001 PHE E 33 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00202 (17040) covalent geometry : angle 0.44820 (22836) SS BOND : bond 0.00049 ( 36) SS BOND : angle 0.69555 ( 72) hydrogen bonds : bond 0.04899 ( 1104) hydrogen bonds : angle 2.92223 ( 3276) *********************** 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 218 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5747 (tpt) cc_final: 0.4787 (ttt) REVERT: A 43 GLU cc_start: 0.8194 (tp30) cc_final: 0.7509 (tp30) REVERT: C 43 GLU cc_start: 0.8025 (tp30) cc_final: 0.7402 (tp30) REVERT: C 207 ASN cc_start: 0.8144 (m-40) cc_final: 0.7538 (t0) REVERT: C 211 ILE cc_start: 0.8000 (mt) cc_final: 0.7734 (mt) REVERT: B 52 MET cc_start: 0.8401 (mmt) cc_final: 0.7932 (mmt) REVERT: B 69 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7948 (tpp80) REVERT: D 43 GLU cc_start: 0.8192 (tp30) cc_final: 0.7518 (tp30) REVERT: E 52 MET cc_start: 0.8418 (mmt) cc_final: 0.7955 (mmt) REVERT: E 69 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7943 (tpp80) REVERT: F 43 GLU cc_start: 0.7997 (tp30) cc_final: 0.7395 (tp30) REVERT: F 207 ASN cc_start: 0.8162 (m-40) cc_final: 0.7547 (t0) REVERT: F 211 ILE cc_start: 0.8019 (mt) cc_final: 0.7753 (mt) REVERT: G 21 MET cc_start: 0.5660 (tpt) cc_final: 0.4692 (ttt) REVERT: G 43 GLU cc_start: 0.8174 (tp30) cc_final: 0.7526 (tp30) REVERT: H 52 MET cc_start: 0.8416 (mmt) cc_final: 0.7956 (mmt) REVERT: H 69 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7947 (tpp80) REVERT: I 43 GLU cc_start: 0.8031 (tp30) cc_final: 0.7412 (tp30) REVERT: I 207 ASN cc_start: 0.8176 (m-40) cc_final: 0.7560 (t0) REVERT: I 211 ILE cc_start: 0.7901 (mt) cc_final: 0.7621 (mt) REVERT: J 21 MET cc_start: 0.5745 (tpt) cc_final: 0.4763 (ttt) REVERT: J 43 GLU cc_start: 0.8204 (tp30) cc_final: 0.7511 (tp30) REVERT: K 52 MET cc_start: 0.8408 (mmt) cc_final: 0.7937 (mmt) REVERT: K 69 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7942 (tpp80) REVERT: L 43 GLU cc_start: 0.7999 (tp30) cc_final: 0.7397 (tp30) REVERT: L 207 ASN cc_start: 0.8151 (m-40) cc_final: 0.7546 (t0) REVERT: L 211 ILE cc_start: 0.8012 (mt) cc_final: 0.7745 (mt) outliers start: 6 outliers final: 6 residues processed: 212 average time/residue: 0.2145 time to fit residues: 73.3491 Evaluate side-chains 212 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain K residue 87 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.184527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131589 restraints weight = 44272.183| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.72 r_work: 0.3426 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- 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 = 0.92 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 = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17076 Z= 0.118 Angle : 0.473 4.469 22908 Z= 0.244 Chirality : 0.039 0.128 2604 Planarity : 0.003 0.024 2736 Dihedral : 6.877 54.359 2772 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.61 % Allowed : 15.00 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.95 (0.19), residues: 1932 helix: 3.58 (0.13), residues: 1344 sheet: 0.48 (0.52), residues: 132 loop : 0.15 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 197 TYR 0.009 0.001 TYR G 67 PHE 0.009 0.001 PHE B 53 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00277 (17040) covalent geometry : angle 0.47167 (22836) SS BOND : bond 0.00094 ( 36) SS BOND : angle 0.83213 ( 72) hydrogen bonds : bond 0.05025 ( 1104) hydrogen bonds : angle 2.96418 ( 3276) *********************** 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 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5630 (tpt) cc_final: 0.4720 (ttt) REVERT: A 43 GLU cc_start: 0.8196 (tp30) cc_final: 0.7533 (tp30) REVERT: C 43 GLU cc_start: 0.8199 (tp30) cc_final: 0.7524 (tp30) REVERT: C 207 ASN cc_start: 0.8149 (m-40) cc_final: 0.7528 (t0) REVERT: C 211 ILE cc_start: 0.8033 (mt) cc_final: 0.7769 (mt) REVERT: C 254 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 52 MET cc_start: 0.8451 (mmt) cc_final: 0.8019 (mmt) REVERT: B 69 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7905 (tpp80) REVERT: B 257 MET cc_start: 0.7815 (mmm) cc_final: 0.7497 (mmm) REVERT: D 21 MET cc_start: 0.5535 (tpt) cc_final: 0.5306 (tpt) REVERT: D 43 GLU cc_start: 0.8187 (tp30) cc_final: 0.7533 (tp30) REVERT: E 52 MET cc_start: 0.8448 (mmt) cc_final: 0.8019 (mmt) REVERT: E 69 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7893 (tpp80) REVERT: E 257 MET cc_start: 0.7815 (mmm) cc_final: 0.7515 (mmm) REVERT: F 43 GLU cc_start: 0.8167 (tp30) cc_final: 0.7499 (tp30) REVERT: F 207 ASN cc_start: 0.8160 (m-40) cc_final: 0.7539 (t0) REVERT: F 211 ILE cc_start: 0.8085 (mt) cc_final: 0.7819 (mt) REVERT: F 254 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7213 (tt) REVERT: G 43 GLU cc_start: 0.8182 (tp30) cc_final: 0.7529 (tp30) REVERT: H 52 MET cc_start: 0.8424 (mmt) cc_final: 0.7988 (mmt) REVERT: H 69 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7893 (tpp80) REVERT: H 257 MET cc_start: 0.7807 (mmm) cc_final: 0.7490 (mmm) REVERT: I 43 GLU cc_start: 0.8200 (tp30) cc_final: 0.7527 (tp30) REVERT: I 207 ASN cc_start: 0.8176 (m-40) cc_final: 0.7556 (t0) REVERT: I 211 ILE cc_start: 0.8179 (mt) cc_final: 0.7895 (mt) REVERT: I 254 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7215 (tt) REVERT: J 43 GLU cc_start: 0.8199 (tp30) cc_final: 0.7533 (tp30) REVERT: K 52 MET cc_start: 0.8435 (mmt) cc_final: 0.7999 (mmt) REVERT: K 69 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7896 (tpp80) REVERT: K 257 MET cc_start: 0.7819 (mmm) cc_final: 0.7517 (mmm) REVERT: L 43 GLU cc_start: 0.8170 (tp30) cc_final: 0.7506 (tp30) REVERT: L 207 ASN cc_start: 0.8160 (m-40) cc_final: 0.7536 (t0) REVERT: L 211 ILE cc_start: 0.8018 (mt) cc_final: 0.7748 (mt) REVERT: L 254 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7171 (tt) outliers start: 11 outliers final: 7 residues processed: 204 average time/residue: 0.2502 time to fit residues: 82.7071 Evaluate side-chains 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 87 CYS Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain J residue 211 ILE 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 60 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.182880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129892 restraints weight = 44630.053| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.72 r_work: 0.3402 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17076 Z= 0.138 Angle : 0.488 4.472 22908 Z= 0.253 Chirality : 0.040 0.126 2604 Planarity : 0.003 0.024 2736 Dihedral : 6.914 43.124 2772 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.67 % Allowed : 15.11 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.91 (0.19), residues: 1932 helix: 3.53 (0.13), residues: 1344 sheet: 1.10 (0.53), residues: 120 loop : -0.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 197 TYR 0.011 0.001 TYR G 67 PHE 0.010 0.001 PHE K 53 TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00333 (17040) covalent geometry : angle 0.48617 (22836) SS BOND : bond 0.00142 ( 36) SS BOND : angle 0.85889 ( 72) hydrogen bonds : bond 0.05298 ( 1104) hydrogen bonds : angle 2.99172 ( 3276) ********************** 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 230 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5562 (tpt) cc_final: 0.5321 (tpt) REVERT: A 43 GLU cc_start: 0.8217 (tp30) cc_final: 0.7536 (tp30) REVERT: C 43 GLU cc_start: 0.8212 (tp30) cc_final: 0.7527 (tp30) REVERT: C 211 ILE cc_start: 0.8131 (mt) cc_final: 0.7927 (mt) REVERT: C 254 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7169 (tt) REVERT: C 269 LEU cc_start: 0.7146 (mt) cc_final: 0.6866 (mt) REVERT: B 52 MET cc_start: 0.8468 (mmt) cc_final: 0.7985 (mmt) REVERT: B 69 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7910 (tpp80) REVERT: B 257 MET cc_start: 0.7809 (mmm) cc_final: 0.7492 (mmm) REVERT: D 21 MET cc_start: 0.5558 (tpt) cc_final: 0.5327 (tpt) REVERT: D 43 GLU cc_start: 0.8204 (tp30) cc_final: 0.7544 (tp30) REVERT: E 52 MET cc_start: 0.8461 (mmt) cc_final: 0.8024 (mmt) REVERT: E 69 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7913 (tpp80) REVERT: E 257 MET cc_start: 0.7831 (mmm) cc_final: 0.7536 (mmm) REVERT: F 43 GLU cc_start: 0.8203 (tp30) cc_final: 0.7531 (tp30) REVERT: F 207 ASN cc_start: 0.8155 (m-40) cc_final: 0.7442 (t0) REVERT: F 211 ILE cc_start: 0.8134 (mt) cc_final: 0.7892 (mt) REVERT: F 254 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7174 (tt) REVERT: F 257 MET cc_start: 0.7790 (mmm) cc_final: 0.7434 (mmm) REVERT: F 269 LEU cc_start: 0.7272 (mt) cc_final: 0.7036 (mt) REVERT: G 21 MET cc_start: 0.5458 (tpt) cc_final: 0.5221 (tpt) REVERT: G 43 GLU cc_start: 0.8262 (tp30) cc_final: 0.7588 (tp30) REVERT: H 52 MET cc_start: 0.8454 (mmt) cc_final: 0.8016 (mmt) REVERT: H 69 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7910 (tpp80) REVERT: H 257 MET cc_start: 0.7817 (mmm) cc_final: 0.7504 (mmm) REVERT: I 43 GLU cc_start: 0.8215 (tp30) cc_final: 0.7540 (tp30) REVERT: I 207 ASN cc_start: 0.8167 (m-40) cc_final: 0.7456 (t0) REVERT: I 211 ILE cc_start: 0.8215 (mt) cc_final: 0.7949 (mt) REVERT: I 254 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7178 (tt) REVERT: I 257 MET cc_start: 0.7797 (mmm) cc_final: 0.7444 (mmm) REVERT: I 269 LEU cc_start: 0.7268 (mt) cc_final: 0.7027 (mt) REVERT: J 21 MET cc_start: 0.5561 (tpt) cc_final: 0.5323 (tpt) REVERT: J 43 GLU cc_start: 0.8222 (tp30) cc_final: 0.7549 (tp30) REVERT: K 52 MET cc_start: 0.8461 (mmt) cc_final: 0.8023 (mmt) REVERT: K 69 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7905 (tpp80) REVERT: K 257 MET cc_start: 0.7822 (mmm) cc_final: 0.7526 (mmm) REVERT: L 43 GLU cc_start: 0.8203 (tp30) cc_final: 0.7526 (tp30) REVERT: L 211 ILE cc_start: 0.8125 (mt) cc_final: 0.7919 (mt) REVERT: L 254 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7181 (tt) REVERT: L 257 MET cc_start: 0.7814 (mmm) cc_final: 0.7459 (mmm) REVERT: L 269 LEU cc_start: 0.7160 (mt) cc_final: 0.6899 (mt) outliers start: 12 outliers final: 8 residues processed: 226 average time/residue: 0.2274 time to fit residues: 82.9414 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain H residue 87 CYS 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 K residue 254 LEU Chi-restraints excluded: chain L residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.184027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131251 restraints weight = 44704.170| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.74 r_work: 0.3422 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17076 Z= 0.107 Angle : 0.457 4.261 22908 Z= 0.237 Chirality : 0.039 0.129 2604 Planarity : 0.003 0.024 2736 Dihedral : 6.474 44.188 2772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.44 % Allowed : 16.06 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.01 (0.19), residues: 1932 helix: 3.61 (0.13), residues: 1344 sheet: 0.41 (0.51), residues: 132 loop : 0.25 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.009 0.001 TYR H 67 PHE 0.006 0.001 PHE B 53 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.000 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00242 (17040) covalent geometry : angle 0.45618 (22836) SS BOND : bond 0.00085 ( 36) SS BOND : angle 0.73152 ( 72) hydrogen bonds : bond 0.04788 ( 1104) hydrogen bonds : angle 2.97328 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.38 seconds wall clock time: 118 minutes 36.51 seconds (7116.51 seconds total)