Starting phenix.real_space_refine on Mon Aug 25 15:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppq_17808/08_2025/8ppq_17808.map" } resolution = 3.9 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= 0.011 sd= 0.172 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 102 5.16 5 C 9271 2.51 5 N 2578 2.21 5 O 2745 1.98 5 H 14659 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s 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: 29355 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7502 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "B" Number of atoms: 7501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7501 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "C" Number of atoms: 7501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 7501 Classifications: {'peptide': 496} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 476} Chain: "a" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2296 Classifications: {'peptide': 147} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 2 Chain: "b" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2251 Classifications: {'peptide': 144} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain breaks: 2 Chain: "c" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2262 Classifications: {'peptide': 144} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.90, per 1000 atoms: 0.20 Number of scatterers: 29355 At special positions: 0 Unit cell: (172, 160.175, 139.75, 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 102 16.00 O 2745 8.00 N 2578 7.00 C 9271 6.00 H 14659 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=1.99 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=1.96 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.00 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 338 " distance=2.02 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.01 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=1.98 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.05 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 290 " distance=2.00 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 338 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.01 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.00 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.04 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.01 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 338 " distance=2.02 Simple disulfide: pdb=" SG CYS a 30 " - pdb=" SG CYS a 65 " distance=1.98 Simple disulfide: pdb=" SG CYS a 49 " - pdb=" SG CYS a 63 " distance=1.99 Simple disulfide: pdb=" SG CYS b 30 " - pdb=" SG CYS b 65 " distance=2.01 Simple disulfide: pdb=" SG CYS b 49 " - pdb=" SG CYS b 63 " distance=2.01 Simple disulfide: pdb=" SG CYS c 30 " - pdb=" SG CYS c 65 " distance=2.02 Simple disulfide: pdb=" SG CYS c 49 " - pdb=" SG CYS c 63 " distance=2.02 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 154 " " NAG B 501 " - " ASN B 154 " " NAG C 501 " - " ASN C 154 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3460 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 34 sheets defined 25.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.556A pdb=" N LEU A 6 " --> pdb=" O CYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.809A pdb=" N HIS A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.660A pdb=" N ASP A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 417 through 421 removed outlier: 4.185A pdb=" N TRP A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 443 removed outlier: 4.536A pdb=" N GLY A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.833A pdb=" N LEU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 490 removed outlier: 4.231A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 4.077A pdb=" N HIS B 5 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 6 " --> pdb=" O CYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 397 through 417 removed outlier: 3.903A pdb=" N GLY B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 removed outlier: 4.055A pdb=" N TRP B 421 " --> pdb=" O GLU B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.693A pdb=" N ASN B 446 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 443 through 447' Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.683A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 490 removed outlier: 4.119A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.723A pdb=" N HIS C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.866A pdb=" N HIS C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 397 through 417 removed outlier: 4.102A pdb=" N GLY C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 421 removed outlier: 4.189A pdb=" N TRP C 421 " --> pdb=" O GLU C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.737A pdb=" N ASN C 446 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 447 " --> pdb=" O ALA C 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 443 through 447' Processing helix chain 'C' and resid 454 through 469 removed outlier: 3.859A pdb=" N LEU C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 490 removed outlier: 4.383A pdb=" N LEU C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 127 Processing helix chain 'a' and resid 127 through 142 Processing helix chain 'a' and resid 144 through 159 Processing helix chain 'a' and resid 160 through 162 No H-bonds generated for 'chain 'a' and resid 160 through 162' Processing helix chain 'b' and resid 113 through 127 Processing helix chain 'b' and resid 127 through 142 Processing helix chain 'b' and resid 144 through 158 Processing helix chain 'c' and resid 113 through 127 Processing helix chain 'c' and resid 127 through 142 Processing helix chain 'c' and resid 144 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.475A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.507A pdb=" N VAL A 21 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 165 removed outlier: 3.560A pdb=" N LYS A 161 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 6.025A pdb=" N ALA A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU A 58 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY A 129 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 54 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 228 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 97 removed outlier: 6.736A pdb=" N SER A 112 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 114 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 120 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 15.404A pdb=" N LYS A 64 " --> pdb=" O TRP a 40 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ASP a 42 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER A 66 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER a 44 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU a 48 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA A 72 " --> pdb=" O GLU a 48 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP a 43 " --> pdb=" O ARG a 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 244 removed outlier: 3.612A pdb=" N GLU A 243 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.550A pdb=" N GLU A 329 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 317 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 327 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.733A pdb=" N GLY A 379 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 394 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 381 " --> pdb=" O TRP A 392 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 392 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 26 removed outlier: 3.814A pdb=" N HIS B 287 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 189 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.588A pdb=" N GLU B 277 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.768A pdb=" N ALA B 54 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.544A pdb=" N LYS B 228 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 63 through 73 removed outlier: 3.750A pdb=" N ALA B 120 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 242 through 244 Processing sheet with id=AB8, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.515A pdb=" N THR B 313 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 319 through 320 removed outlier: 3.625A pdb=" N THR B 319 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AC2, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.907A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.566A pdb=" N VAL C 21 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS C 287 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.922A pdb=" N ARG C 57 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 131 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C 55 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 90 through 97 removed outlier: 5.203A pdb=" N LYS C 118 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASP C 67 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 120 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 65 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 16.069A pdb=" N LYS C 64 " --> pdb=" O TRP c 40 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N ASP c 42 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C 66 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER c 44 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU c 48 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA C 72 " --> pdb=" O GLU c 48 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP c 43 " --> pdb=" O ARG c 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG c 77 " --> pdb=" O ASP c 43 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL c 71 " --> pdb=" O CYS c 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 244 removed outlier: 3.707A pdb=" N GLU C 243 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 255 " --> pdb=" O GLU C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AD1, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AD2, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AD3, first strand: chain 'C' and resid 342 through 346 Processing sheet with id=AD4, first strand: chain 'a' and resid 21 through 24 removed outlier: 3.993A pdb=" N THR a 21 " --> pdb=" O ILE a 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE a 32 " --> pdb=" O THR a 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 2 through 4 removed outlier: 7.459A pdb=" N ASP b 43 " --> pdb=" O ARG b 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 22 through 25 removed outlier: 3.534A pdb=" N PHE b 64 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 21 through 25 removed outlier: 3.735A pdb=" N THR c 21 " --> pdb=" O ILE c 32 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1503 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: 7.26 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 14650 1.12 - 1.30: 2556 1.30 - 1.47: 5675 1.47 - 1.65: 6620 1.65 - 1.82: 147 Bond restraints: 29648 Sorted by residual: bond pdb=" CD2 HIS B 104 " pdb=" HD2 HIS B 104 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS C 64 " pdb=" H LYS C 64 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 PHE C 165 " pdb=" HE1 PHE C 165 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 TYR B 255 " pdb=" HD2 TYR B 255 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG B 401 " pdb="HH11 ARG B 401 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 29643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 47256 3.09 - 6.19: 5653 6.19 - 9.28: 720 9.28 - 12.37: 14 12.37 - 15.46: 10 Bond angle restraints: 53653 Sorted by residual: angle pdb=" CB ASN C 154 " pdb=" CG ASN C 154 " pdb=" ND2 ASN C 154 " ideal model delta sigma weight residual 116.40 100.94 15.46 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " pdb=" ND2 ASN A 154 " ideal model delta sigma weight residual 116.40 101.04 15.36 1.50e+00 4.44e-01 1.05e+02 angle pdb=" N ASN A 154 " pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " ideal model delta sigma weight residual 110.32 97.69 12.63 1.82e+00 3.02e-01 4.81e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 119.50 -6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" C ALA A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta sigma weight residual 120.99 133.64 -12.65 1.86e+00 2.89e-01 4.63e+01 ... (remaining 53648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 12435 17.62 - 35.23: 921 35.23 - 52.85: 325 52.85 - 70.46: 232 70.46 - 88.08: 17 Dihedral angle restraints: 13930 sinusoidal: 7648 harmonic: 6282 Sorted by residual: dihedral pdb=" CB CYS c 49 " pdb=" SG CYS c 49 " pdb=" SG CYS c 63 " pdb=" CB CYS c 63 " ideal model delta sinusoidal sigma weight residual 93.00 166.50 -73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS a 49 " pdb=" SG CYS a 49 " pdb=" SG CYS a 63 " pdb=" CB CYS a 63 " ideal model delta sinusoidal sigma weight residual 93.00 147.87 -54.87 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" N ASN A 154 " pdb=" C ASN A 154 " pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " ideal model delta harmonic sigma weight residual 122.80 109.04 13.76 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 13927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1378 0.079 - 0.159: 706 0.159 - 0.238: 222 0.238 - 0.318: 43 0.318 - 0.397: 8 Chirality restraints: 2357 Sorted by residual: chirality pdb=" CA ARG A 2 " pdb=" N ARG A 2 " pdb=" C ARG A 2 " pdb=" CB ARG A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA THR a 35 " pdb=" N THR a 35 " pdb=" C THR a 35 " pdb=" CB THR a 35 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA TRP A 44 " pdb=" N TRP A 44 " pdb=" C TRP A 44 " pdb=" CB TRP A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2354 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 44 " 0.424 2.00e-02 2.50e+03 1.62e-01 1.04e+03 pdb=" CG TRP C 44 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP C 44 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 TRP C 44 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP C 44 " -0.132 2.00e-02 2.50e+03 pdb=" CE2 TRP C 44 " -0.052 2.00e-02 2.50e+03 pdb=" CE3 TRP C 44 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 44 " 0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 44 " -0.094 2.00e-02 2.50e+03 pdb=" CH2 TRP C 44 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP C 44 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP C 44 " -0.204 2.00e-02 2.50e+03 pdb=" HE3 TRP C 44 " -0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 44 " 0.263 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 44 " -0.118 2.00e-02 2.50e+03 pdb=" HH2 TRP C 44 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 44 " -0.278 2.00e-02 2.50e+03 1.61e-01 1.04e+03 pdb=" CG TRP A 44 " -0.166 2.00e-02 2.50e+03 pdb=" CD1 TRP A 44 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP A 44 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP A 44 " 0.096 2.00e-02 2.50e+03 pdb=" CE2 TRP A 44 " -0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP A 44 " 0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 44 " -0.144 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 44 " 0.113 2.00e-02 2.50e+03 pdb=" CH2 TRP A 44 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP A 44 " 0.119 2.00e-02 2.50e+03 pdb=" HE1 TRP A 44 " 0.327 2.00e-02 2.50e+03 pdb=" HE3 TRP A 44 " 0.099 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 44 " -0.278 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 44 " 0.205 2.00e-02 2.50e+03 pdb=" HH2 TRP A 44 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 154 " -0.307 2.00e-02 2.50e+03 2.24e-01 7.53e+02 pdb=" CG ASN C 154 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN C 154 " 0.136 2.00e-02 2.50e+03 pdb=" ND2 ASN C 154 " 0.022 2.00e-02 2.50e+03 pdb="HD21 ASN C 154 " 0.325 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.270 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1470 2.17 - 2.77: 49462 2.77 - 3.38: 74980 3.38 - 3.99: 94428 3.99 - 4.60: 137998 Nonbonded interactions: 358338 Sorted by model distance: nonbonded pdb=" OD1 ASP c 7 " pdb=" HG SER c 9 " model vdw 1.558 2.450 nonbonded pdb=" O ALA A 47 " pdb=" HG1 THR A 140 " model vdw 1.582 2.450 nonbonded pdb=" HG SER C 321 " pdb=" OG1 THR C 325 " model vdw 1.587 2.450 nonbonded pdb=" O ILE B 358 " pdb=" HG1 THR B 359 " model vdw 1.589 2.450 nonbonded pdb=" HG1 THR A 325 " pdb=" OE2 GLU A 373 " model vdw 1.602 2.450 ... (remaining 358333 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2) \ ) or resid 6 through 501)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'a' and (resid 1 through 95 or resid 112 through 161)) selection = (chain 'b' and (resid 1 through 95 or resid 112 through 161)) selection = (chain 'c' and resid 1 through 161) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.210 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.013 0.078 15016 Z= 0.803 Angle : 1.926 15.463 20392 Z= 1.280 Chirality : 0.102 0.397 2357 Planarity : 0.019 0.196 2574 Dihedral : 13.259 88.077 5415 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.19), residues: 1899 helix: 2.07 (0.26), residues: 412 sheet: -0.41 (0.22), residues: 537 loop : -1.43 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG c 77 TYR 0.191 0.035 TYR b 47 PHE 0.067 0.017 PHE C 220 TRP 0.247 0.031 TRP C 44 HIS 0.043 0.005 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.01259 (14989) covalent geometry : angle 1.91886 (20335) SS BOND : bond 0.02883 ( 24) SS BOND : angle 2.59422 ( 48) hydrogen bonds : bond 0.20329 ( 558) hydrogen bonds : angle 7.27531 ( 1503) link_NAG-ASN : bond 0.01678 ( 3) link_NAG-ASN : angle 7.33469 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8552 (t) cc_final: 0.7876 (p) REVERT: A 34 THR cc_start: 0.8444 (p) cc_final: 0.8193 (m) REVERT: A 48 ILE cc_start: 0.8514 (mt) cc_final: 0.8242 (mt) REVERT: A 58 GLU cc_start: 0.6767 (tt0) cc_final: 0.6394 (tt0) REVERT: A 82 LEU cc_start: 0.8308 (mt) cc_final: 0.8091 (mt) REVERT: A 96 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 116 CYS cc_start: 0.5317 (m) cc_final: 0.4902 (m) REVERT: A 187 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7421 (ttm110) REVERT: A 227 TRP cc_start: 0.8129 (p-90) cc_final: 0.7914 (p-90) REVERT: A 285 SER cc_start: 0.6911 (t) cc_final: 0.6648 (p) REVERT: A 294 LEU cc_start: 0.8303 (tp) cc_final: 0.7997 (tp) REVERT: A 306 MET cc_start: 0.5747 (ttt) cc_final: 0.5392 (ttt) REVERT: A 471 MET cc_start: 0.2646 (mpp) cc_final: 0.2362 (mpp) REVERT: B 23 LEU cc_start: 0.7521 (mt) cc_final: 0.7309 (mt) REVERT: B 24 VAL cc_start: 0.8286 (m) cc_final: 0.7956 (p) REVERT: B 117 VAL cc_start: 0.8441 (t) cc_final: 0.8198 (m) REVERT: B 209 LEU cc_start: 0.7636 (mt) cc_final: 0.7410 (mt) REVERT: B 356 MET cc_start: 0.5792 (ttm) cc_final: 0.4941 (tpt) REVERT: C 33 ILE cc_start: 0.8055 (mt) cc_final: 0.7811 (mt) REVERT: C 65 LEU cc_start: 0.7899 (mt) cc_final: 0.7598 (mt) REVERT: C 174 LEU cc_start: 0.7189 (mp) cc_final: 0.6938 (mp) REVERT: C 211 THR cc_start: 0.6975 (p) cc_final: 0.5244 (m) REVERT: C 380 ASP cc_start: 0.7891 (m-30) cc_final: 0.7461 (p0) REVERT: a 13 ARG cc_start: 0.7174 (ptm160) cc_final: 0.6833 (ttm170) REVERT: a 23 VAL cc_start: 0.7855 (t) cc_final: 0.7653 (p) REVERT: b 13 ARG cc_start: 0.6575 (ptm160) cc_final: 0.5068 (ptp-170) REVERT: c 24 ARG cc_start: 0.5498 (mmt180) cc_final: 0.5196 (ptt-90) REVERT: c 59 VAL cc_start: 0.8887 (t) cc_final: 0.8646 (p) REVERT: c 61 VAL cc_start: 0.8526 (m) cc_final: 0.8267 (p) REVERT: c 119 ARG cc_start: 0.7346 (ttt180) cc_final: 0.6919 (ttm110) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.2584 time to fit residues: 164.4820 Evaluate side-chains 363 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145340 restraints weight = 65713.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152241 restraints weight = 26902.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156588 restraints weight = 14316.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159206 restraints weight = 9290.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160993 restraints weight = 6999.434| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15016 Z= 0.166 Angle : 0.697 13.558 20392 Z= 0.376 Chirality : 0.046 0.263 2357 Planarity : 0.006 0.082 2574 Dihedral : 5.913 66.000 2105 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.52 % Allowed : 8.22 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.19), residues: 1899 helix: 1.90 (0.26), residues: 415 sheet: -0.47 (0.21), residues: 594 loop : -1.71 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 99 TYR 0.017 0.002 TYR b 47 PHE 0.028 0.002 PHE c 64 TRP 0.022 0.002 TRP B 44 HIS 0.017 0.003 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00374 (14989) covalent geometry : angle 0.67825 (20335) SS BOND : bond 0.00469 ( 24) SS BOND : angle 1.48376 ( 48) hydrogen bonds : bond 0.05878 ( 558) hydrogen bonds : angle 6.22622 ( 1503) link_NAG-ASN : bond 0.01038 ( 3) link_NAG-ASN : angle 6.94027 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 360 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8493 (t) cc_final: 0.7939 (p) REVERT: A 34 THR cc_start: 0.8336 (p) cc_final: 0.8076 (m) REVERT: A 82 LEU cc_start: 0.8290 (mt) cc_final: 0.7996 (mt) REVERT: A 98 ASP cc_start: 0.7932 (t0) cc_final: 0.7579 (p0) REVERT: A 116 CYS cc_start: 0.4918 (m) cc_final: 0.4633 (m) REVERT: A 161 LYS cc_start: 0.8458 (mptt) cc_final: 0.8179 (mptt) REVERT: A 187 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.6997 (ttm110) REVERT: A 230 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 285 SER cc_start: 0.6857 (t) cc_final: 0.6499 (p) REVERT: A 294 LEU cc_start: 0.8270 (tp) cc_final: 0.7935 (tp) REVERT: A 471 MET cc_start: 0.2985 (mpp) cc_final: 0.2569 (mpp) REVERT: A 478 MET cc_start: 0.3828 (mmp) cc_final: 0.3091 (mmp) REVERT: B 285 SER cc_start: 0.7665 (t) cc_final: 0.7370 (m) REVERT: C 24 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7250 (p) REVERT: C 66 SER cc_start: 0.8275 (p) cc_final: 0.8048 (t) REVERT: C 211 THR cc_start: 0.6734 (p) cc_final: 0.4994 (m) REVERT: C 234 ASN cc_start: 0.7899 (m-40) cc_final: 0.7656 (m-40) REVERT: C 324 ASP cc_start: 0.7690 (t0) cc_final: 0.7333 (t0) REVERT: C 380 ASP cc_start: 0.7659 (m-30) cc_final: 0.7261 (p0) REVERT: C 392 TRP cc_start: 0.7825 (t-100) cc_final: 0.7614 (t-100) REVERT: b 13 ARG cc_start: 0.6259 (ptm160) cc_final: 0.4962 (ptp-170) REVERT: c 43 ASP cc_start: 0.7967 (t0) cc_final: 0.7657 (t0) REVERT: c 59 VAL cc_start: 0.8879 (t) cc_final: 0.8673 (p) REVERT: c 74 GLU cc_start: 0.5286 (pt0) cc_final: 0.5007 (pt0) REVERT: c 119 ARG cc_start: 0.7280 (ttt180) cc_final: 0.6942 (ttm110) outliers start: 24 outliers final: 18 residues processed: 368 average time/residue: 0.2447 time to fit residues: 136.4917 Evaluate side-chains 353 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 334 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 52 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 57 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.187228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145851 restraints weight = 67999.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152595 restraints weight = 28628.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156882 restraints weight = 15578.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159799 restraints weight = 10266.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161380 restraints weight = 7660.301| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15016 Z= 0.188 Angle : 0.624 6.731 20392 Z= 0.338 Chirality : 0.044 0.164 2357 Planarity : 0.004 0.074 2574 Dihedral : 5.808 58.618 2105 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.96 % Allowed : 11.26 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.19), residues: 1899 helix: 1.97 (0.26), residues: 416 sheet: -0.50 (0.21), residues: 579 loop : -1.89 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.027 0.002 TYR b 47 PHE 0.020 0.002 PHE c 64 TRP 0.021 0.002 TRP B 44 HIS 0.011 0.002 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00406 (14989) covalent geometry : angle 0.61283 (20335) SS BOND : bond 0.00565 ( 24) SS BOND : angle 1.51061 ( 48) hydrogen bonds : bond 0.04983 ( 558) hydrogen bonds : angle 5.85520 ( 1503) link_NAG-ASN : bond 0.01037 ( 3) link_NAG-ASN : angle 4.50985 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 341 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8575 (t) cc_final: 0.8074 (p) REVERT: A 82 LEU cc_start: 0.8246 (mt) cc_final: 0.7994 (mt) REVERT: A 95 ASP cc_start: 0.8173 (t70) cc_final: 0.7827 (t0) REVERT: A 116 CYS cc_start: 0.4882 (m) cc_final: 0.4524 (m) REVERT: A 161 LYS cc_start: 0.8454 (mptt) cc_final: 0.8218 (mptt) REVERT: A 187 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7175 (ttm110) REVERT: A 230 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 285 SER cc_start: 0.6936 (t) cc_final: 0.6521 (p) REVERT: A 294 LEU cc_start: 0.8349 (tp) cc_final: 0.8025 (tp) REVERT: A 471 MET cc_start: 0.3012 (mpp) cc_final: 0.2531 (mpp) REVERT: B 20 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7399 (mtp180) REVERT: B 285 SER cc_start: 0.7615 (t) cc_final: 0.7314 (m) REVERT: B 374 MET cc_start: 0.6222 (mmm) cc_final: 0.6018 (mmm) REVERT: C 24 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7399 (p) REVERT: C 211 THR cc_start: 0.6640 (p) cc_final: 0.4939 (m) REVERT: C 234 ASN cc_start: 0.7769 (m-40) cc_final: 0.7500 (m-40) REVERT: C 324 ASP cc_start: 0.7739 (t0) cc_final: 0.7361 (t0) REVERT: C 380 ASP cc_start: 0.7713 (m-30) cc_final: 0.7390 (p0) REVERT: C 392 TRP cc_start: 0.7891 (t-100) cc_final: 0.7516 (t-100) REVERT: b 13 ARG cc_start: 0.6638 (ptm160) cc_final: 0.4768 (ptt180) REVERT: c 43 ASP cc_start: 0.7906 (t0) cc_final: 0.7664 (t0) REVERT: c 74 GLU cc_start: 0.5340 (pt0) cc_final: 0.5122 (pt0) REVERT: c 119 ARG cc_start: 0.7271 (ttt180) cc_final: 0.6921 (ttm110) REVERT: c 121 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6619 (mp0) outliers start: 31 outliers final: 28 residues processed: 356 average time/residue: 0.2533 time to fit residues: 137.6291 Evaluate side-chains 363 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 2 VAL Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.187426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146197 restraints weight = 67737.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152962 restraints weight = 28441.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157260 restraints weight = 15403.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160093 restraints weight = 10121.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.161541 restraints weight = 7642.037| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15016 Z= 0.149 Angle : 0.587 7.387 20392 Z= 0.316 Chirality : 0.044 0.216 2357 Planarity : 0.004 0.060 2574 Dihedral : 5.579 53.023 2105 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.96 % Allowed : 12.59 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.19), residues: 1899 helix: 2.10 (0.26), residues: 416 sheet: -0.51 (0.21), residues: 581 loop : -1.84 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.020 0.002 TYR b 47 PHE 0.019 0.001 PHE c 64 TRP 0.018 0.001 TRP B 44 HIS 0.011 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00329 (14989) covalent geometry : angle 0.57519 (20335) SS BOND : bond 0.00443 ( 24) SS BOND : angle 1.68742 ( 48) hydrogen bonds : bond 0.04401 ( 558) hydrogen bonds : angle 5.63133 ( 1503) link_NAG-ASN : bond 0.00936 ( 3) link_NAG-ASN : angle 4.39287 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 333 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8358 (t) cc_final: 0.7809 (p) REVERT: A 82 LEU cc_start: 0.8246 (mt) cc_final: 0.8027 (mt) REVERT: A 98 ASP cc_start: 0.8022 (t0) cc_final: 0.7534 (p0) REVERT: A 116 CYS cc_start: 0.4796 (m) cc_final: 0.4416 (m) REVERT: A 146 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6492 (t-90) REVERT: A 161 LYS cc_start: 0.8519 (mptt) cc_final: 0.8303 (mptt) REVERT: A 164 SER cc_start: 0.8601 (p) cc_final: 0.8361 (p) REVERT: A 187 ARG cc_start: 0.7543 (ttt-90) cc_final: 0.7160 (ttm110) REVERT: A 230 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 285 SER cc_start: 0.6905 (t) cc_final: 0.6495 (p) REVERT: A 294 LEU cc_start: 0.8325 (tp) cc_final: 0.8014 (tp) REVERT: A 471 MET cc_start: 0.3021 (mpp) cc_final: 0.2786 (mpp) REVERT: B 20 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7391 (mtp180) REVERT: B 84 GLU cc_start: 0.7148 (mp0) cc_final: 0.6812 (mp0) REVERT: B 285 SER cc_start: 0.7636 (t) cc_final: 0.7323 (m) REVERT: C 24 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7394 (p) REVERT: C 92 CYS cc_start: 0.5431 (m) cc_final: 0.5053 (m) REVERT: C 211 THR cc_start: 0.6587 (p) cc_final: 0.4890 (m) REVERT: C 234 ASN cc_start: 0.7729 (m-40) cc_final: 0.7443 (m-40) REVERT: C 324 ASP cc_start: 0.7762 (t0) cc_final: 0.7409 (t0) REVERT: C 333 SER cc_start: 0.7767 (m) cc_final: 0.7214 (p) REVERT: C 356 MET cc_start: 0.2239 (ttp) cc_final: 0.1940 (ttm) REVERT: C 380 ASP cc_start: 0.7644 (m-30) cc_final: 0.7374 (p0) REVERT: C 392 TRP cc_start: 0.7923 (t-100) cc_final: 0.7478 (t-100) REVERT: b 13 ARG cc_start: 0.6584 (ptm160) cc_final: 0.4641 (ptt180) REVERT: c 43 ASP cc_start: 0.7910 (t0) cc_final: 0.7688 (t0) REVERT: c 74 GLU cc_start: 0.5415 (pt0) cc_final: 0.5177 (pt0) REVERT: c 119 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6911 (ttm110) REVERT: c 121 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6741 (mp0) outliers start: 31 outliers final: 25 residues processed: 347 average time/residue: 0.2378 time to fit residues: 124.2912 Evaluate side-chains 352 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain b residue 33 LEU Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 1 THR Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145867 restraints weight = 62943.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152654 restraints weight = 25532.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156880 restraints weight = 13454.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159575 restraints weight = 8553.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161051 restraints weight = 6338.715| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15016 Z= 0.123 Angle : 0.562 8.186 20392 Z= 0.301 Chirality : 0.043 0.225 2357 Planarity : 0.003 0.055 2574 Dihedral : 5.309 47.820 2105 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.64 % Allowed : 13.54 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.19), residues: 1899 helix: 2.25 (0.27), residues: 416 sheet: -0.47 (0.21), residues: 581 loop : -1.71 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.017 0.002 TYR b 47 PHE 0.029 0.001 PHE B 371 TRP 0.017 0.001 TRP A 227 HIS 0.009 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00279 (14989) covalent geometry : angle 0.54856 (20335) SS BOND : bond 0.00403 ( 24) SS BOND : angle 1.76307 ( 48) hydrogen bonds : bond 0.03991 ( 558) hydrogen bonds : angle 5.44620 ( 1503) link_NAG-ASN : bond 0.00899 ( 3) link_NAG-ASN : angle 4.44854 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 332 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8283 (t) cc_final: 0.7745 (p) REVERT: A 59 TYR cc_start: 0.6918 (m-80) cc_final: 0.6651 (m-80) REVERT: A 82 LEU cc_start: 0.8287 (mt) cc_final: 0.8062 (mt) REVERT: A 98 ASP cc_start: 0.8041 (t0) cc_final: 0.7503 (p0) REVERT: A 116 CYS cc_start: 0.4747 (m) cc_final: 0.4381 (m) REVERT: A 161 LYS cc_start: 0.8440 (mptt) cc_final: 0.8197 (mptt) REVERT: A 164 SER cc_start: 0.8588 (p) cc_final: 0.8355 (p) REVERT: A 187 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.7121 (ttm110) REVERT: A 230 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 294 LEU cc_start: 0.8331 (tp) cc_final: 0.7990 (tp) REVERT: A 471 MET cc_start: 0.3076 (mpp) cc_final: 0.2828 (mpp) REVERT: A 478 MET cc_start: 0.3554 (mmp) cc_final: 0.3212 (mmp) REVERT: B 20 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7324 (mtp180) REVERT: B 84 GLU cc_start: 0.7229 (mp0) cc_final: 0.6882 (mp0) REVERT: B 285 SER cc_start: 0.7624 (t) cc_final: 0.7324 (m) REVERT: C 24 VAL cc_start: 0.7556 (OUTLIER) cc_final: 0.7296 (p) REVERT: C 92 CYS cc_start: 0.5390 (m) cc_final: 0.5071 (m) REVERT: C 211 THR cc_start: 0.6536 (p) cc_final: 0.4822 (m) REVERT: C 234 ASN cc_start: 0.7741 (m-40) cc_final: 0.7438 (m-40) REVERT: C 324 ASP cc_start: 0.7879 (t0) cc_final: 0.7526 (t0) REVERT: C 333 SER cc_start: 0.7753 (m) cc_final: 0.7253 (p) REVERT: C 356 MET cc_start: 0.1961 (ttp) cc_final: 0.1686 (ttm) REVERT: C 380 ASP cc_start: 0.7718 (m-30) cc_final: 0.7426 (p0) REVERT: C 392 TRP cc_start: 0.7934 (t-100) cc_final: 0.7460 (t-100) REVERT: b 13 ARG cc_start: 0.6568 (ptm160) cc_final: 0.4670 (ptt180) REVERT: c 43 ASP cc_start: 0.7956 (t0) cc_final: 0.7742 (t0) REVERT: c 57 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7031 (mm-30) REVERT: c 119 ARG cc_start: 0.7203 (ttt180) cc_final: 0.6896 (ttm110) outliers start: 26 outliers final: 22 residues processed: 345 average time/residue: 0.2419 time to fit residues: 128.4765 Evaluate side-chains 352 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 329 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.182840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143765 restraints weight = 62519.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150429 restraints weight = 25424.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154504 restraints weight = 13432.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157221 restraints weight = 8651.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158847 restraints weight = 6404.341| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15016 Z= 0.213 Angle : 0.619 9.720 20392 Z= 0.334 Chirality : 0.044 0.230 2357 Planarity : 0.004 0.050 2574 Dihedral : 5.478 49.403 2105 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.21 % Allowed : 15.18 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.19), residues: 1899 helix: 2.14 (0.27), residues: 416 sheet: -0.66 (0.21), residues: 581 loop : -1.94 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 2 TYR 0.029 0.003 TYR b 47 PHE 0.026 0.002 PHE B 371 TRP 0.025 0.002 TRP A 227 HIS 0.012 0.002 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00472 (14989) covalent geometry : angle 0.60833 (20335) SS BOND : bond 0.00636 ( 24) SS BOND : angle 1.75131 ( 48) hydrogen bonds : bond 0.04394 ( 558) hydrogen bonds : angle 5.47685 ( 1503) link_NAG-ASN : bond 0.01078 ( 3) link_NAG-ASN : angle 4.10065 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8520 (t) cc_final: 0.8042 (p) REVERT: A 82 LEU cc_start: 0.8349 (mt) cc_final: 0.8133 (mt) REVERT: A 98 ASP cc_start: 0.8015 (t0) cc_final: 0.7585 (p0) REVERT: A 116 CYS cc_start: 0.4745 (m) cc_final: 0.4383 (m) REVERT: A 161 LYS cc_start: 0.8472 (mptt) cc_final: 0.8226 (mptt) REVERT: A 164 SER cc_start: 0.8627 (p) cc_final: 0.8384 (p) REVERT: A 187 ARG cc_start: 0.7510 (ttt-90) cc_final: 0.7099 (ttm110) REVERT: A 230 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 285 SER cc_start: 0.7042 (t) cc_final: 0.6595 (p) REVERT: A 294 LEU cc_start: 0.8369 (tp) cc_final: 0.8001 (tp) REVERT: A 471 MET cc_start: 0.3106 (mpp) cc_final: 0.2835 (mpp) REVERT: A 478 MET cc_start: 0.3534 (mmp) cc_final: 0.3207 (mmp) REVERT: B 20 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7248 (mtp180) REVERT: B 26 GLU cc_start: 0.6858 (tp30) cc_final: 0.6631 (tp30) REVERT: B 84 GLU cc_start: 0.7274 (mp0) cc_final: 0.6839 (mp0) REVERT: B 203 ASP cc_start: 0.7770 (t0) cc_final: 0.7517 (t0) REVERT: B 285 SER cc_start: 0.7769 (t) cc_final: 0.7447 (m) REVERT: B 374 MET cc_start: 0.5615 (mmm) cc_final: 0.5374 (mmm) REVERT: C 24 VAL cc_start: 0.7564 (OUTLIER) cc_final: 0.7286 (p) REVERT: C 92 CYS cc_start: 0.5336 (m) cc_final: 0.5032 (m) REVERT: C 211 THR cc_start: 0.6597 (p) cc_final: 0.4967 (m) REVERT: C 234 ASN cc_start: 0.7760 (m-40) cc_final: 0.7416 (m-40) REVERT: C 324 ASP cc_start: 0.7860 (t0) cc_final: 0.7483 (t0) REVERT: C 333 SER cc_start: 0.7815 (m) cc_final: 0.7359 (p) REVERT: C 356 MET cc_start: 0.1911 (ttp) cc_final: 0.1626 (ttm) REVERT: C 380 ASP cc_start: 0.7761 (m-30) cc_final: 0.7451 (p0) REVERT: b 13 ARG cc_start: 0.6893 (ptm160) cc_final: 0.5699 (ptp-170) REVERT: c 43 ASP cc_start: 0.7981 (t0) cc_final: 0.7771 (t0) REVERT: c 57 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7123 (mm-30) REVERT: c 119 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6903 (ttm110) outliers start: 35 outliers final: 31 residues processed: 346 average time/residue: 0.2336 time to fit residues: 124.0211 Evaluate side-chains 364 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 43 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 179 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN C 248 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.184725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145458 restraints weight = 62767.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152266 restraints weight = 25491.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156504 restraints weight = 13432.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159262 restraints weight = 8522.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160894 restraints weight = 6296.467| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15016 Z= 0.124 Angle : 0.562 10.027 20392 Z= 0.299 Chirality : 0.043 0.208 2357 Planarity : 0.003 0.041 2574 Dihedral : 5.178 47.093 2105 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.83 % Allowed : 16.07 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.19), residues: 1899 helix: 2.31 (0.27), residues: 416 sheet: -0.60 (0.21), residues: 557 loop : -1.74 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 88 TYR 0.017 0.002 TYR b 47 PHE 0.017 0.001 PHE c 64 TRP 0.019 0.001 TRP A 227 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00282 (14989) covalent geometry : angle 0.54966 (20335) SS BOND : bond 0.00424 ( 24) SS BOND : angle 1.60715 ( 48) hydrogen bonds : bond 0.03811 ( 558) hydrogen bonds : angle 5.31667 ( 1503) link_NAG-ASN : bond 0.00920 ( 3) link_NAG-ASN : angle 4.31972 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8425 (t) cc_final: 0.7833 (p) REVERT: A 82 LEU cc_start: 0.8305 (mt) cc_final: 0.8090 (mt) REVERT: A 95 ASP cc_start: 0.8213 (t70) cc_final: 0.7846 (t0) REVERT: A 116 CYS cc_start: 0.4786 (m) cc_final: 0.4445 (m) REVERT: A 161 LYS cc_start: 0.8452 (mptt) cc_final: 0.8217 (mptt) REVERT: A 164 SER cc_start: 0.8551 (p) cc_final: 0.8307 (p) REVERT: A 187 ARG cc_start: 0.7481 (ttt-90) cc_final: 0.7122 (ttm110) REVERT: A 230 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 294 LEU cc_start: 0.8326 (tp) cc_final: 0.7982 (tp) REVERT: A 471 MET cc_start: 0.3130 (mpp) cc_final: 0.2827 (mpp) REVERT: B 20 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7194 (mtp180) REVERT: B 26 GLU cc_start: 0.6795 (tp30) cc_final: 0.6571 (tp30) REVERT: B 203 ASP cc_start: 0.7772 (t0) cc_final: 0.7572 (t0) REVERT: B 285 SER cc_start: 0.7717 (t) cc_final: 0.7406 (m) REVERT: B 374 MET cc_start: 0.5605 (mmm) cc_final: 0.5382 (mmm) REVERT: C 24 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7315 (p) REVERT: C 92 CYS cc_start: 0.5293 (m) cc_final: 0.4978 (m) REVERT: C 211 THR cc_start: 0.6558 (p) cc_final: 0.4909 (m) REVERT: C 234 ASN cc_start: 0.7742 (m-40) cc_final: 0.7422 (m-40) REVERT: C 324 ASP cc_start: 0.7831 (t70) cc_final: 0.7485 (t0) REVERT: C 333 SER cc_start: 0.7755 (m) cc_final: 0.7288 (p) REVERT: C 356 MET cc_start: 0.1914 (ttp) cc_final: 0.1624 (ttm) REVERT: C 380 ASP cc_start: 0.7728 (m-30) cc_final: 0.7476 (p0) REVERT: b 13 ARG cc_start: 0.6678 (ptm160) cc_final: 0.5614 (ptp-170) REVERT: c 43 ASP cc_start: 0.7968 (t0) cc_final: 0.7752 (t0) REVERT: c 57 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7158 (mm-30) REVERT: c 119 ARG cc_start: 0.7212 (ttt180) cc_final: 0.6885 (ttm110) outliers start: 29 outliers final: 24 residues processed: 346 average time/residue: 0.2191 time to fit residues: 116.6756 Evaluate side-chains 353 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 175 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143516 restraints weight = 62658.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150238 restraints weight = 25574.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154466 restraints weight = 13511.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157141 restraints weight = 8589.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158923 restraints weight = 6356.025| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15016 Z= 0.166 Angle : 0.583 8.737 20392 Z= 0.310 Chirality : 0.043 0.210 2357 Planarity : 0.004 0.042 2574 Dihedral : 5.189 48.031 2105 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.90 % Allowed : 16.26 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.19), residues: 1899 helix: 2.29 (0.27), residues: 416 sheet: -0.64 (0.21), residues: 557 loop : -1.81 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 88 TYR 0.023 0.002 TYR b 47 PHE 0.017 0.001 PHE c 64 TRP 0.020 0.001 TRP A 227 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00374 (14989) covalent geometry : angle 0.57089 (20335) SS BOND : bond 0.00473 ( 24) SS BOND : angle 1.65188 ( 48) hydrogen bonds : bond 0.03950 ( 558) hydrogen bonds : angle 5.28724 ( 1503) link_NAG-ASN : bond 0.00978 ( 3) link_NAG-ASN : angle 4.24166 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 SER cc_start: 0.8402 (t) cc_final: 0.7907 (p) REVERT: A 82 LEU cc_start: 0.8368 (mt) cc_final: 0.8166 (mt) REVERT: A 95 ASP cc_start: 0.8199 (t70) cc_final: 0.7814 (t0) REVERT: A 116 CYS cc_start: 0.4775 (m) cc_final: 0.4409 (m) REVERT: A 161 LYS cc_start: 0.8453 (mptt) cc_final: 0.8191 (mptt) REVERT: A 164 SER cc_start: 0.8572 (p) cc_final: 0.8323 (p) REVERT: A 187 ARG cc_start: 0.7478 (ttt-90) cc_final: 0.7110 (ttm110) REVERT: A 230 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 242 VAL cc_start: 0.8553 (t) cc_final: 0.8210 (m) REVERT: A 294 LEU cc_start: 0.8372 (tp) cc_final: 0.8013 (tp) REVERT: A 471 MET cc_start: 0.3121 (mpp) cc_final: 0.2815 (mpp) REVERT: B 20 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7179 (mtp180) REVERT: B 84 GLU cc_start: 0.7339 (mp0) cc_final: 0.6862 (mp0) REVERT: B 203 ASP cc_start: 0.7801 (t0) cc_final: 0.7543 (t0) REVERT: B 268 LEU cc_start: 0.8570 (tp) cc_final: 0.8165 (tp) REVERT: B 285 SER cc_start: 0.7740 (t) cc_final: 0.7411 (m) REVERT: C 24 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7277 (p) REVERT: C 92 CYS cc_start: 0.5287 (m) cc_final: 0.4985 (m) REVERT: C 211 THR cc_start: 0.6574 (p) cc_final: 0.4963 (m) REVERT: C 234 ASN cc_start: 0.7768 (m-40) cc_final: 0.7389 (m-40) REVERT: C 324 ASP cc_start: 0.7868 (t70) cc_final: 0.7485 (t0) REVERT: C 333 SER cc_start: 0.7839 (m) cc_final: 0.7382 (p) REVERT: C 356 MET cc_start: 0.1740 (ttp) cc_final: 0.1444 (ttm) REVERT: C 380 ASP cc_start: 0.7768 (m-30) cc_final: 0.7495 (p0) REVERT: b 13 ARG cc_start: 0.6824 (ptm160) cc_final: 0.5790 (ptp-170) REVERT: c 43 ASP cc_start: 0.7986 (t0) cc_final: 0.7781 (t0) REVERT: c 57 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7203 (mm-30) REVERT: c 119 ARG cc_start: 0.7224 (ttt180) cc_final: 0.6894 (ttm110) outliers start: 30 outliers final: 26 residues processed: 342 average time/residue: 0.2106 time to fit residues: 110.6749 Evaluate side-chains 355 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.184095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144818 restraints weight = 62435.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151572 restraints weight = 25444.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155791 restraints weight = 13450.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158545 restraints weight = 8573.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159999 restraints weight = 6350.569| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15016 Z= 0.141 Angle : 0.567 8.473 20392 Z= 0.301 Chirality : 0.043 0.206 2357 Planarity : 0.003 0.038 2574 Dihedral : 5.077 47.943 2105 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.90 % Allowed : 16.70 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.19), residues: 1899 helix: 2.36 (0.27), residues: 416 sheet: -0.57 (0.21), residues: 557 loop : -1.76 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.020 0.002 TYR b 47 PHE 0.017 0.001 PHE c 64 TRP 0.019 0.001 TRP A 227 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00320 (14989) covalent geometry : angle 0.55554 (20335) SS BOND : bond 0.00410 ( 24) SS BOND : angle 1.60236 ( 48) hydrogen bonds : bond 0.03742 ( 558) hydrogen bonds : angle 5.20959 ( 1503) link_NAG-ASN : bond 0.00930 ( 3) link_NAG-ASN : angle 4.28058 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 327 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8339 (mt) cc_final: 0.8130 (mt) REVERT: A 95 ASP cc_start: 0.8223 (t70) cc_final: 0.7839 (t0) REVERT: A 116 CYS cc_start: 0.4798 (m) cc_final: 0.4447 (m) REVERT: A 161 LYS cc_start: 0.8487 (mptt) cc_final: 0.8219 (mptt) REVERT: A 164 SER cc_start: 0.8521 (p) cc_final: 0.8272 (p) REVERT: A 187 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7162 (ttm110) REVERT: A 230 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 294 LEU cc_start: 0.8336 (tp) cc_final: 0.7981 (tp) REVERT: A 471 MET cc_start: 0.3034 (mpp) cc_final: 0.2747 (mpp) REVERT: B 20 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7171 (mtp180) REVERT: B 203 ASP cc_start: 0.7790 (t0) cc_final: 0.7548 (t0) REVERT: B 285 SER cc_start: 0.7737 (t) cc_final: 0.7410 (m) REVERT: C 24 VAL cc_start: 0.7582 (OUTLIER) cc_final: 0.7331 (p) REVERT: C 211 THR cc_start: 0.6508 (p) cc_final: 0.4811 (m) REVERT: C 234 ASN cc_start: 0.7721 (m-40) cc_final: 0.7383 (m-40) REVERT: C 324 ASP cc_start: 0.7884 (t70) cc_final: 0.7533 (t0) REVERT: C 333 SER cc_start: 0.7800 (m) cc_final: 0.7387 (p) REVERT: C 356 MET cc_start: 0.1926 (ttp) cc_final: 0.1620 (ttm) REVERT: C 380 ASP cc_start: 0.7795 (m-30) cc_final: 0.7512 (p0) REVERT: b 13 ARG cc_start: 0.6748 (ptm160) cc_final: 0.5728 (ptp-170) REVERT: c 43 ASP cc_start: 0.7958 (t0) cc_final: 0.7747 (t0) REVERT: c 57 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7224 (mm-30) REVERT: c 119 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6885 (ttm110) outliers start: 30 outliers final: 27 residues processed: 339 average time/residue: 0.2189 time to fit residues: 112.4793 Evaluate side-chains 350 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 322 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 0.2980 chunk 91 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145421 restraints weight = 62397.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152206 restraints weight = 25439.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156449 restraints weight = 13434.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.159113 restraints weight = 8541.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160960 restraints weight = 6333.119| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15016 Z= 0.123 Angle : 0.562 8.406 20392 Z= 0.296 Chirality : 0.043 0.203 2357 Planarity : 0.003 0.042 2574 Dihedral : 4.948 47.077 2105 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.58 % Allowed : 17.27 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.19), residues: 1899 helix: 2.43 (0.27), residues: 416 sheet: -0.50 (0.21), residues: 590 loop : -1.72 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.018 0.002 TYR b 47 PHE 0.017 0.001 PHE c 64 TRP 0.018 0.001 TRP A 227 HIS 0.006 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00284 (14989) covalent geometry : angle 0.54861 (20335) SS BOND : bond 0.00382 ( 24) SS BOND : angle 1.71565 ( 48) hydrogen bonds : bond 0.03610 ( 558) hydrogen bonds : angle 5.15594 ( 1503) link_NAG-ASN : bond 0.00901 ( 3) link_NAG-ASN : angle 4.33211 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8374 (mt) cc_final: 0.8145 (mt) REVERT: A 95 ASP cc_start: 0.8202 (t70) cc_final: 0.7839 (t0) REVERT: A 116 CYS cc_start: 0.4778 (m) cc_final: 0.4426 (m) REVERT: A 161 LYS cc_start: 0.8423 (mptt) cc_final: 0.8155 (mptt) REVERT: A 164 SER cc_start: 0.8519 (p) cc_final: 0.8270 (p) REVERT: A 187 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7081 (ttm110) REVERT: A 230 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 294 LEU cc_start: 0.8373 (tp) cc_final: 0.7996 (tp) REVERT: A 471 MET cc_start: 0.3005 (mpp) cc_final: 0.2723 (mpp) REVERT: B 20 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7171 (mtp180) REVERT: B 203 ASP cc_start: 0.7796 (t0) cc_final: 0.7547 (t0) REVERT: B 268 LEU cc_start: 0.8556 (tp) cc_final: 0.7898 (tp) REVERT: B 285 SER cc_start: 0.7761 (t) cc_final: 0.7436 (m) REVERT: C 211 THR cc_start: 0.6466 (p) cc_final: 0.4787 (m) REVERT: C 234 ASN cc_start: 0.7755 (m-40) cc_final: 0.7402 (m-40) REVERT: C 324 ASP cc_start: 0.7899 (t70) cc_final: 0.7532 (t0) REVERT: C 333 SER cc_start: 0.7798 (m) cc_final: 0.7381 (p) REVERT: C 356 MET cc_start: 0.1731 (ttp) cc_final: 0.1426 (ttm) REVERT: C 371 PHE cc_start: 0.7786 (t80) cc_final: 0.7568 (t80) REVERT: C 380 ASP cc_start: 0.7785 (m-30) cc_final: 0.7482 (p0) REVERT: b 13 ARG cc_start: 0.6742 (ptm160) cc_final: 0.5732 (ptp-170) REVERT: c 43 ASP cc_start: 0.7973 (t0) cc_final: 0.7766 (t0) REVERT: c 119 ARG cc_start: 0.7227 (ttt180) cc_final: 0.6903 (ttm110) outliers start: 25 outliers final: 24 residues processed: 338 average time/residue: 0.2521 time to fit residues: 129.7135 Evaluate side-chains 351 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 327 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain b residue 65 CYS Chi-restraints excluded: chain c residue 68 VAL Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 54 optimal weight: 0.0170 chunk 132 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 183 optimal weight: 0.0060 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.0030 chunk 59 optimal weight: 4.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148363 restraints weight = 68401.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155230 restraints weight = 28869.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159684 restraints weight = 15813.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162556 restraints weight = 10439.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163790 restraints weight = 7866.489| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 15016 Z= 0.102 Angle : 0.538 8.226 20392 Z= 0.282 Chirality : 0.043 0.193 2357 Planarity : 0.003 0.045 2574 Dihedral : 4.694 44.221 2105 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.08 % Allowed : 17.71 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.20), residues: 1899 helix: 2.87 (0.27), residues: 401 sheet: -0.50 (0.20), residues: 598 loop : -1.55 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 187 TYR 0.012 0.001 TYR b 47 PHE 0.018 0.001 PHE A 332 TRP 0.017 0.001 TRP A 227 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00235 (14989) covalent geometry : angle 0.52537 (20335) SS BOND : bond 0.00314 ( 24) SS BOND : angle 1.54106 ( 48) hydrogen bonds : bond 0.03288 ( 558) hydrogen bonds : angle 5.02169 ( 1503) link_NAG-ASN : bond 0.00822 ( 3) link_NAG-ASN : angle 4.44065 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5033.53 seconds wall clock time: 86 minutes 21.69 seconds (5181.69 seconds total)